Our Research Interests Include

Our research group is a multidisciplinary, working on diverse areas such as Extremophilic Bioprocessing, Biocatalysis, Biomaterials, Gas to liquid fuels, Genome editing of bacteria, Homo/heterologous expression of genes, Metabolic engineering, Space biology, and Bioelectrochemical systems. We have been focusing on extremophiles isolated from the deepest mine (Homestake Gold Mine; 7,800 ft. deep) to develop unique extremophilic bioprocesses for different applications including production of biofuels, biopolymers, and value-added products under thermophilic conditions (≥60℃). Homestake Gold Mine, known as Sanford Underground Research Facility (SURF), is located in the Black Hills, Lead, South Dakota

  • Rules of Life in Biofilms grown on 2D materials
  • Biogas to Liquid fuels (BioGTL, Genome Editing)
  • Thermophilic Bioprocessing of Solid Wastes to Biofuels and Value-added Products (Molecular Biology, Biotechnology, and Metabolic Engineering)
  • Space Biology (Effects of mg on Extremophiles)
  • Biocatalysis (Protein Engineering, Simulations/Modeling, and Bioinformatics)
  • Biomaterials/Biopolymers (EPSs and PHAs: Biomedical applications)

Research Scientists 2
Postdoctoral fellow 1
Graduate students 13
Undergraduate students 3
Teachers 4

1. Building Genome-to-Phenome Infrastructure for Regulating Methane in Deep and Extreme Environments (BuG ReMeDEE)

Type of Funding: NSF RII Track-2 FEC
Award:1736255 (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1736255)
Time Frame: 2017-2021
Award: $6,000,000

Methane remains the second largest contributor to the radiative forcing of climate change. Its global warming potential is 34-fold more extensive than that of carbon dioxide over 100 years. Globally, 60% of methane emissions are related to anthropogenic sources, most of which are attributed to microbial methanogenesis. A significant gap in scientific knowledge is associated with methane emission and oxidation from the earth’s deep and thermally impacted biospheres. To more deeply understand these processes, this Research Infrastructure Improvement Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC) award, led by Professor Rajesh Sani, has formed a BuG ReMeDEE consortium of 75 participants (faculty and students).

This collaborative consortium (South Dakota School of Mines and Technology, Montana State University and University of Oklahoma) uses the Sanford Underground Research Facility (SURF) and Yellowstone National Park (YNP) as testbeds for extreme environments in deep biosphere and thermal systems, respectively.

The BuG ReMeDEE will accomplish:

  • Unexplored microbial species: Regulate methane in deep and extreme environments
  • Genome editing of novel (previous unexplored) methane-oxidizing microbes
  • Fundamental info on industrial techniques of converting methane into value added products (e.g., Methanol, Biopolymer, and Bioelectricity) as shown in figure.

2. Composite and Nanocomposite Advanced Manufacturing – Biomaterials Program (CNAM-Bio)

Type of Funding: Funded by Governor’s Office of Economic Development, South Dakota
Time Frame: 2018-2023
Award: $1,806,427

The world is moving relentlessly towards bio-based chemicals and materials. In principle, these bio-based products can be virtually the same, or provide additional functionality and value, compared to petroleum-based counterparts, but are manufactured from renewable resources. The research, funded by Governor’s Office of Economic Development, South Dakota for developing the agriculturally based economy in the state, is exceptionally positioned to bring together strong academic teams in biocatalysis, metabolic engineering, extremozymes, plant genetics, interfacial chemistry, polymer processing, composites manufacturing, and biomimetic modeling. The overall goal of this program is to synthesize low-cost biopolymers from renewable sources using extremophilic bioprocessing, and the development of commercially viable processes for the transformation of these materials into valuable polymers and high-performance biocomposites and bio-nano composites, at high yields and low cost.

We are focusing on the production of biopolymers such as polyhydroxyalkanoates, nanocellulose, and extracellular polysaccharides, as the targeted products, using corn stover (abundantly available feedstocks) as the raw material. Our group has isolated four strains thermophilic microbial strains that can efficiently breakdown unprocessed lignocellulose without expensive pretreatment and produce biopolymers (primarily polyhydroxyalkanoates, PHAs) in one step. There is no report to date on single-step consolidated bioconversion of unprocessed lignocellulosic wastes to bioplastics. Currently, we are applying, systems biology tools and theories, electrocatalytic, and electrochemical approaches to enhance the synthesis of PHAs with mechanical and thermal properties suited to high-performance composite applications. Besides,

we are also engineering extremophilic microorganisms to produce PHAs from unpurified methane at high yields. Microbial breakdown of the biomass is being attempted to release cellulose nanocrystals and nanofibrils which are known to possess high strength and stiffness (similar to Kevlar® aramid fibers), a reactive surface, and a unique combination of electrical, electromagnetic and piezoelectric properties, suitable for designing biocomposites with advanced multifunctional properties. Significant further value will be added to these bioprocesses through the generation of byproducts such as biofuels. In addition, microbial electrochemical systems will be developed for accelerating biopolymer production while simultaneously removing the substrates via microbial electrosynthesis, and for purifying the polymers at a low cost in an environmentally benign manner

3. Extremophiles, gene manipulation, and fermentation: Gravitational effects on recombinant extremophiles.

Type of Funding: NASA
Time Frame: 2016-2019
Award: $750,000

We were also awarded a project by NASA where we proposed to develop and validate a bio-electrochemical module that produces electricity from crews’ solid wastes using thermophiles under microgravity conditions.  We are investigating the effects of microgravity on thermophile (Geobacillus sp.) growth, cellular physiology, and cell-cell interactions in exogenic biofilms on the electrode surface under thermophilic conditions.  To stimulate the effects of microgravity on Geobacillus sp. growth as well as electricity generation, we are using a rotating bioreactor known as the NASA bioreactor.

