Industrial Biotechnology

1. Industrial Biotechnology Lesson 4 ISOLATION, SCREENING AND STRAIN IMPROVEMENT

2. Isolation and Screening of IndustrialStrain • Isolation of from the environment is by: • Collecting samples of free living microorganism from anthropogenic or natural habitats. • These isolates are then screened for desirable traits. • Or by sampling from specific sites: • Mos with desired characteristics are found among the natural microflora • After sampling of the organism the next step is of enrichment.

3. Enrichment • Enrichment in batch or continuous system on a defined growth media and cultivation conditions are performed to encourage the growth of the organism with desired trait. • This will increase the quantity of the desired organism prior to isolation and screening.

4. Screening • Subsequent isolation as pure cultures on solid growth media involves choosing or developing the appropriate selective media and growth conditions. • Next step to enrichment and isolation is Screening. • The pure cultures must be screened for the desired property; production of a specific enzyme, inhibitory compound, etc. • Selected isolates must also be screened for other important features, such as stability and, where necessary, non-toxicity.

5. Screening • These isolation and screening procedures are more easily, applied to the search for a single microorganism. • The industrial microorganism should ideally exhibit: • 1. genetic stability • 2. efficient production of the target product, whose, route of biosynthesis, should preferably be well characterized.

6. Screening • 3. limited or no need for vitamins and additional growth factors. • 4. utilization of a wide range of low-cost and readily available carbon sources • 5. amenability to genetic manipulation; • 6. safety, non-pathogenic and should not produce toxic agents, unless there is the target product; • 7. ready harvesting from the fermentation; . • 8. production of limited byproducts to ease subsequent purification problems.

7. Culture Preservation • Streptomyces aureofaciens NRRL 2209 was the first microorganism deposited in a culture collection in support of a microbially based patent application. • Preservation of microbial cultures was critical for all individuals and firms engaged in the search for patentable products from and patentable processes by microorganisms.

8. Culture Preservation • Preservation of cultures by freezing, drying, or a combination of the two processes is highly influenced by resistance of the culture to the damage caused by rapid freezing, the dehydrating effects of slow freezing, or damage caused during recovery. • To minimize damage, agents have been used that protect against ice formation by causing the formation of glasses upon cooling.

9. Culture Preservation • Methods to protect against the negative effects of dehydration include adaptation to lower effective water activity by pre-incubation in high osmotic pressure solutions. • Damage caused by thawing after freezing can be minimized by rapid melting and by the composition of the medium used for growth after preservation.

10. Culture Preservation • There are various preservation methods . • To date, preservation in liquid nitrogen is still the most successful long-term method.

11. Serial Transfer • Based upon its ease of use, serial transfer is often the first “preservation” technique used by microbiologists. • The disadvantages of relying upon this method for culture maintenance include contamination, loss of genetic and phenotypic characteristics, high labor costs, and loss of productivity.

12. Preservation in Distilled Water • This method (Castellani method, 50 years ago) was extensively tested on 594 fungal strains: • 62% of the strains growing and maintaining their original morphology. • In another study, 76% of yeasts, filamentous fungi, and actinomycetes survived storage in distilled water for 10 years.

13. Preservation in Distilled Water • The pathogen Sporothrix schencki concluded that even though long-term survival was good when this procedure was used, there was a noted loss in virulence. • Castellani technique should be considered as one of the options for practical storage of fungal isolates.

14. Preservation under Oil • One of the earlier preservation methods was the use of mineral oil to prolong the utility of stock cultures. • Mineral oil has been found to prevent evaporation from the culture and • Decrease the metabolic rate of the culture by limiting the supply of oxygen. • This method is more suitable than lyophilization for the preservation of non-sporulating strains.

15. Lyophilization • One of the best methods for long-term culture preservation of many microorganisms is freeze-drying (lyophilization). • The commonly used cryoprotective agents are skim milk (15% [wt/vol] for cultures grown on agar slants and 20% for pelleted broth cultures) or sucrose (12% [wt/vol] final concentration). • It should be noted that some plasmid--containing bacteria are successfully preserved by this method.

16. Storage over Silica Gel • Neurospora has successfully been preserved over silica gel. • Preservation on Paper • Drying the spores on some inert substrates can preserve spore-forming fungi, actinomycetes, and unicellular bacteria. • Fruiting bodies of the myxobacteria, containing myxospores, may be preserved on pieces of sterile filter paper and stored at room temperature or at 6°C for 5 to 15 years. • Preservation on Beads • The method involving preservation on beads (glass, porcelain) , developed by Lederberg, is successful for many bacteria.

17. Liquid Drying • To avoid the damage that freezing can cause, a liquid—drying preservation process is applied. • It has effectively preserved organisms such as anaerobes that are damaged by or fail to survive freezing. • This procedure was preferred over lyophilization for the maintenance of the biodegradation capacity of six gram--negative bacteria capable of degrading toluene. • Malik’s liquid-drying method was also found to be markedly superior to lyophilization for the preservation of unicellular algae.

