Metagenomic study of diversity of microorganisms in the salt mine of Pakistan
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ABSTRACT:
PROVIDER: PRJEB28016 | ENA |
REPOSITORIES: ENA
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Project description:Hypersaline regions are terrestrial analogs of the Earth's primitive ecosystem and extraterrestrial environment. The salt range in Pakistan is considered among a few of the ancient salt deposits in the subcontinent. Karak salt mine is situated at the Northwest end in Pakistan. Despite the fact that halophiles initiated the formation of terrestrial ecosystems, their products and identities remain hidden. Some preliminary studies limited to culture-dependent isolations have been reported. Characterizing the microbiome that spans over centuries of ecosystem development is crucial, given their role in shaping landscape succession and biogeochemical cycles. Here, we used metagenomics techniques to explore the microbial diversity of the Karak salt mine. We used 16S rRNA Illumina amplicon sequencing to characterize the halophilic communities entrapped in Karak mine. The results were interpreted using Illumina Basespace, QIIME, and Cytoscape. Cultures were isolated at 16-25% salinity. Metagenomics data was consistent with our preliminary culturing data, indicating remarkable species to strain-level diversity of unique halophiles. A total of 107,099 (brine) and 122,679 (salt) reads were obtained. 16S rRNA based sequencing revealed a microbiome with bacteria (66% brine and 72% salt) dominated by Bacteroidetes and Proteobacteria with a strikingly high abundance of Archaea (18% brine and 13% salt). Alpha diversity has higher values in salt than in the brine. The study of the halophiles in the Karak salt mine provides clues for species contributing to the maintenance of biogeochemical cycles of the ecosystem. This is the first report of a metagenomic study of any hypersaline region of Pakistan.
| S-EPMC7386132 | biostudies-literature
Project description:The aim of the project was to find new catalysts capable of chlorolactone biotransformation. Three bicyclic chlorolactones with structures possessing one or two methyl groups in their cyclohexane ring were subjected to screening biotransformation using seven bacterial strains and one fungal strain from a salt mine. Three strains of bacteria (Micrococcus luteus Pb10, Micrococcus luteus WSP45, Gordonia alkanivorans Pd25) and one fungal strain (Aspergillus sydowii KGJ10) were able to catalyse hydrolytic dehalogenation of one substrate. The classification of the strains that were effective biocatalysts was confirmed by 16S rDNA analysis. The best result (76%) was obtained using Aspergillus sydowii KGJ10. All strains catalysed hydrolytic dehalogenation without changing the conformation. The equatorial position of the chlorine atom in the substrate turned out to be warrant of the positive result of the biotransformation process.
| S-EPMC5957361 | biostudies-literature
Project description:Ground water Arsenic (As) toxicity is a global problem and millions of people are exposed to elevated levels (more than WHO advised maximum limit of 10µg/L) through drinking water. The exposure is associated with various cancerous and non-cancerous diseases. It may alter DNA methylation profiles of inviduals and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also has reported elevated ground water As levels in various investigations since 2005. However, a very limited biomonitoring studies have been conducted in this context while no study reports molecular changes associated with drinking water As exposure in Pakistan. Within this context, the present study aimed to investigate genome-wide DNA methylation profiles of the exposed subjects in two districts of Punjab Province Pakistan, i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. Genome-wide DNA methylation profiles were obtained using MeDIP in combination with NimbleGen 2.1M Deluxe Promotor arrays.
2021-10-27 | GSE157111 | GEO
Project description:Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
| S-EPMC5809485 | biostudies-literature
Project description:Ground water Arsenic toxicity is the global problem and millions of people are exposed to elevated levels through drinking water than WHO permiscible limit of 10µg/L. The exposure is associated with various cancerous and non-cancerous diseases. It may alter the gene expression profile of invidual and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also have different areas reported to have elevated Ground water As. levels since 2005. The Present Study aimed to investigate Transcriptome profile of the exposed subjects in two districts of Punjab Province Pakistan. i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. We used Agilent Microarrays platform for Transcriptomics analysis and Linear mixed model was used to find differential gene expression associated with Arsenic exposure
2019-12-26 | GSE110852 | GEO
Project description:The Bochnia Salt Mine metagenome sequencing
| PRJNA848445 | ENA
Project description:Clinical isolate from Pakistan
| PRJNA33789 | ENA