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Title Slide

  • Copyright: University of Reading

  • Topic: Limitless Potential | Limitless Opportunities | Limitless Impact

  • Lecture: Benefits of Microbes: Industrial and Biotechnological Applications

  • Instructor: Dr. Glyn Barrett (glyn.barrett@reading.ac.uk)

  • Course Code: BI1FM1 Fundamentals of Microbiology

Learning Outcomes

  • Overview of important uses of microbes in various fields including:

    • Natural Product Production:

    • Biopolymers

    • Pharmaceuticals

    • Antibiotics

    • Biocontrol Agents:

    • Biological pesticides in agriculture

    • Biotechnology:

    • Recombinant DNA Technology: CRISPR/Cas9

    • Bioremediation:

    • Removal and/or breakdown of pollutants from contaminated land or water.

Natural Products

  • Exploitation of Bacteria:

    • Bacteria can be exploited for various natural products:

    • Antibiotics: Natural antimicrobial agents

    • Amino Acids: Building blocks of proteins

    • Organic Acids: Essential metabolic products

    • Biopolymers: Repeating units that form larger structures

    • Medically Important Compounds: Various compounds critical for health

    • Zones of Clearing on a Petri Dish: areas where microbial activity has ddestroyed / inhibited the growth of other organisms creating clear zones

    • The zones are observed in experiments test for

    • clear zones are observed in experiments testing foe antimicrobial

Production of Antibiotics

  • Natural Origins:

    • Most antibiotics are derived from microorganisms or are their natural products.

  • Governance by Environmental Conditions:

    • Production of antibiotics is often influenced by the surrounding environmental conditions.

  • Mechanisms of Production:

    • Usually produced as a by-product of secondary metabolism.

    • Example: Streptomyces spp. which produce antibiotics, specifically the metabolite Geosmin.

Using Microbes Against Other Microbes

  • Historical Context:

    • Penicillin was the first antibiotic discovered.

  • Mechanisms of Action:

    • Antibiotics can act in several key ways:

    • Prevent replication: Inhibit the growth of bacteria

    • Kill directly: Destroy bacterial cells

    • Damage cell wall or prevent its synthesis: Compromise the structural integrity of bacterium precedes cell lysis

Secondary Metabolism

  • Definition and Context:

    • Microorganisms modify their metabolism when under stress, particularly under growth/nutrient limitations or specific growth phases.

  • Survival Strategy:

    • Alterations in metabolism are thought to aid in survival and competition elimination.

Production and Scale of Secondary Metabolites

  • Complexity of Production:

    • Secondary metabolites are often large organic molecules requiring extensive enzymatic pathways for production.

  • Example:

    • Tetracycline production necessitates at least 72 separate enzymatic steps involving approximately 300 genes with complex regulatory mechanisms.

Production of Biopolymers

  • Overview of Microbially Produced Polymers:

    • Key roles in cell growth and division, widely utilized in:

    • Food Industry: Modify texture

    • Pharmaceuticals: Serve as gelling agents

    • Types include:

    • Polynucleotides: RNA/DNA

    • Polypeptides: Chains of amino acids

    • Polysaccharides: Sugars and starches

Applications of Biopolymers

  • Diverse Uses of Biopolymers:

    • Applications extend to:

    • Paints

    • Absorbents

    • Plastics production

    • Food thickeners

    • Drilling lubricants

    • Asphalt

Xanthan Gum

  • Definition:

    • An exopolysaccharide produced by the bacterium Xanthomonas campestris, known for causing black rot in cauliflower.

  • Production Method:

    • Laboratory media cultivation and precipitation with alcohol, followed by drying and milling.

  • Use:

    • Increases viscosity in liquids; serves as a thickening agent.

Biocontrol

  • Definition:

    • The control of pest species using other living organisms.

  • Objectives:

    • Aimed at reducing pest numbers rather than eradicating them, utilizing natural ecological balance.

  • Examples:

    • Use of bacteria (or fungi or viruses) or their products as bioinsecticides, notably Bacillus thuringiensis (Bt) is widely utilized.

Bacillus thuringiensis

  • Characteristics:

    • Common soil bacterium available in various forms (species & strains).

  • Mode of Action:

    • Produces proteins toxic to insects; commonly used in garden sprays and commercial agriculture, including organic farming.

  • Human Health & Environmental Safety:

    • Well known for its safety regarding human health and environmental impact.

Bt Toxin

  • Longevity and Release:

    • Used globally for over 40 years, with no accumulation in soil or non-target species. Readily degraded under abiotic conditions.

