Microbial Biotechnology

The following sections are included:

• List of Contributors

• Preface

• Contents

The use of microorganisms for large-scale industrial purposes has a long history, which is long before the realization of the activities of the microorganisms. For centuries, beer, wine, vinegar, soy sauce and other fermented foods were produced through spontaneous fermentation of natural occurring microorganisms or the use of carry-over microbial seeds from the previous batch of production. The quality and productivity of these early products were very often inconsistent. The development of scientific screening and isolation methods allows the selection of desirable natural occurring or mutated microorganisms for specific purposes. These methods, coupled with the advancement of the technical know-how in large-scale sterilization of culture media, in provision of adequate oxygen supply and in mixing homogeneity of the culture systems, enable the exploitation of both anaerobic (yeast and some bacteria) and aerobic microorganisms (fungi and some bacteria). Common examples are: the development of large-scale processes for the production of citric acid, amino acids and antibiotics; in improved biotransformation of steroid hormones, as well as the mass production of many enzymes. The diverse catalytic activities of microorganisms are being used more and more widely to perform specific chemical reactions in the industrial production processes…

The following sections are included:

• Introduction

• Screening for New Antibiotics

• Screening for Beneficial Cultures

• Screening for Antimicrobial Peptides

• Screening for Low Molecular Weight Peptides

• Screening for Potential Bacteriocins

• Screening for Non-Proteinaceous Fermented By-Products

• Requirements of Screens

• Screening Process

• Screening Methods

• New Screening Technology

• Further Readings

Bioprocess technology is the industrial application of biological processes involving living cells or their components to effect desired transformation of substrates. The major advantages of bioprocesses over traditional chemical processes are that they require mild reaction conditions, are more specific and efficient, and produce renewable by-products (biomass). The development of recombinant DNA technology has expanded and extended the potential of bioprocesses.

The following sections are included:

• Enzymes as Catalysts

• Nomenclature

• Cofactors

• Regulation of Enzyme Activity

• The Michaelis-Menten Equation

• Inhibition of Enzyme Activity

• Industrial Applications of Enzymes

• References

• Further Readings

• Relevant World Wide Web Sites

This chapter focuses on the ways in which molecular genetic techniques can be used to manipulate genes in order to alter the expression and production of microbial products, including the expression of novel recombinant products. “Classical” (in vivo) genetic techniques are essentially limited by two factors. Firstly, they can only be applied to the existing genetic complement of an organism, i.e. they are restricted to naturally occurring genes or relatively minor modifications of these genes. It is not possible to get an organism to make a product totally foreign to that organism using these techniques. Secondly, with classical techniques, one can only work on the basis of phenotype and mutants are selected by their effect on the observable characteristics of the organism. This not only limits the changes that can be selected, but also means that it can be difficult to determine the nature of the mutation that has caused the alteration in the phenotype…

The following sections are included:

• Introduction

• Gene Cloning

• DNA and Protein Sequencing

• Outline of a Search Strategy

• Data Mining for Gene Hunting

• Sequence Comparisons and Alignment

• Protein Structure Prediction

• Useful Tools and Websites on the Internet for Microbiological Research

• Summary

• Further Readings

The fermented foods industry today is a big business and is the result of developments from traditional, small-scale production methods. Over the millennia, mankind has learnt to manipulate microorganisms and the environment of food to encourage the growth of desirable organisms that result in valuable foods which have good keeping quality and flavors…

Fermented foods are those that have been transformed by microbial action or enzymes to produce desirable biochemical and physical changes. Fermentation, from the perspective of the microorganism, is an oxygen free process (anaerobic) in which an organic compound endogenous to the organism acts as the final electron acceptor. However, in food fermentations some microorganisms use oxygen as the final electron acceptor. These processes are also referred to as fermentations (Fig. 6.1). In addition, another food fermentation commonly referred to is the tea fermentation that is not a microbial process at all but an endogenous enzymic oxidation process. The microorganisms responsible for food fermentation include bacteria, yeasts and moulds…

In ancient times, alcoholic beverages were an important part of the diet. They provided a way of storing the food value in otherwise perishable agricultural products and provided important nutrients, including vitamins, in the diet. Today, these products are consumed for their flavors, their alcoholic content and its effects, and food value. The quality of the final beverage rests as much on the ethanol production as it does on the development of flavoring compounds in the final product. Production of ethanol may be the prime purpose of production methods but the final flavor does not depend on the ethanol producers alone. In addition to yeasts other than S. cerevisiae, bacteria play a role in the development of the final desirable flavor of an alcoholic beverage…

The following sections are included:

• Flavors and Fragrances

• Antioxidants

• Essential Amino Acids

• Essential Fatty Acids

• Polysaccharides

• Microbial Meat Substitute — RHM Mycoprotein

• Organic Acids
  • Citric acid
  • Lactic acid

• Colorant
  • Monascus pigments
  • Algal pigments

• Further Readings

The discovery of enzymes and their isolation opened up the possibility of using the enzymes to modify foods. Microbial enzymes can be produced cheaply in large quantities and because microorganisms grow under a wide range of environmental conditions, the enzymes can be used in relatively extreme conditions. Enzymes have been isolated to modify fats, carbohydrates and proteins as well as in other applications.