18. Cryopreservation • Microorganisms may be preserved at - 5 to - 20°C for 1, to 2 years by freezing broth cultures or cell suspensions in suitable vials. • Deep freezing of microorganisms requires a cryoprotectant such as glycerol or dimethyl sulfoxide (DMSO) when stored at -70°C or in the liquid nitrogen at -156 to -196°C.

19. Cryopreservation • Broth cultures taken in the mid--logarithmic to late logarithmic growth phase are mixed with an equal volume of 10 to 20% (vol/vol) glycerol or 5 to 10% (vol/vol) DMSO. • Alternatively, a 10% glycerol-sterile broth suspension of growth from agar slants may be prepared.

20. Preservation in Liquid Nitrogen • Storage in liquid nitrogen is clearly the preferred method for preservation of culture viability.

21. Protocol for Cryopreservation with Cryoprotectants by a Two-stage Freezing Process, and Revival of Culture • After centrifugation the supernatant is removed and the pellet, consisting of microbial cells, is dissolved in an ice-cold solution containing polyvinyl ethanol (10% [wt/vol]) and glycerol (10% [wt/vol]) in a 1:1 ratio. • Due to the presence of polyvinyl ethanol, a viscous thick cell suspension is obtained, which is kept for about 30 minutes in an ice bath for equilibration.

22. Protocol for Cryopreservation with Cryoprotectants by a Two-stage Freezing Process, and Revival of Culture • During equilibration, an aliquot of 0.5 to 1.0 ml of the cell suspension is dispensed into each plastic cryovial or glass ampoule. • They are tightly closed, clamped onto labeled aluminum canes, and placed at -30°C for about 1 h or for a few minutes in the gas phase of liquid nitrogen to achieve a freezing rate of about 1°C/min. • The canes are then placed into canisters, racks, or drawers and frozen rapidly at -80°C or in liquid nitrogen.

23. Protocol for Cryopreservation with Cryoprotectants by a Two-stage Freezing Process, and Revival of Culture • For revival of cultures, the frozen ampoules are removed from the liquid nitrogen. • For thawing, they are immediately immersed to the neck in a water bath at 37°C for a few seconds. • The thawed cell contents of the ampoule or vial are immediately transferred to membranes to form a thick layer. • The resulting bacterial membranes with immobilized cells are used as a biological component of a biosensor for activity measurements.

24. Inoculum Development • The primary purpose of inoculum development is to provide microbial mass, of predictable phenotype, at a specific time, and at a reasonable cost for the productive stage of a microbial activity. • Until now, inoculum development has been more art than science. There remains a need, especially at the shake flask or spore-generating stages of the process, for time and “it looks good” criteria to be replaced with biochemical, physiological, or morphological markers as both descriptors of an optimum inoculum and indicators for optimum timing of inoculum transfer: • Inoculum Source

25. Inoculum development • When fungal spores are used as the inoculum source, it is common for conidia produced on an agar slant to be dispersed in sterile distilled water containing 0.01 to 0.1 % Tween 80. • Spore formation of Streptomyces coelicolor on agar was dependent upon the type of agar used, the inclusion of trace elements, the nitrogen source, and a C/N ration between 40 and 100 (68).

26. Inoculum development • Nabais and de Fonseca have optimized a medium for sporulation by Streptomyces clavuligerus. • Spore storage, however, could be a problem, since the spores lost 72% of their viability after storage for 1 week in buffer at 4°C. • Many strains isolated from nature and often strains that have been subjected to a mutation program result in an “unstable” culture, whose productivity can be rapidly lost. • For such strains, a single spore selection step or its equivalent is a necessity for maintenance of productivity.

27. Acclimatization • A number of commercial-level microbiological processes use as the inoculum, at least in part, culture growth that has been part of a previous “production phase. • For fermentation processes involved in the degradation of waste materials, a very important variable is the extent of acclimatization of the inoculum source.

28. Acclimatization • The process lag before initiation of biodegradation decreases with increased numbers of competent microorganisms. • High degradation rates are obtained when acclimated sewage sludge operated in a plant with low retention times is used as the inoculum.

29. Acclimatization h • The use of an acclimatized inoculum has been reported to result in significant improvements in operational efficiencies for xylose conversion to xylitol by Candida guilliermondii grown on a sugar cane hemi-cellulosic hydrolysate. • In the brewery industry, the reuse or pitching of yeast is a common practice.

30. The effect of serial pitching of the yeast inoculum on subsequent re-fermentation has not been well characterized. • The condition of the yeast cell surface as measured by flocculation can be predictive before subsequent fermentation performance.

31. Seed Media • For the design of media used for the production of cell mass, the determination of an elemental material balance is a useful exercise. • For defined media, the determination is a straightforward calculation from the components. • For complex media, Traders’ Co. and other manufacturers of complex nutrients provide the basic data needed to estimate the contribution of various components to the sum of an element.

