Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India

BACKGROUND: Traditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS. RESULTS: The glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported. CONCLUSION: Results indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.

Productivity and profitability assessment of organically grown vegetables embedded in rice based cropping sequences in Sikkim Himalayas, North East India

Aim: The objective of the present study was to identify economically viable, profitable and resource efficient vegetables embedded rice-based cropping sequences under organic management for marginal and small farmers of Sikkim Himalayas, India.Methodology: Three-year fixed plot study was conducted to evaluate seven rice–based cropping sequences viz., rice–fallow (farmers’ practice), rice–fenugreek (leafy vegetable), rice–coriander (leaves), rice–radish, rice–broccoli, rice–potato and rice–vegetable pea were replicated four-times in a completely randomized block design. Results: Among the various rice – based cropping sequences, cultivation of rice–coriander (leaves) recorded higher production (67.3 kg ha-1 day-1), system productivity (24.6 t ha-1), relative economic efficiency (1040%) and net returns (376.1x103). However, rice-broccoli and rice–vegetable pea sequences recorded 8.6 and 4.4% higher B: C ratio, respectively, over the rice–coriander system. With regards to soil health, rice – vegetable pea cropping sequences resulted in maximum improvement in soil organic carbon (SOC) (1.26%), available soil N (415.2 kg ha-1), P (22.8 kg ha-1) and K (411.5 kg ha-1), soil microbial biomass carbon (SMBC) (344.7 µg MBC g-1 soil), dehydrogenase activity (DHA) (24.0 µg TPFg-1 soil h-1) and fluorescin di acetate (FDA) (38.8 µg FDAg-1 soil h-1) among the cropping sequences. Interpretation: Induction of vegetables in rice–fallow system under assured irrigation condition of Sikkim Himalayas, India not only enhances the farm productivity and profitability but also sustain the soil health on long term basis. Thus, rice-vegetable pea/coriander/broccoli based production systems under organic management hold great promises for sustaining livelihood of organic growers in Sikkim Himalayas over conventional rice– fallow system.

Bioprospecting of phosphorus solubilizing bacteria from Renuka Lake Ecosystems, Lesser Himalayas

In the present study, diversity and plant growth promoting traits of bacteria isolated from Renuka Lake,Himachal Pradesh was investigated. A total of three samples, including sediment (pH-7.3), sub-surface water(pH-8.1), and surface water (pH-8.2), were collected. A total of 65 bacterial isolates were obtained on differentgrowth media. Among 65 isolates 18 isolates were found to be solubilizers of phosphorus. The maximumamount of phosphorus was solubilized by EU-RL 54 (7,976 ± 0.01 µg/l) followed by EU-RL 53 (6,322 ± 0.01µg/l). Phosphorus solubilizers also possessed other plant growth promoting traits, such as the production ofammonia, hydrogen cyanide, zinc solubilization, production of hydrolytic enzymes. The isolates were identifiedbelonging to different genera Acinetobacter, Bacillus, Enterobacter, Klebsiella, Proteus, Pseudomonas, andStaphylococcus. This is the first report for these plant growth promoting bacteria to solubilize a considerableamount of phosphorus isolated from Ecosystems, Lesser Himalayas.

Identification of molecular markers to study the Garcinia spp. diversity.

The genus Garcinia shows a considerable variation in its morphological characters such as leaf, flower and fruit with taxonomic ambiguity. It is a potential under-exploited multipurpose crop that gained considerable attention for the presence of (-) hydroxycitric acid, an anti-obesity compound, in its fruit rind and leaves. Here, we evaluated the genetic relationship through molecular markers among the selected 9 species commonly available in the Western Ghats and the Northeastern Himalayan foot hills of India. The nucleotide sequence data obtained from two prominent monomorphic bands generated in ISSR profiling of the species was utilized for the study. The selected bands were found to be of ITS region (700 bp) and partial region of KNOX-1 gene (600 bp). The evolutionary cluster was formed using MEGA5 software. The study indicated 2 major clusters, influenced by floral morphology of the species and availability of (-) hydroxycitric acid in their fruit rinds. In the subclusters, one species from the Western Ghats were paired with another from Northeastern Himalayas with relatively similar morphological traits.