The capability of Geobacillus sp. to produce ethanol and lactate from solid wastes can be undesirable in terms of bioelectricity production.  Therefore, we are blocking alcohol dehydrogenase (aldh) and lactate dehydrogenase (ldh) genes so we could divert the flux towards higher production of acetate.  To increase the yield of electricity, we are also overexpressing acetate kinase (ackA), phosphotransacetylase (pta), and acetyl-CoA transferase (pimB) in Geobacillus sp. to convert acetate into acetyl-CoA at greater rates. As a result, acetyl-CoA can enter the TCA cycle and produce NADH and FADH2 molecules which can be oxidized by NADH and FADH2 dehydrogenases, respectively.  Released protons will synthesize ATP using proton motive force and ATP synthase, and electrons will be carried to the electrode by Geobacillus sp. electron carrier proteins to produce electricity (please see figure R5). The NASA-funded research, for the first time, will develop a robust recombinant thermophile Geobacillus sp. for conversion of complex solid wastes to electricity in a bio-electrochemical module.

4. Data Driven Material Discovery (DDMD) Center for Bioengineering Innovation

Type of Funding: NSF RII Track-2 FEC
NSF Award: 1920954 (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1920954&HistoricalAwards=false)
Time Frame: 2019-2023
Award: $6,000,000

South Dakota School of Mines & Technology (SDSM&T), Montana State University (MSU), University of South Dakota (USD) and University of Nebraska-Omaha (UNO) will collaborate to develop Big Data Tools for understanding rules of life in biofilms on technologically relevant materials. We propose to form the Data Driven Material Discovery (DDMD) Center for Bioengineering Innovation which will bring together diverse infrastructure (human experts and hardware) in bioscience, computer science, and material science from the three jurisdictions (SD, MT, NE) to develop a Biofilms Data and Information Discovery system (Biofilm-DIDs). This system will integrate metadata from accessible materials and biofilms data sources, employs it to process natural language processing (NLP) queries from users to predict biofilm phenotype on a material. Specifically, Biofilm-DIDs will analyze gene responses and biofilm phenotypes based on nanostructure properties of underlying materials. Our goals are to:

  1. facilitate convergent research among investigators across the four institutions, the three jurisdictions and across disciplines of computational theory, data mining, machine learning, 2D materials science and engineering, and systems biology;
  2. develop automated approaches to material properties analysis, with the aim of better investigating nanoscopic properties that control biofilm phenotypes;
  3. accelerate development of nanostructured materials for bioengineering applications;
  4. train researchers, faculty, and students in big data and rules of life research; and
  5. enhance career pathways for middle and high school students, graduate students, research scientists, and junior faculty including under-represented Native American population.

5. Building on The 2020 Vision: Expanding Research, Education and Innovation in South Dakota

Type of Funding: NSF RII Track-1 FEC
Award: 1849206 (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1849206&HistoricalAwards=false)
Time Frame: 2019-2024
Award: $20,000,000

Biofilm development is controlled by gene expression and genetic responses to environmental conditions. While spatial and temporal genotypic variations inducing the heterogeneous biofilm phenotypes have been well-studied, the question of how the nano-scale heterogeneity of surface properties impact microenvironments in biofilms remains unanswered, especially those grown on recently discovered two dimensional (2D) materials and their Van der Waals heterostructures. The South Dakota Biofilm Science and Engineering Center (SDBSEC) will conduct convergent research by coalescing bioscience, material science, computational science and engineering experts from 3 research institutions, 3 predominately undergraduate institutions, 2 private universities, 2 tribal colleges and a tribal university. SDBSEC will identify fundamental rules of life that govern biofilm phenotypes of biocorrosion stress resistance on metal

surfaces (Area 1) and resilience against competition for colonization of plant root surfaces (Area 2) modified with 2D materials, thus addressing two National Academy of Engineering grand challenges related to urban infrastructure and the nitrogen cycle, respectively. SDBSEC addresses all five research sectors in South Dakota’s S&T plan, Vision 2020. The collaborative infrastructure will enable the development of novel, nanoscale coatings to regulate biofilm formation on technologically relevant surfaces.

Dr. Sani’s group will contribute to achieving the following:

  • Development of collaborative infrastructure in three jurisdictions
  • For the first time
    • Gene and metabolic regulatory networks
    • Gene response to 2D materials
    • Upregulated, adhesive, metal resistance, nanofilament formation genes
    • Are there in changes at DNA levels (epigenomes)?
    • What signal molecules are involved? Roles in G20 biofilms
  • Genome editing of a Sulfate reducing bacteria
  • Strengthen the research capability of junior faculty
  • Provide multidisciplinary training to trainees
  • Address issue of Biocorrosion