1. Industrial Production & Bioremediation
Microbes for industrial production
Preservation of cultures
Methods of industrial production
Major products of industrial microbiology
Bioremediation
Biosensors & microarrays

2. Microbes for industrial production
Finding microorganisms in nature
Only a small percentage of microbial species have been cultured
Bioprospecting: Hunting for new microorganisms with potential for commercial exploitation
Great deal of interest in microbes from extreme environments
Challenge is to develop cost-effective techniques for their culture

3. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

4. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

5. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

6. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

7. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

8. Microbes for industrial production
Genetic manipulation
Altering the characteristics of existing known species to produce new and desirable characteristics
Mutations can be induced with mutagenic agents or UV irradiation
Example: Development of high-yield cultures of Penicillium for penicillin production
Protoplast fusion can be used to fuse cells of eukaryotic microbes and microbes that are not phylogenetically related; used especially for genetic manipulation in yeasts & molds

9. Microbes for industrial production
Genetic manipulation
Site-directed mutagenesis is the insertion of short segments of DNA (using recombinant DNA technology) into a gene to lead to desired changes in its protein product
Recombinant DNA can be transferred between different organisms, creating combinations of genes with exhibit desired characteristics
Shuttle vectors: Vectors (such as bacterial plasmids) that can replicate in more than one species
Expression vectors: Vectors that have transcriptional promoters capable of mediating gene expression in the target species.

10. Microbes for industrial production
Genetic manipulation
Gene expression can be modified by altering transcriptional regulation, fusing proteins, and removing feedback regulation controls
This is used for pathway architecture, or metabolic pathway engineering, to increase or regulate production.
Natural genetic engineering
Growing cultures under marginal (“stressful”) growth conditions and selecting for new strains (spontaneous mutations) that have increased growth in those conditions

11. Preservation of cultures
Periodic transfer + refrigeration
Mineral oil slant + refrigeration
Washed culture + refrigeration
Freezing
Freezing with 50% glycerol
Drying
Lyophilization (freeze drying)
Ultracold freezing

12. Methods of industrial production
Medium development
Lower-cost ingredients, such as crude plant or animal by-products, are used for cost-effectiveness
Manipulating the levels of a limiting nutrient may be critical to trigger or optimize the production of a desired product

13. Methods of industrial production
Scaleup
Successive optimization of growth & product yield from a small scale (such as a shaking flask or small fermenter) to a large scale (such as industrial scale fermenters)
Mixing, aeration, pH control, foaming, & formation of filamentous growth or biofilms are significant issues in scaleup

14. Methods of industrial production
Methods for mass culture
Batch fermentation
Continuous culture (chemostat)
Lift-tube fermentation
Solid-state fermentation
Fixed-bed reactors
Fluidized-bed reactor
Dialysis culture unit

15. Methods of industrial production
Primary & secondary metabolites
Primary metabolites are produced during the growth phase of the microbe. Examples: amino acids, nucleotides, fermentation end products, and many types of enzymes
Secondary metabolites accumulate during periods of nutrient limitation and waste buildup. Examples: many antibiotics and mycotoxins

16. Major products Antibiotics Recombinant DNA products
Examples: penicillin & streptomycin
The yield of both of these antibiotics are optimized by nutrient limitation (carbon & nitrogen)
Recombinant DNA products
Proteins produced from genes introduced into microbes via recombinant DNA techniques, such as enzymes, peptide hormones, recombinant vaccines

17. Major products Amino acids
Glutamic acid (monosodium glutamate) is produced by regulatory mutants of Corynebacterium glutamicum that have a modified Krebs cycle that can be manipulated to shift -ketoglutarate to glutamate production
Lysine is produced by a Corynebacterium glutamicum strain in which homoserine lactone synthesis is blocked

18. Major products Other organic acids “Speciality” compounds Biopolymers
Acetic acid, citric acid, fumaric acid, gluconic acid, itaconic acid, kojic acid, lactic acid
“Speciality” compounds
A variety of drugs (cholesterol drugs, immunosuppressants, antitumor drugs), ionophores, enzyme inhibitors, pesticides
Biopolymers
Microbial-produced polymers, mostly polysaccharides, useful as thickening or gelling agents in foods, pharmaceuticals, paints, etc.

19. Major products Biosurfactants Bioconversions
Microbial-produced detergents, such as glycolipids; used in bioremediation applications such as oil spill cleanups
Bioconversions
Using a microbe as a biocatalyst to convert a substrate into a desired product; for example, in the modification of steroid hormones

20. Bioremediation Biodegradion in natural communities Includes:
minor changes in organic molecules, leaving the main structure still intact
fragmentation of an organic molecule into smaller organic molecules, still resembling the original structure
complete mineralization of an organic molecule to CO2
Recalcitrant compounds are organic compounds that are resistant to biodegradation

21. Bioremediation Biodegradion in natural communities
Halogenated compounds, especially halogenated aromatic compounds (such as polychlorinated biphenyls) are often recalcitrant
The presence of halogens in a meta position makes the compound more recalcitrant
Often one stereoisomer of an organic compound will be biodegradable, while another isomer will be recalcitrant
Specific organisms in an environment may be able to degrade recalcitrant compounds, at varying rates depending on the conditions

22. Bioremediation Biodegradation in natural communities
Sometimes partial degradation of a compound may yield compounds that are worse; for example, trichloroethylene can be degraded to form highly carcinogenic vinyl chloride
Another example of detrimental biodegradation is microbial corrosion of metal pipes

23. Bioremediation Stimulating biodegradation
Biodegradation by naturally-occurring organisms may be stimulated by
Adding essential nutrients to the contaminated area
Providing aeration or limiting aeration, depending on whether the contamination is better degraded under aerobic or anaerobic conditions
Using plants and the microbial communities of their rhizospheres (phytoremediation)
Using microbes for metal bioleaching from minerals

24. Bioremediation Bioaugmentation
Adding microbes not normally found in an environment to try to alter or accelerate the biodegradation process
When the microbes are added without consideration of their “normal” habitat (e.g., just adding a pure culture), there may be short-term improvement but the added microbe usually fails to establish a stable population
Better results are may be seen when the added organism’s microenvironment (nutrients, oxygen, aeration, etc.) are included in the bioaugmentation strategy

25. Biosensors & microarrays
Devices in which a biospecific molecule (e.g., a monoclonal antibody or a hormone receptor protein) is attached to a “transducer” (often a piezoelectrically-active quartz chip)
When the biosensor binds to its target, it slighty “twists” the transducer, creating a small electrical current that can be amplified, detected, and measured

26. Biosensors & microarrays
A series of microscopic DNA spots on a glass, plastic, or silicon backing; used to monitor levels of gene expression for thousands of genes simultaneously, or to determine differences in genotype