Influence of phenolic compounds of Kangra tea [Camellia sinensis (L) O Kuntze] on bacterial pathogens and indigenous bacterial probiotics of Western Himalayas

Phenolic compounds of nutraceutical importance viz., catechins (C), (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epigallocatechin-3-gallate (EGCG) and (-)-epicatechin-3-gallate (ECG) were estimated in fresh green tea shoots of Camellia sinensis (L) O Kuntze cultivar. The total polyphenols and total catechins were in the range of 219.90 to 317.81 and 140.83 to 271.39 g/kg, respectively in monthly samples of tea. The values of C, EC, EGC, EGCG and ECG in tea powders as analyzed through high performance liquid chromatography (HPLC) were in the range of 1.560 to 3.661, 13.338 to 27.766, 26.515 to 39.597, 62.903 to 102.168 and 18.969 to 39.469 mg/g, respectively. Effect of tea extracts and standard flavanols against five pathogenic bacteria viz., Listeria monocytogenes (MTCC-839), Pseudomonas aeruginosa (MTCC-741), Bacillus cereus (MTCC-1272), Staphylococcus aureus (MTCC-96) and Escherichia coli (MTCC-443), and eleven indigenous potential bacterial probiotics belonging to genera Enterococcus, Bacillus and Lactobacillus spp. obtained from fermented foods of Western Himalayas, was investigated. EGCG, ECG and EGC exhibited antibacterial activity but, C and EC did not show this activity. Tea extracts having high concentrations of EGCG and ECG were more potent in antibacterial action against bacterial pathogens. Tea extracts and standard flavan-3-ols augmented viability of potential probiotics in an order of EGCG > EGC > ECG > EC > C. Tea extracts and standard flavanols had no antibacterial activity against Escherichia coli (MTCC-443) but, in combination with probiotic culture supernatants, this activity was seen. The Kangra tea thus, exerts antibacterial effect on bacterial pathogens through EGCG, ECG and EGC constituents while stimulatory effect on growth of indigenous potential probiotics.

Natural selection among Kinnaura of the Himalayan highland: A comparative analysis with other Indian and Himalayan populations.

The present investigation on fertility and mortality differential among Kinnaura of the Himalayan highland is based on data collected from 160 post-menopausal women belonging to the middle and high altitude region of Kinnaur district of Himachal Pradesh (Indian Himalayas). Selection potential based on differential fertility and mortality was computed for middle-and high-altitude women. Irrespective of the methodology, the total index of selection was found to be highest among middle-altitude women (0.386) as compared with high-altitude (0.370) women, whereas for the total population it is estimated to be 0.384. It was found that the Kinnaura of the Himalayan highland showing moderate index of total selection and relative contribution of the mortality component (Im) to the index of total selection is higher than the corresponding fertility component (If). The analysis of embryonic and post-natal mortality components shows that the post-natal mortality components are higher in comparison with the embryonic mortality components among highlanders and needs special intervention and health care. The present findings are compared with other Indian tribes as well as non-tribes of the Himalayan region and other parts of the country. It reveals that this index among Kinnaura is moderate than the other population groups; among the Himalayan population, the highest was reported for Galong (It = 1.07) of Arunachal, whereas the lowest was reported from Ahom (It = 0.218) of Manipur. The correlation and regression analysis between total index of selection (It) and fertility (If) and mortality (Im) components for pooled data of populations of the Indian Himalayan states show that If and Im account for 21.6 and 29.1% variability, respectively. In Crow's total index of selection (It) along with strong association, which is significant at the 1% level, this indicates that mortality plays a greater role in natural selection in comparison with fertility among populations of the Indian Himalayas.