Microbiology

Microbiology has applications across several fields, including:

• Agriculture, horticulture and food production
• Food technology and management (from cheese making and brewing to food processing and preserves)
• Disease control and management (Human and veterinary)
• Human Nutrition and Digestion
• Environmental microbiology
• Industrial (mining) microbiology
• Pharmaceuticals
• Genetic engineering

In this course, you'll learn about the taxonomy of microbes, different types of microbes, how to grow cultures, and how several types of microbe affect human health. Bacteria are one of the smallest living things, being just single-celled organisms (though they are slightly larger than viruses). They enter plants through wounds or natural openings such as stomata (tiny epidermal pores on the surface of leaves or stem) or water pores (hydathodes). Most cannot break directly through the cell walls of the 'surface' of a plant though some, e.g. potato scab, can enter through thin tuber walls. Some penetrate through root hairs e.g. root nodule bacteria of legumes. Others enter through specialised cells that produce nectar during flowering, e.g. apple, pear, and quince blight. Bacterial invasion can cause rots, blights, spots, galls, scabs and other symptoms (note: fungi can also cause many of these).

Lesson Structure

There are 9 lessons in this course:

1. Scope and Nature of Microbiology
2. Scope and Nature of Microbiology
   • Why study microorganisms
   • Bacteria
   • Actinomycetes
   • Fungi
   • Viruses
   • Other multicellular microscopic organisms - nematodes, mites
3. Microscopes
   • Types - light, electron and helium ion microscopes
   • Types of light microscope - stereoscope, compound microscope, confocal microscope
   • Electron microscopy - scanning election microscope, transmission electron microscope
   • Helium ion microscope
   • Preparing samples for microscopy
   • Case study - diagnosis of plant disease
   • Selecting pathogen for verification
   • Preparation of pathogens
   • Culture methods and isolation techniques
   • Inoculation
4. Cultures
   • Types of culture - pure, mixed, contaminated
   • Types of glassware
   • Sterilisation
   • Autoclaves
   • Arnold steam sterilisation
   • Dry heat sterilisation
   • Disinfection
   • Filtration sterilisation
   • Low temperature sterilisation
   • Radiation
   • What is used in media
   • Types of media - synthetic, complex, enrichment, selective, differential etc
   • Common examples - MacConkey's agar, Mannitol salt agar
   • Preparing agar plates
   • Streak plate method
   • Pour plate method
   • Staining
   • Maintaining cultures
   • Aseptic technique
   • Preserved cultures
   • Factors affecting microbial growth -pH, temperature, oxygen, moisture, pressure, vitamins, radiation, carbon, nitrogen, etc
   • Stages in development of a plant disease
   • Virus replication cycle
   • The microbiology laboratory
   • Setting up a simple home laboratory
   • Starting out
5. Microbial Taxonomy
   • What is taxonomy - varying opinions
   • Morphology
   • Prokaryotes and eukaryotes
   • Bacteria - Eubacteriales, Pseudomonadales, Clamidobacteriales, Spirochaetales, etc
   • Archaea - Crenarchaeota, Euryarchaeota, Korarchaeota
   • Viruses - ICTV, Baltimore classification
   • Fungi -Oomycotes, Zygomycota, Ascomycota, Basidiomycota, Deuteromycota
   • Others - Helminths,Arthropods
   • Good and bad microorganisms
   • Good things that microorganisms do
   • Bacteria
6. Viruses
   • Virus structure
   • Anatomy of a virion - nucleic acids, capsid, capsomeres, envelopes
   • The infected cell
   • Virus reproduction
   • The infectious cycle
   • Attachment
   • Penetration
   • Un-coating
   • Replication
   • Assembly
   • Release
   • Virus taxonomy
   • Animal viruses
   • Prototype classification
   • Viral diseases
   • Crystallisation of viruses
   • Transmission - body fluid, vector
   • Viral diseases in humans
   • Control and treatments - vaccines, drugs, hygiene
   • Case Study - human swine flu
   • Viral disease in plants - including different specific examples
   • Viral diseases in animals - including different specific examples
7. Other Microbes
   • Fungus biology
   • Case study - candida
   • Protists
   • Plant like protists - Euglenophytes, Chrysophytes, Diatoms, Dinoflagellates
   • Fungus like protists
   • Animal like protists -Amoebae (pseudopods), Flagellates, Ciliates, Sporozoa
   • Helminths
8. Immunology
   • Types of immunity - Acquired Immunity, Active Immunity, Passive Immunity
   • Antitoxins
   • Agglutinins
   • Precipitans
   • Antigens
   • Antibodies
   • Titre
   • Antiserum
   • Immunisation -Sub-unit vaccines, Inactivated vaccines, Live, attenuated vaccines, Toxoid vaccines, Conjugate vaccines
   • General immune response
   • Recognition of self or non self
   • Specificity
   • Heterogeneity
   • Memory
   • Herd immunity
   • Immunological disorders
   • Autoimmune disease
9. Applied Applications
   • Agriculture and horticulture applications
   • Mycorrhizae -Ectomycorrhizae, Endomycorrhizae, Ectendomycorrhiza
   • Soil biological management
   • Nitrogen cycle - Ammonification,Nitrification, Denitrification, Nitrogen Fixation, Immobilisation
   • Improving soil biology
   • Rhizobium Bacteria and Soil Fertility
   • The Rhizobium Bacteria
   • Microbiology and Plant Pathology
   • How Bacteria, Fungi and other Microorganisms Infect Plants
   • Lifecycle of Nematodes
   • Fungi
   • The Role of Insects in the Spread of Disease
   • Food Technology Applications
   • Food microbiology - yeast, algae
   • Microbes - food spoilage factors pH, water, oxygen, food structure
   • Reducing food spoilage
   • Environmental Applications
   • Water disposal
   • Environmental cleanup
   • Reducing greenhouse gases
   • Biological pesticides
   • Water analysis
   • Industrial Microbiology - production, mining
   • Pharmaceuticals
   • Drug therapies
   • Antibiotics, vaccines
   • Obtaining steroids from microorganisms
   • Microbes in Humans
   • Hospital acquired infections
   • Infection control
   • MRSAs
   • Virology
   • Animal/Human interactions -zoonoses
   • Microbiological health management in animals