Molecular biological methods have becoming increasingly applicable to the diagnosis of infectious diseases and vaccines development in veterinary medicine. The commonly employed microbiology and virology assays and the conventional serological test to identify microorganisms are often not specific and sensitive enough to make the diagnosis in a short period of time. However, with advances in diagnostic methods based on immunology and molecular biology technology, these methods are rapidly invading into laboratories as the preferred choice for diagnosis of animal diseases. The reasons are that these methods are user friendly, safe, cost effective, reproducible and some are automated to facilitate the evaluation of large numbers of specimens…

We have charted an amazing growth rate in the human population in the last two centuries. From 1804 to about 1900, the world population had increased from one billion to more than two billion people. However, by 1974, the human population had doubled to four billion people. To date, there are more than six billion people in the world, with the figure still growing daily (Fig. 10.1). This rapid increase signals some major problems, like the shortage of food to meet human demand…

Plant biotechnology has opened a new era of agricultural revolution by introducing genes from different organisms to generate new varieties of plants — genetically modified (GM) plants. Among them, the new food crops (such as grain crops, vegetables and fruits ) will have higher yield, better nutritional qualities, resistance against pests (insects, diseases, nematodes, weeds and abiotic stresses), others will help us to produce new industrial raw materials (oil, starches and biodegradable plastics) and pharmaceutical products. Despite the great economical and humanitarian potentials, plant biotechnology has caused great concerns about the safety of the genetically modified (GM) foods, the environmental impact of GM plants, and moral issues. In this chapter, both technical and regulatory aspects of plant biotechnology will be discussed in detail. The future success of plant biotechnology depends on science-based facts, proper governmental regulations and public education efforts…

The staggering breakthroughs in medical and microbial biotechnology, notably in molecular biology, have led to great strides in the understanding and treatment of human diseases. Monoclonal antibodies, gene probes and polymerase chain reaction offer improved diagnosis of infectious diseases and other ailments. Microbial and animal host cells, transgenic animals and plants generate genetically-engineered, high value pharmaceuticals and vaccines in large quantity. Sophisticated structural studies and computer modeling of complex molecules permit the design of novel drugs. Previously intractable infections are now preventable by novel immunization strategies using recombinant DNA technology, and amenable to new anti-microbial agents discovered from nature. Complemented by the enormous Human Genome Project, gene therapy is at the threshold of a new dimension in medical science. Recognizing the impact of these advances on human health and economic development, scientists are harnessing these enabling technologies to meet the new challenges in medicine, including the disciplines of medical microbiology and infectious diseases.

The 21st Century is hailed as a potentially significant milestone in human history that will witness the next new wave of technology, namely the Biotechnological Revolution whose seeds were sown with the advent of many critical advances in molecular biology. Biotechnology is the integrated and practical application of bioscientific and engineering disciplines to the industrial processing of materials by biological agents to provide useful products and serve other desirable purposes. Recent advances in biotechnology have tremendous impact on numerous fields of human endeavor, including the food and agricultural industry, environmental management, and notably medicine. Fundamental scientific research in medicine, genetics, immunology and communicable diseases accelerated the discovery of new biotechnological innovations, especially in molecular biology over the last 30 years culminating in this “golden age of biology”. This leads to a better understanding of the principles of human health, disease etiopathogenesis, prevention and management, with important implications in clinical medicine and health care. For example, significant advances in unraveling the molecular mechanisms of cancer, a major global health problem, have been accomplished through the study of oncogenic viruses…

Robert Koch was a medical doctor and a great microbiologist who first identified Bacillus anthracis as the causative agent of anthrax in the late 1880’s. Since then, many other bacteria were identified and later shown to be responsible for different infectious diseases. Examples of some bacteria that can cause infections include Vibrio cholerae (causes cholera), Pseudomonas aeruginosa (wound infection), Corynebacterium diphtheriae (diphtheria), Clostridium perfringens (gas gangrene), Clostridium botulinum (botulism), Shigella dysenteriae (shigellosis), and Bordetella pertussis (whooping cough).

