Browsing by Author "Zain Abbas"

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    Binning and annotation of saline soil metagenome
    (UMT, Lhr, 2023) Zain Abbas
    There are about 10 million to 14 million estimated number of earth’s current species. Of them, reporting of 1.2 million has been done and 86% of them have not yet been described. To establish a tree of life and to get a comprehensive idea of all types of species existing on this planet and their phylogenetic relation, genome sequencing of all forms of life has to be done. Extreme environments are fascinating regions on Earth where organisms have adapted to survive and thrive under extreme conditions that are generally inhospitable to most life forms. It is estimate that 1 gram of soil contains billions of microbial species and reporting of only 1-2% will have been done. Modern NGS technologies with their exploitation in microbial field has discovered enormous number of species. The term metagenomics discovered to study the diversity of microbes present in different habitat. In this study, hypersaline soil samples were collected from the Khewra region. The samples were pooled together and total DNA was extracted using MO BIO's PowerSoil DNA Isolation Kit. The sample was sequenced from University of Minnesota, Genomics Center using PacBio SMRT sequencing technology. The reads obtained were further processed for quality control and trimming. There were 965 contigs found out with 65 percent GC content. The structural and functional annotation was done through IMG JGI database system. The binning and phylogenetic analysis was done through Busybee Web for comprehensive and differential composition-based metagenomic binning. It was found out that there were 186 RNA genes and 19909 protein coding genes. Functional annotation showed a fraction of protein coding genes that have function in inorganic ions transport and metabolism, cell wall/envelope biogenesis making the microbes able to survive in extreme saline conditions. The distribution of halophiles such as Haloterrigena, Halorubrum, Streptomyces, Paraoceanicella, Mesorhizobium, and Natronomonas across the saline habitat suggesting their important role in this environment. Further pathway analysis output showed involvement of genes in different pathways such as energy metabolism, amino acid metabolism, xenobiotics degradation, motility. We successfully characterized the saline soil microbial community of khewra mines using PacBio SMRT sequencing technology.
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    Molecular identification of the most prevalent fungal specie present in mesophilic and thermophilic stage of municipal solid waste composting and its evaluation as an inoculum to check growth of plants
    (UMT Lahore, 2021) Zain Abbas
    Composting is a biodegradative and aerobic process of organic constituents, which results in more stable organic products. The microbial communities present in the soil play a significant role in the accessibility of nutrients to plants by the decomposition of organic material. Fungi are the most prevailing microbes during the process of aerobic composting, most of them belonging to the Aspergillus species. During the compost formation process, organic material goes through various phases: Mesophilic phase, Thermophilic phase, Cooling phase, or Maturation phase. The process of composting is helpful for the management of municipal solid waste from landfills. Compost, being humus-like as an ultimate product of composting, when added to the soil, increases its fertility, increases the availability of nutrients for the plant's development, and increases the water-retaining capacity of the soil. This study is designed to molecularly identify the fungi present in the mesophilic and thermophilic phases of aerobic composting and evaluate them as an inoculum to check the growth of different plants.