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Rsani Research

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
  • Methane to Value to Value Added Products
  • Carbon dioxide sequestration by extremophiles
  • Extremophilic Bioprocessing of Solid Wastes (Agri-Wastes) to Biomaterials/Biopolymers (EPSs, PHAs, and Nano-Cellulose)
  • Genome Editing of Extremophiles (Thermophiles, Sulfate Reducing Bacteria, Methanotrophs)
  • Meta-Omics (Epigenetics, Transcriptomics, Metagenomics, Meta-transcriptomics)
  • In-silico (Simulations/Modeling of Proteins, and Bioinformatics)
  • Space Biology (Effects of Micro-Gravity on Extremophiles)
  • Anaerobic digestion of Food wastes to Biofuels (Ethanol, Butanol, Hydrogen)
Research Scientists 0
Postdoctoral fellow 2
Graduate students 12
Undergraduate students 7
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,

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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. 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.
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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.

4. 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
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5. NSF 2026: EAGER: Accelerated carbon mineralization sequestration in cation rich rock formations via microbial augmentation and stimulation

Type of Funding: CBET, National Science Foundation
TimeFrame: 2021-2022
Award: $300,000.00

With support from the Division of Chemical, Bioengineering, Environmental and Transport Systems and the NSF 2026 Program in the Office of Integrated Activities, this project aims to explore biologically accelerated carbon mineralization processes in cation rich rock formations. One approach for mitigating excessive carbon dioxide (CO2) in the atmosphere, a factor that contributes to extreme weather and wildfires, is to reduce excessive CO2 levels by capture and storage. However, storage runs the risk that CO2 injected underground as a fluid can migrate and escape. Fortunately, nature has provided a solution through carbonate mineralization in deep rock, which has recently been shown to sequester large quantities of CO2. This award develops laboratory data that would be needed for the design of a potentially high-capacity, long-term carbon sequestration system. As opposed to other processes that rely on fluid CO2 to stay contained below a caprock, this system stores the carbon in the rock as part of the rock itself. A future benefit of such a system is that, as opposed to fracking which induces seismicity, this can be used to reduce seismicity through binding of deep faults. Another potential impact of such technology, if deployed at scale, would be to contribute to sustainability and resilience by reducing extreme weather and wildfire risks. The educational goal of the project is to create interest and curiosity among a diverse range of students by developing demonstrations on greenhouse gas biomineralization.
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6. Bio-Mediated Technique to Control Phase Changes of Porous Media in Seasonally Frozen Ground

Type of Funding:  National Science Foundation
TimeFrame: 2021-2024
Award: $453,047

The growth of ice-lens in porous soil media is a complex thermomechanical process that does not occur just due to the volume expansion of water but rather dependent on freezing rate, heat extraction, the equilibrium of thermal, mechanical, and chemical forces, and effective stress on soil skeleton.The goal of this project is to investigate, optimize, and develop a bio-mediated sustainable approach using the antifreeze proteins (AFPs) from psychrophilic (cold-loving) microorganisms to control the phase change transformations of the pore-water present in the porous media of seasonally frozen ground. The specific objectives of the award are as follows: (1) Conduct fundamental studies with moderate to hyperactive AFPs from different psychrophiles to determine and characterize the antifreeze properties; (2) Investigate the bio-treated soils’ thermal characteristics including thermal hysteresis, phase changes, freezing point and evaluate corresponding ice inhibition, ice shaping, and ice recrystallization activities; and (3) Evaluate the resiliency of the bio-mediated technique to freeze-thaw cycles and investigate the strength and deformation characteristics of the untreated and bio-treated soils. This project will allow the PI to advance the knowledge base in rules of life of psychrophiles, ice mechanics, and soil-ice interfaces, and long-term career in developing resiliency of cold region infrastructure.
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