By the turn of the last millenium, the rapid development in various areas such as microbiology, genetics, biochemistry and chemical engineering has led to tremendous advances in the knowledge and applications in biotechnology. The previous chapters of this book describe the applications and development of biotechnology in industry, agriculture and medicine. In Part V of this book, the development of biotechnology in environmental applications will be introduced. Because there are numerous applications in this area, only selected topics will be discussed in detail with emphasis on the applications of microorganisms in the biotechnological processes for solving environmental problems…

The specific application of biotechnology to environmental management and pollution control is generally referred to as environmental biotechnology. It is used in waste and wastewater treatment as well as environmental cleanup encompassing toxic waste decontamination and the biodegradation of oils, pesticides and other organics. Microorganisms are in general more effective than multicellular organisms in environmental treatment, although higher plants are frequently used in phytoremediation and hydrophyte treatment systems. Municipal systems are usually mixed-substrate, mixed-culture continuous operations. Most processes are aerobic, but few are anaerobic. Some processes such as composting and anaerobic digestion are multi-stage and involve both mesophilic (15–40°C) and thermophilic (45–70°C) organisms under different operational conditions. The majority of treatment processes makes use of the indigenous populations in the wastes and provides favorable conditions for the growth and metabolic activity of these microorganisms. Industrial treatment systems often use pure strain (monoculture) of artificially screened microorganisms, while the degradation of xenobiotics may employ genetically engineered microorganisms in laboratory trials or pilot scale systems…

The following sections are included:

• Removal of Inorganic Pollutants
  • Removal of metal ions in industrial wastewater
  • Metal pollution in Hong Kong
  • Toxicity of metal ions in the environment
  • Methods of removal of metal ions from industrial effluent

• Removal of Organic Pollutants from Industrial Wastewater
  • Azo dyes
  • Treatment of industrial effluent containing azo dyes

• References

The following sections are included:

• Composting

• Bioremediation of Contaminated Surface and Subsurface Sites

• Microbes in Mining

• Microbial Desulfurization of Coal

• Biodegradable Plastics

• Detoxification of Metal Ions
  • Demethylation and reduction of mercury
  • Reduction of chromium

• Further Readings

Photosynthetic microorganisms, such as micro-algae and cyanobacteria are able to harness low-intensity solar energy and store it as latent chemical energy in the biomass, which can then be released via biochemical conversion. Various photobioreactors have been developed to allow maximum uptake and storage of solar energy. The structural and storage carbohydrates in biomass have low energy content and it is necessary to concentrate the energy content further for fuel application. Anaerobic microbial fermentation is an efficient and widely used method for such conversion processes. Useful renewable fuels produced by microorganisms include hydrocarbons, ethanol, methane and hydrogen. Biofuel cells that are able to release energy in fuel chemicals to generate electrical energy at ambient temperatures have been developed.

The 1973 oil embargo and accompanying soaring oil prices together with the recognition that natural fuel reserves are being rapidly depleted, led to a worldwide interest in the development of alternative renewable fuels. Microbial production of fuels has the potential for helping to meet world energy demands. Living organisms assimilate and concentrate energy in their biomass and products. Hence, biomass in its various forms is an attractive alternative source of energy. Through photosynthesis, biomass collects and stores low-intensity solar energy, which can then be harvested and released via biochemical conversion. Biological processes are involved in both the harnessing of solar energy and upgrading of low energy feed stocks to biomass fuels. Useful fuels produced by microorganisms include biodiesel (produced from algal oils), ethanol, methane and hydrogen.

Most governments see at least part of national future prosperity in the expansion of life sciences research, either by exploiting natural resources such as indigenous medicinal plants and thermophilic bacteria, or by supporting a workforce skilled enough to compete in the de novo design of new drugs, as well as genetically modified animals and crops. So much money will be spent on development that those who finance it will insist that wherever possible its fruits will be protected from exploitation by others, that is, patented. All scientists, including microbiologists, would do well to be aware of the prerequisites and procedures involved.¹ Put briefly, the invention must be novel (not already identifiable in practice or in the literature), it must involve an inventive step (something not obvious to those already in the field) and it must have some industrial application. In return for meeting these criteria, the invention will be protected against exploitation by others for twenty years. In regard to exactly what may be patented however, there are certain exclusions, such as devices, which offend public morality, as well as theories and discoveries. Methods of medical treatment were previously non-patentable but are now of debatable status.²

The following sections are included:

• Territorial Nature of Patents

• Inventive Step

• Industrial Application

• Procedure and Form
  • Search
  • Claims
  • Embodiments
  • Filing
  • Priority
  • International application
  • Publication
  • Grant

• Recent Trends in Biotechnology and Microbiology Patents
  • Microbial products
  • Base and amino acid sequences
  • Life forms per se
  • Algorithms, methods and processes
  • Mosaicism

• Potential Licensees

• References and Notes

The following sections are included:

• Index