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The main goal of this area of research is to “characterize key microbes that can play a beneficial function in enhancing resistance against environmental stress in a specific ecosystem (aquatic and terrestrial).”


We try to understand important questions like:

  • What are microbial symbionts in the microbiome of keystone halophytes and extremophiles?
  • How does core-microbiome function with plants living in extreme conditions and what helps them survive episodes of extreme climate changes?
  • How can the core microbiome be isolated to produce stress-competent microbes to increase yield and function of productivities (plants, metabolites or enzymes)?
  • What are biosynthetic pathways for essential metabolites and nutrients during plant-microbiome-stress interaction?
  • How does the unhealthy plant microbiome can influence the human gut microbiome?

Global Climate Change such as the increase or decrease of temperature, lack or abundance of water, changes in nutrients, and essential chemical composition of soil and water can influence an ecosystem’s natural resource cycling. Plants and microbes, a necessary part of human subsistence for food, shelter, medicine and income can be drastically impacted by reducing the desired natural productivity and sustainable functioning of the ecosystem. A microbiome refers to the total genetic material of microbial communities associated with plants in either of the modes, whereas ‘holobiome’ or ‘holobionts’ is a sum of host and associated biota genomic material that can also include prokaryotic and eukaryotic organisms. Microorganisms (bacteria, fungi, and archaea) are the silent wheel to function as the cradle of the plant ecosystem. These microbes’ composition, structure, and richness are variable across different environmental systems and associated with organisms. A newer concept of ‘eco-holobionts’ argues exponentially on the ecological or ecosystem-based interaction of microbiome to identify soil-plant-animal-environmental functionalities. Recently, the plant and the soil-associated microbiome has been coined as “second genome” that is highly variable in diversity, abundance and composition. Microbiome diversity and abundances in food crops alternatively influence the human gut microbiome. Healthy soil and crop microbiome is key to healthy human growth.


  • Samples collections from different environments (extreme, natural habitats, agriculture)
  • Large-scale DNA extractions from soil, plant, microbes
  • Sequencing the amplicon 16S/ITS gene using MiSeq Illumina
  • Sequencing the metagenome of microbial DNA using NovaSeq 6000 Illumina
  • Bioinformatic analysis with the help of UH cluster and available computational resources in the lab
  • Extra-Cellular enzymes, biochemical, phytohormonal, and organic acids assessment with the help of GC/MS SIM, fluorescence spectroscopy, and HPLC
  • Metabolomics analysis of targeted and non-targeted ones using LC/MS-MS and Chemo-informatics using available libraries
  • Soil and water physical, chemical, and nutrients assessments using ICP-MS and spectrophotometry
  • Adopting workflow of gene-editing technologies to improve production and yield of important traits such metabolites production and nutrient acquisition