MICROBIOLOGY

Microbiology is Critical to all Horticulture

If you have not studies microbiology, and you work in horticulture; your daily work is akin to someone trying to do a two handed job with one hand tied behind their back.

Every Gardener or Horticulturist will Benefit from a solid Understanding of Microbiology.

This course is a comprehensive introduction to both theoretical and applied microbiology. It helps you to better manage plant production, workplace safety and much more.

• Learn about viruses, bacteria and other disease organisms - understanding the organism is the first step to controlling it
• Learn about the tools of the microbiologist, from microscopes to laboratory equipment.
• Learn about the techniques used to detect, study, and analyse living organisms that can't be seen with the naked eye, but which can impact dramatically upon the success of work in any sector of horticulture

Lesson Structure

There are 8 lessons in this course:

1. Scope and Nature of Microbiology
   • Why study microorganisms
   • Bacteria
   • Actinomycetes
   • Fungi
   • Viruses
   • Other multicellular microscopic organisms - nematodes, mites
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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

What are 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 mites and leafhoppers and again, infected plants usually have to be destroyed.   

How Viruses are Classified

Viruses are typically not divided into conventional taxonomic groups. Instead they are grouped according to properties, such as the nature of the nucleic acid they contain.

In the plant world, viruses have also been classified in a number of ways. In the past, plant virologists have used group names based on the first-discovered, or prototype, virus. More recently, however, plant virologists have come to use the Baltimore classification (into seven groups as below)as the upper level of nomenclature or naming, then use the same order, family, genus, and species taxa listed above.

The "Baltimore Classification" is as follows:

Group I: Double-stranded DNA viruses (dsDNA viruses) e.g. Adenoviruses, Herpesviruses, Poxviruses.

Group II: Single-stranded DNA viruses (ssDNA viruses) e.g. Parvoviruses.

Group III: Double-stranded RNA viruses (dsRNA viruses) e.g. Reoviruses, Birnaviruses.

Group IV: Single-stranded RNA viruses - Positive-sense (+ssRNA viruses) e.g. Picornaviruses, Togaviruses.

Group V: Single-stranded RNA viruses - Negative-sense (-ssRNA viruses) e.g. Orthomyxoviruses, Rhabdoviruses.

Group VI: RNA reverse transcribing viruses; positive-sense single-stranded RNA viruses that replicate through a DNA intermediate (ssRNA-RT viruses) e.g. Retroviruses.

Group VII: DNA reverse transcribing viruses; double-stranded DNA viruses that replicate through a single-stranded RNA inter mediate (dsDNA-RT viruses) e.g. Hepadnaviruses.

VIRAL DISEASES IN PLANTS

Viruses can have a wide variety of different effects on the organism they infect. One of the most common symptoms in plants is a change of colour in leaves and/or flowers.  Infected leaves frequently show light green or yellow patches (i.e. a variegated effect) due to the interruption of chlorophyll production, and hence photosynthesis is reduced.  This type of infection can cause reduction of crop yield or quality, or a general stunting of the plant.

One of the most severe effects of a virus would be death, although this is not common (viruses can only live in a host organism whilst the host is alive - if the host dies, the virus dies and hence eliminates itself). Growth patterns can be disturbed and changed by viruses.  In some cases, stunting (mild or severe) will be the only obvious effect.  In other cases, a virus can cause distortion in the growth (i.e. twisting, blistering or other distorted formations in leaves, stems, roots or flowers).  In extreme cases, leaves can be reduced to a central midrib (i.e. no leaf blade at all).  

Flowering and seed production can be stopped completely by a virus.  Viruses can also induce leaf rolling, leaf yellowing, plant wilting, or changes to the physiological processes in the plant so that some functions of a cell's metabolism cease completely. One or several of these symptoms might occur.  

Plants which are very commonly affected by serious viral problems include: gladioli, carnations, chrysanthemums, strawberries, passionfruit, Daphne and tulips.  There are others, but you should watch these in particular.