Hot springs are the high temperature environments that serve as the ideal habitats for a number of thermophilic microorganisms. Exploration of microbial communities of these environments has both basic and applied aspects. The limit of the traditional culture based methods to access microbial world has now been extended many folds by the culture-independent approach of metagenomics. World over metagenomic studies of hot springs have resulted in the identification of several novel prokaryotic life forms as well gene(s) of immense industrial applications. There are several thermal springs located within the territorial boundary of India and quite a few of them have been explored for metagenomic investigations as well. This review describes community structure elucidation as well as functional gene identification in the community genome of some hot springs in India.

Identification

10.36953/ecj.2018.191220

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Genetic and functional diversity among root-associated psychrotrophic Pseudomonad’s isolated from the Himalayan plants

Archives of Microbiology (2013)

Shekhar Chandra Bisht Pankaj Kumar Mishra Gopal Joshi

10.1007/s00203-013-0908-4

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Citations (38)

De novotranscriptome profiling of mustard aphid (Lipaphis erysimi) and differential expression of transcripts associated with developmental stages, feeding and non-feeding conditions

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Rubina Chongtham Kirti Kulkarni Rohit Shukla Gopal Joshi Amar Kumar

Abstract Lipaphis erysimi is a Brassicaceae specialist aphid, which causes significant losses in yield and/or reduction of oil content of vegetable and oilseed brassicas and is a major pest in the Indian subcontinent. This study reports the de novo transcriptome of L. erysimi for the first time. We also present a comparative analysis of nymphs and adult transcriptomes to study the differential expression profiles associated with different developmental stages as well as different feeding conditions. For this, RNA-seq was performed on three different biological samples adults, nymphs (with all nymph stages pooled) and adults starved for 3 hours (referred to as Adult Feeding, AF; Nymphs Feeding, NF, and Adult Starved_3 hr, ANF samples henceforth). A final transcriptome comprising 52,652 transcripts of 1064bp average length and N50 value of 1806 bp was generated. A total of 27,112 transcripts were annotated with insect proteins from SwissProt, of which 4128 transcripts were components of 165 KEGG pathways. A total of 17,296 transcripts were classified based on their Gene Ontology. Potential transcripts for host selection, detoxification, salivary proteins and effectors, molecular chaperones and developmental genes were identified. A total of 23,532 transcripts that remained unannotated were subjected to BLAST against aphid sequences available at AphidBase and a total of 3091 transcripts had hits with sequences of other aphids in the database, out of which 1380 had protein hits. A total of 20441 found to share no homology to any sequence available in the public domain and could therefore represent novel aphid genes or sequences that are unique to L. erysimi . This is an exploratory study with no biological replicates. However, the significant repertoire of feeding- and development-related genes and their differential expression profiles generated in this study adds to the limited data available on L. erysimi and it would facilitate studies on the molecular basis of aphid feeding and development. This could also allow identification of novel target genes for development of RNAi-based aphid control methods.

Lipaphis erysimi

KEGG

10.1101/717470

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Cryotolerance strategies of Pseudomonads isolated from the rhizosphere of Himalayan plants

SpringerPlus (2013)

Shekhar Chandra Bisht Gopal Joshi Shafiul Haque Pankaj Kumar Mishra

The cold stress biology of psychrotrophic Pseudomonas strains isolated from the rhizosphere of Himalayan plants have been explored to evaluate their cryotolerance characteristcs. Pseudomonas strains were examined for stress metabolites, viz., exopolysaccharide (EPS) production, intracellular sugar, polyols and amino acid content, ice nucleation activity, and their freezing survival at -10 and -40°C, respectively. High freezing survival was observed for the Pseudomonas strains that were grown at 4°C prior to their freezing at -10 or -40°C. Increased EPS production was noticed when Pseudomonas strains were grown at lower temperatures, i.e., 4 and 15°C, in comparison with their optimal growth temperature of 28°C. All Pseudomonas strains showed low level of type-III class ice nucleation activity at -10°C after 96 h. Considerable differences were noticed in accumulated contents of various intracellular sugars, polyols, amino acids for all Pseudomonas strains when they grown at two different temperatures, i.e., 4 and 28°C, respectively. The unusual complement of stress protectants especially, raffinose, cysteine and aspartic acid that accumulated in the bacterial cells at low temperature was novel and intriguing finding of this study. The finding that raffinose is a key metabolite accumulated at low temperature is an exciting discovery, and to the best of our information this is first report ever signifying its role in bacterial cold tolerance.