Aims

• Discuss the nature and scope of microbiology and its potential application to human life and society.
• Determine appropriate tools for studying microorganisms, and how to utilise those tools in a variety of different contexts.
• Describe how to culture different microorganisms in a laboratory.
• Differentiate between different types of microorganisms.
• Determine appropriate ways of finding and applying current information to differentiate between microorganisms you are not familiar with.
• Explain the taxonomy, function and significance of a range of different types of bacteria.
• Explain the taxonomy, function and significance of a range of different types of viruses.
• Explain immunity in plants, animals and humans.
• Identify and explain different practical applications for an understanding of the applications of microbiology.

TYPES OF MICOORGANISMS

There are many different types of microorganisms; active in a world that is largely out of sight; but as we learn more; no longer out of mind.
Microorganisms impact upon humans and everything else in our world, far more than what we commonly recognise.

Bacteria

Although bacteria often join together to form a mass of cells, each one is independent of the others. They multiply by cell division and this can occur at a rapid rate with cell division occurring several times in an hour under favourable conditions. Due to their relatively large surface area and the large number of cells produced they are able to attack plant tissue rapidly if the conditions are right.

Bacteria which feed on dead plant (or animal) tissue are known as 'saprophytes'. Disease causing bacteria are known as ‘parasites’. Many bacteria can live as both parasites and saprophytes. They will often survive on dead plant material until a new plant or crop becomes available, e.g. they can over-winter on dead tissue.

Some species of pathogenic bacteria have external hair-like appendages known as 'flagella' which can be vibrated to enable them to move small distances in water and plant juices. Those without flagella can still be relocated through the splashing of water or wind-blown droplets, for instance. They can also be spread by movement of soil from one location to another.

Once bacteria have entered the plant tissue they may move about in the plant juices within or between cells, or they can be transported within the sap stream. Usually bacteria are found between the cells at the onset of disease but as the cell walls become damaged they are able to penetrate the cells.

The symptoms produced by a plant in response to bacterial invasion are often indicative of the disease e.g. galls, wilts, spots etc. These symptoms and their effects are similar to those of fungal infections. Galls normally only affect one part of the plant, wilts affect the whole plant, and rots may affect one part or the whole plant. Bacterial infections are very difficult to treat because very few chemicals or fungicides can control them.