  • Genetic Engineering:

    • Gene for Bt toxin, cry, was cloned into plants around 1996, resulting in commercialization of Bt-corn, Bt-potato, and Bt-cotton.

  • Global Impact:

    • Utilized extensively in both developed and developing countries.

Mechanism of Bt Toxin Action

  • Process:

    • Toxin ingested by insects; alkaline conditions convert it, resulting in:

    • Fragmentation into protoxin

    • Reaction with proteases creates active toxin

    • Active toxin binds to gut receptors, causing cell lysis.

Recombinant Products

  • Genetic Engineering Basics:

    • Involves inserting genes from one organism into a different organism.

  • Historical Significance:

    • Pioneering work demonstrated by Stanley and Cohen in the early 1970s.

  • Universal DNA:

    • DNA is the same across different life forms, allowing for such genetic manipulations.

Production of Insulin via Recombinant DNA

  • Process Overview:

    • Human insulin gene is inserted into an E. coli plasmid and the bacteria then produce insulin.

  • Technical Steps:

    • Insert human gene into high copy number plasmid.

    • Transform E. coli with the recombinant plasmid to yield human insulin.

Ethical Considerations with Recombinant Insulin

  • Concerns:

    • Ethical issues surrounding the use of animal-derived products; advantages include:

    • Free from infectious agents like BSE

    • Differences in amino acid composition in porcine and bovine insulin, facilitating modification of insulin properties (absorption, distribution, metabolism, and excretion).

CRISPR/Cas9 Overview

  • Definition of CRISPR:

    • Clustered Regularly Interspaced Short Palindromic Repeats: Consists of repeated palindromic sequences interspersed with viral DNA fragment sequences.

  • Functionality:

    • Acts as a bacterial immune system to detect and cleave foreign viral DNA with ribonucleases and helicases.

Applications of CRISPR/Cas9

  • Gene Editing Capabilities:

    • Enables researchers to perform precise gene knockouts, insertions, deletions, and SNPs in organisms.

    • Requires two chief components: Cas9 (endonuclease) and guide RNA (gRNA).

  • Mechanism of Action:

    • gRNA guides Cas9 to specific DNA sequences, where it unwinds and cleaves both strands.

Practical Applications of CRISPR

  • Use Cases:

    • Rapid diagnostics, modification of genes, correcting genetic mutations to counter disease, removal of malaria from mosquitoes, and targeting cancer cells for destruction.

Bioremediation

  • Definition:

    • The use of microorganisms (or plants) to restore environments affected by contaminants.

  • Main Types:

    • Biostimulation: Adding nutrients and oxygen to stimulate growth of existing bacteria.

    • Bioaugmentation: Introducing specific microorganisms capable of degrading certain harmful contaminants.

Biostimulation Explained

  • Process Overview:

    • Adding nutrients and oxygen to enhance existing microbial activity.

    • Monitoring the disappearance of contaminants to assess remediation effectiveness.

Bioaugmentation Explained

  • Process Summary:

    • Introducing specialized microorganisms into contaminated environments, typically more effective when the cleaning agents are removed from the original site.

Case Study: Atrazine Bioremediation

  • Example:

    • Bioremediation methods utilizing biodegradable beads containing bacteria designed to remove atrazine, an herbicide from municipal water treatment facilities.

Bioremediation Benefits

  • Advantages:

    • Cost-effective and capitalizes on natural remediation processes, minimizes disturbance to the environment, and efficiently mineralizes contaminants.

Limitations of Bioremediation

  • Challenges:

    • Failures may arise due to microbes not thriving in substrate-rich conditions, lack of access to contaminants, nutrient deficiencies, competition, or if other substrates are preferred by the introduced organisms.

Other Considerations

  • Site Specificity:

    • Unique conditions at each site can complicate successful bioremediation. Laboratory controlled conditions may not align with field conditions.

  • Ethical Concerns:

    • Objections to introducing foreign species or genetically manipulated organisms into ecosystems.

Further Reading

  • Reference Texts:

    • Prescott, Harley and Klein

    • Specific sections pertaining to each topic of focus for further studies:

    • Microorganisms as/in Food – pp. 1023-1048

    • Natural Products – pp. 1070-1074

    • Recombinant Products – pp. 357-382

    • Biocontrol – pp. 1083-1086

    • Bioremediation – pp. 1075-1082

    • Sewage Treatment – pp. 1055-1060