Strain (injury)

10.1186/2193-1801-2-667

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Production and characterization of bioactive metabolites from piezotolerant deep sea fungusNigrosporasp. in submerged fermentation

Journal of Applied Microbiology (2014)

Ganesh Arumugam Savitha Srinivasan Gopal Joshi Gopal Dharani Kirubagaran Ramalingam

To produce and characterize bioactive metabolites from piezotolerant marine fungus Nigrospora sp. in submerged fermentation.A distinct marine strain, Nigrospora sp. NIOT has been isolated from a depth of 800 m at the Arabian Sea. The 18S rRNA and internal transcribed spacers (ITS) analysis demonstrates its close association with the genus Nigrospora. Effect of pH, temperature, salinity, carbon source and amino acids was studied to optimize the fermentation conditions. Optimal mycelia growth and secondary metabolites production were observed at 6·0-8·0 pH, 20-30°C temperature, 7·5% salinity, sucrose as carbon source and tryptophan as amino acid source. The extracellular secondary metabolites exhibited high antimicrobial activities against both gram-positive and gram-negative pathogenic bacteria with minimal inhibitory concentration (MIC) values higher than 30 μg ml(-1). Strongest cytotoxicity was observed in all cell lines tested, GI50 (growth inhibition by 50%) was calculated to be 1·35, 3·2, 0·13 and 0·35 μg ml(-1) against U937, MCF-7, A673 and Jurkat, respectively. Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) analyses of secondary metabolites confirmed the production of antimicrobial and anticancer substances.A piezotolerant fungus Nigrospora sp. NIOT isolated from deep sea environment was successfully cultured under submerged fermentation. The secondary metabolites produced from this organism showed potent antimicrobial and anticancer activities with immediate application to cosmetics and pharmaceutical industries.This is the first study exploring Nigrospora sp. from 800 m in marine environment. This deep sea fungus under optimized culture conditions effectively produced bioactive secondary metabolites such as griseofulvin, spirobenzofuran and pyrone derivatives at higher concentrations.

Christian ministry

Ocean science

10.1111/jam.12693

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Citations (42)

ILC Reference Design Report: ILC Global Design Effort and World Wide Study

(2007) (2007)

J. E. Brau T. Mimashi Jin‐Young Jung Haitao Wang Cai Tu Shi

Source

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Genome-wide identification and characterization of miRNAome from tomato (Solanum lycopersicum) roots and root-knot nematode (Meloidogyne incognita) during susceptible interaction

PLoS ONE (2017)

Pritam Kaur Neha Shukla Gopal Joshi Cheeni VijayaKumar Arun Jagannath

Root-knot nematodes (RKNs, Meloidogyne spp.) are the most damaging plant parasites causing severe losses to crop production. The present study reports genome-wide identification and characterization of both tomato and RKN miRNAs simultaneously from RKN-infected susceptible tomato roots using high-throughput sequencing technique. RNAseq data from 11 small RNA libraries derived from 5 disease development stages identified 281 novel miRNAs of tomato in addition to 52 conserved and 4 variants of conserved miRNAs. Additionally, the same set of RNAseq data identified 38 conserved and 290 novel RKN miRNAs. Both tomato and RKN miRNAs showed differential expression at 5 stages of disease development based on digital expression profiles. In tomato, further validation through qRT-PCR confirmed that majority of miRNAs were significantly upregulated during susceptible response whereas downregulated during resistance response. The predicted targets of 8 conserved and 1 novel miRNAs were validated through 5'RLM-RACE. A negative correlation between expression profiles of a few conserved miRNAs (miR156, miR159, miR164 and miR396) and their targets (SBP, GAMYB-like, NAC and GRF1 transcription factor) was confirmed. A novel Sly_miRNA996 also showed a negative correlation with its target MYB-like transcription factor. These results indicate that the conserved and novel tomato miRNAs are involved in regulating developmental changes in host root during RKN infection. In RKN, the targets of conserved miRNAs were also predicted and a few of their predicted target genes are known to be involved in nematode parasitism. Further, the potential roles of both tomato and RKN miRNAs have been discussed.

Root-knot nematode

MYB

10.1371/journal.pone.0175178

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A Comprehensive Genome-Wide Study on Tissue-Specific and Abiotic Stress-Specific miRNAs in Triticum aestivum

PLoS ONE (2014)

Ritu Pandey Gopal Joshi Ankur R. Bhardwaj Manu Agarwal Surekha Katiyar‐Agarwal

Productivity of wheat crop is largely dependent on its growth and development that, in turn, is mainly regulated by environmental conditions, including abiotic stress factors. miRNAs are key regulators of gene expression networks involved in diverse aspects of development and stress responses in plants. Using high-throughput sequencing of eight small RNA libraries prepared from diverse abiotic stresses and tissues, we identified 47 known miRNAs belonging to 20 families, 49 true novel and 1030 candidate novel miRNAs. Digital gene expression analysis revealed that 257 miRNAs exhibited tissue-specific expression and 74 were associated with abiotic stresses. Putative target genes were predicted for miRNAs identified in this study and their grouping into functional categories indicated that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three known miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by the corresponding miRNAs. Mapping of the sequenced data onto the wheat progenitors and closely related monocots revealed a large number of evolutionary conserved miRNAs. Additional expression profiling of some of these miRNAs in other abiotic stresses underline their involvement in multiple stresses. Our findings provide valuable resource for an improved understanding of the role of miRNAs in stress tolerance as well as plant development.

10.1371/journal.pone.0095800

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Citations (82)