Actinomycetes

These organisms are somewhat similar to bacteria but they are not motile (capable of independent or spontaneous movement). The only species of importance to plant pathology are the Streptomycetes spp. known to cause common potato scab.  Acid scab (Streptomyces acidiscabies) of potatoes for example most frequently occurs in very acid soil conditions i.e. a pH under 5.2 (producing the typical superficial lesions on the surface of the potato known as scab). The second pathogen (that occurs on less acidic through to alkaline soils) is S. scabiei, this produces raised lumps and raised lesions on the surface of the potato.

Fungi  

Fungi are members of the 'thallophyte' group of plants and do not produce chlorophyll. Since fungi do not generate their own energy from photosynthesis, they must feed off other organic material.  Like bacteria, they are either usually parasites or saprophytes, but most can alternate between the two states. There are over 15,000 species known, with estimates of more than 100,000 in existence, and many are responsible for major plant diseases. They are thread-like organisms which grow among the tissue they derive their nutrition from, and the individual threads or 'hyphae' are collectively known as 'mycelium'. To reproduce, they grow fruiting bodies from a mass of mycelia and spores are produced in these fruiting bodies. Fruiting bodies serve as a useful form of identification.

Mycelia are microscopic and therefore many fungal diseases have to be diagnosed by symptoms rather than the presence of the organism. However, in some species where the mycelia come together to form bracket fungi or toadstools for example, identification is easier.

Viruses

Viruses are very small microscopic particles composed of nucleic acid and protein. They are more similar to chemicals than living organisms and represent the greatest cause for concern of all the pathogens. They exhibit many, but not all, characteristics of living organisms and, as such, are sometimes called a life form. Mostly, they are not considered a life form. Viruses can only replicate inside a living host cell.

Viruses only contain only one kind of nucleic acid, either DNA or RNA. This nucleic acid may be single- or double-stranded, and is enclosed by a protein coat called a capsid. Some viruses also contain enzymes, and some are surrounded by a bilayer membrane called an envelope.
Viruses can mutate. They cause many serious diseases and frequently cause variegation or mottling of leaf colour. Some viruses are considered beneficial because of the variations they provide in leaf colour – this is how we have come by many of our variegated-leaf plants. To retain the leaf variegation though, plants have to be propagated vegetatively, as seed grown plants will revert back to the appearance of the parent plant. Whether considered beneficial or not, viruses cause a general weakening of the plants they infect, making the plant more susceptible to other problems and often stunting growth to some degree.

Viruses are able to multiply rapidly in plant material. Most are introduced to plants by the action of insect pests, such as aphids. These act as vectors, carrying and spreading the virus. Some viruses may be spread by pollen or seeds. Others may enter wounds caused by mechanical damage, e.g. foot traffic or strong winds or by an infected plant coming into contact with a non-infected one.

Typically, viruses invade all the cells of an infected plant which makes the virus incurable. In both horticulture and agriculture these infected plants have to be destroyed by burning.

Another pathogen, referred to as 'mycoplasmas' are somewhere between the size of viruses and bacteria. These are transmitted by pests such as mealy bug, aphids, mites and leaf hoppers. Infected plants usually should be destroyed.   

Other multi-cellular organisms

Other multi-cellular organisms include a whole range of tiny living things from nematodes to mites. These are generally impossible to see with the naked eye, but can be far larger and more complex than bacteria, viruses and protozoa.

HOW THEN IS MICROBIOLOGY APPLIED?

Microbes need to be managed in many different situations; sometimes to eliminate or preclude them; but at other times to introduce or support their activity. Examples include:

• In human or animal bodies - Disease causing microbes can be killed or brought under control by many methods, from using pharmaceuticals on animals and humans, to spraying pesticides on plants. Sometimes beneficial microorganisms need to be encouraged as well. Using probiotics can help digestion in humans. Managing exposure to damaging microbes is another important way of controlling disease.
• In soil certain microbes (eg. mycorrhizae and rhizobia) are helpful in facilitating plant nutrition. Other microorganisms decompose organic matter into nutrient chemicals which plants can absorb.Compost making would not happen without microbes.
• Excluding microbes from propagation areas is important to the success of propagating plants.
• Microbiologists use their skills in research, laboratory and pathology testing.
• Commercial examples include brewing and wine making, mushroom production; production of vaccines and pharmaceuticals, production of yeast for baking, the use of bacteria in making cheese and yogurt, etc.
• Bioremediation e.g. microbes used to manage oil spills, pollution, degrading of organic compounds etc.
• Production of biofuels relies on the action of microbes.