32. pH • Nutritionally balanced seed media often result in pH values not far from the optimum for culture growth. • To prevent pH extremes in shake flasks, phosphate salts and CaCO3 and/or buffers such as 2-(N-morpholino) ethanesulfonic acid (MES) or 3-(N-morpholino) propanesulfonic acid (MOPS) are often used. • In fermenter inoculum development stages, buffers are usually replaced with the more economical online pH control.

33. Immobilization • The production of microbial inoculum for use in bioremediation, agricultural applications, and waste treatment is limited by the ability of the microorganism to compete in these environments and to be metabolically effective. • One of the methods by which microbial inocula are being improved for these applications is the use of immobilization technology.

34. Immobilization • The unique characteristics of immobilized inocula include • (i) enhanced inoculum viability, • (ii) protection from stress during manufacture, • (iii) enhanced ecological competence, • (iv) increased metabolite production, • (v) UV resistance, • (vi) the opportunity to use immobilized cells as a source of continuous inoculum, • (vii) the opportunity to introduce mixed culture inocula into a process.

35. Immobilization • Storage of the immobilized inoculum is enhanced if cells in beads are incubated in nutrient or supplemented with nutrient when prepared. • A protocol for alginate immobilization is required as homework?

36. Contamination • Microbial contaminant detection usually relies upon the use of differential media and conditions to encourage the growth of likely contaminant in the presence of the inoculated microbe. • It is difficult to detect of contamination in mixed culture fermentation.

37. Contamination • PCR has provided a rapid, effective technique for the detection of a contaminant present at low levels in a sample. • PCR protocols can be applied to mixed culture fermentations either for the detection of a particular contaminant of interest (Listeria monocytogenes) • or for the detection of an indicator organism, such as the detection of E. coli as an indicator of fecal contamination..

38. Phages • Phage contamination is a constant threat to the productivity of any bacterial fermentation process, particularly in fermentations of dairy products. • How to overcome such a problem? • Selection of plasmids that confer phage resistance ( e. g. for lactic streptococci). • Selection of phage-resistant strains (preffered).

39. Phages • The report that alginate-immobilized streptococci were protected from attack by phages is potentially an interesting alternative approach.

40. Mites • They can devastate a culture source or a series of culture sources either by eating the cultures and leaving no viable source or, • more commonly, by causing marked levels of bacterial and fungal cross contamination. • Often the first indication of a problem is agar plates with bacterial or fungal tracks forming in a random-walk pattern across the plate.

41. Mites • Treatment of incubators with acaricides on a preventative-maintenance schedule is also worth considering.

42. Strain Improvement • What is the Need? • With the exception of the food industry, only a few commercial fermentation processes use wild strains isolated directly from nature. • Mutated and recombined mo’s are used in production of antibiotics, enzymes, amino acids, and other substances.

43. Strain Improvement • What Should We Look for when We Plan a Strain Improvement Program? • In general economic is the major motivation. • Metabolite concentrations produced by the wild types are too low for economical processes. • For cost effective processes improved strain should be attained.

44. Strain Improvement • Depending on the system, it may be desirable to isolate strains: • · Which shows rapid growth • · Which shows Genetic stability • · Which are non-toxic to humans • · Which has large cell size, for easy removal from the culture fluid. • ·,

45. Strain Improvement • Having ability to metabolize inexpensive substrate. • Do not show catabolite repression • Permeability alterations to improve product export rates. • which require shorter fermentation times, • which do not produce undesirable pigments, • which have reduced oxygen needs,

46. Strain Improvement • with lower viscosity of the culture so that oxygenation is less of a problem, • which exhibit decreased foaming during fermentation, • with tolerance to high concentrations of carbon or nitrogen sources,

47. Strain Improvement • The success of strain improvement depends greatly on the target product: • Raising gene dose simply increase the product, from products involving the activity of one or a few genes, such as enzymes. • This may be beneficial if the fermentation product is cell biomass or a primary metabolite.

48. Strain Improvement • However, with secondary metabolites, which are frequently the end result of complex, highly regulated biosynthetic processes, a variety of changes in the genome may be necessary to permit the selection of high-yielding strains. • Mutants, which synthesize one component as the main product, are preferable, since they make possible a simplified process for product recovery.

49. Methods of Strain Improvement Up here (mohamed) • The use of recombinant DNA techniques. • Protoplast fusion, • Site-directed mutagenesis, • Recombinant DNA methods have been especially useful in the production of primary metabolites such as amino acids, • but are also finding increasing use in strain development programs for antibiotics.

50. 1. Mutation • In a balanced strain development program each method should complement the other. • Spontaneous and Induced Mutations • Mutations occur in vivo spontaneously or after induction with mutagenic agents. • Mutations can also be induced in vitro by the use of genetic engineering techniques.