Microbial Ecology and Environmental Genomics Laboratory

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Dr. Mostafa Elshahed



Our laboratory is currently active in four main research areas: 1.) Discovering the diversity, ecophysiology, and metabolic capabilities of novel microorganisms. 2.) Study of the bacterial diversity in soil habitats, with special emphasis on the rare members of the community (members of the rare soil biosphere), and utilization of various phylogenetic and statistical approaches to identify, quantify, and describe the observed patterns of bacterial diversity in soil. 3.) Investigating the potential of anaerobic fungi in biofuel research. 4.) Identifying natural bacterial communities in oil and natural gas reservoirs, and exploring new approaches for the use of microorganisms to enhance oil recovery and improve oil quality. We are always looking for bright and motivated undergraduate and graduate students.

Our laboratory is located in a brand new 1,100 ft2 laboratory at Venture 1 building, an Oklahoma State research facility that aims at fostering interdisciplinary research within the University scientific community.



Zodletone Spring microbial observatory

We study the phylogenetic diversity, metabolic capabilities, and ecological roles of microorganisms in Zodletone spring, an anaerobic, hydrocarbon-impacted sulfide and sulfur rich spring in southwestern Oklahoma. We utilize, develop, and evaluate a variety of procedures to achieve these goals. An integrative approach that combines large-scale, culture-independent phylogenetic surveys, environmental genomic (metagenomic) approaches, and isolation and characterization of novel microorganisms are all ombined to study an ecosystem and/or a microbial group of interest. Microbial groups of interest include several bacterial candidate phyla with no pure cultured representatives (Candidate phyla OD1, SR1, OP11, WW1, and TM7), genera of halophilic Archaea (Family Halobacteriaceae) that survives in low salt environments, and members of the heterotrophic Planctomycetes. Our work by the National Science Foundation microbial observatories and microbial interactions (MO/MI) program.



Bacterial diversity in soil

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Therefore, adetailed phylogenetic analysis of rare members of the community is a difficult task, and the contributions of members of the rare biosphere to ecosystem functions are not yet understood. Our studies integrate Sanger sequencing and pyro sequencing to investigate the novelty, uniqueness of members of the rare soil biosphere, and use such information to propose ecological roles for these lineages. We also seek to document, quantify, and understand the ecological and evolutionary reasons behind diversity rankings patterns observed in soils i.e. why specific microbial phyla in soil (e.g. Planctomycetes) are always more diverse than others (e.g. Verrucomicrobia). Finallly, we seek to develop tools that allows efficient comparison of species richness estimates in datasets with different sizes, as well as between Sanger sequencing and pyrosequencing-generated datasets



Investigating the role of anaerobic fungi in biofuel research

Conversion of cellulosic biomass to fuel requires effective degradation of plant polymers (cellulose, hemicellulose, and potentially lignin) to sugar monomers and eventually to biofuels such as ethanol, and biogas. We are initiating an effort to evaluate the potential of strict anaerobic Fungi (Phylum Neocallimastigomycota) as a source of plant polymers-degrading enzymes, as well as biological agents for direct conversion of energy crops and plant residues to ethanol and biogas. We are isolating members of the Neocallimastigomycota. from the rumen and feces of cows and other herbivores and evaluate the cellulase and hemicellulase enzyme activities in the strains isolated, as well as the ability to directly produce ethanol (in pure culture) and biogas (in co-culture with hydrogen and acetate-utilizing methanogens) from intact switch grass. The results should provide a solid evaluation of the potential of this yet-unexploited group of microorganisms in biofuel research. Our work in this are is currently funded by the Oklahoma Bioenergy fund.



Petroleum microbiology: Utilizing the power of microorganisms to improve oil recovery and oil quality

The demand for energy will continue to climb in the near and intermediate future, and due to a combination of economic, historic, technical, and geopolitical reasons, oil and natural gas will continue to be the major global source of energy through most, if not the entire, twenty first century. However, the rate of discovery of major oil reserves worldwide has been readily declining during the last 40 years, and has now slowed to a trickle. This overall picture of climbing demands and diminishing reserves requires the implementation of innovative strategies to maximize or reinitiate production from nearly depleted or recently depleted oil wells, and to provide better stewardship and maintenance of currently producing oil reservoirs.
Microorganisms represent a powerful tool that could be utilized to achieve these two goals. We are currently initiating research projects with multiple objectives that aim at either increasing the amount of oil extracted in oil reservoirs (microbially enhances oil recovery), or improve the quality of oil produced (Clean oil technology).
Objectives that aim to enhance oil recovery include 1. The use of phylogenetic and metagenomic approaches to mine microbial communities in oil reservoir and other environments for novel products e.g. biosurfactants and hydrocarbon-degradation genes and enzymes, followed by the use of synthetic biology to mass produce such products in stable expression vectors. 2. The use of novel, high throughput isolation approaches under aerobic and anaerobic conditions to obtain novel microbial strains that could be used in various microbially enhanced oil recovery approaches at various reservoir conditions. And 3. Use of molecular biological, genetic, and nutritional approaches to manipulate the genomes of bacterial strains to enhance production of biosurfactants and other useful products, and tailor such products to specific reservoir conditions. Objectives that aim to enhance quality of produced oil include the evaluation and refinement of nitrate-injection protocols for souring control, and understanding their effect on the reservoir community. Such knowledge will lead to accurate predictions of success and optimization of injection protocol depending on reservoir conditions.

Contact Me:
Dr. Mostafa Elshahed
Assistant Professor
Dept. Microbiology and Molecular Genetics

Oklahoma State University
1110 S. Innovation Way
Stillwater, Ok, 74074
Phone: 405-744-3005
Fax: 405-744-1112
Email: Mostafa@okstate.edu


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