Environmental microbiology pertains to microorganisms found in air, water, soil, and wastewater that can affect public health or decompose organic matter. The document discusses taxonomy, which is the classification of organisms, and epidemiology, which is the study of disease patterns in populations. It also examines airborne pathogens and their lifecycles, noting that microbes are often suspended in air droplets and face stresses like desiccation and temperature changes as they are launched, transported, and deposited in the atmosphere.

1. Environmental Microbiology

2. Contents
 Taxonomy and Phylogeny
 Epidemiology
 Air Borne Pathogens

3. Microbiology
 Greek micros, small, bios, life, and logos, study of
 Hence microbiology is a study of microorganisms and their activities
 Environmental microbiology pertains to microorganism found in water,
wastewater, air and soil that may affect public health, decompose organic matter
or perform a useful function.

4. Taxonomy
 Taxa: Order or arrangement
 Nomos: law
 Nemein: to distribute or govern
Taxonomy is the branch of biology dealing with the classification of life.
 Formal system originated by Carl von Linne (1701-1778)
 Identifying and classifying organisms according to specific criteria
 Each organism placed into a classification system

5. History of Taxonomy
 1700s – 2 kingdoms – plant and animal
 1800s – 3 kingdoms – Plant, animal and Protista
 1950-1990s – 5 kingdoms - Plant, animal, protista, Fungi, Monera
 Present – 6 kingdoms – eubacteria, archaebacteria, Protista, animal, plant, fungi

6. Domain – 3 Domain System
 Eubacteria – true bacteria
 Archaea – odd bacteria that lives in
extreme environments, high salt,
heat etc (usually called
extremophiles)
 Eukayra – have a nucleus and
organelles (humans, animals, plants)
A phylogenetic tree based on rRNA data
showing Woese's three-domain system. All
smaller branches can be considered kingdoms.

7. 5 Kingdom System
 Kingdom Procaryotae – Oldest known cells, lack a
nucleus and membrane bound organelle
 Kingdom Protista – Mostly Unicellular, lack tissue
organization, most have flagella during life
 Kingdom Fungi – May be unicellular(yeasts), or
multicellular (molds), Many are saprotrophs.
 Kingdom Plantae – Multicellular, photosynthetic
 Kingdom Animalia – Multicellular, heterotrophs that
ingest food through mouth or oral cavity

8. Taxonomy
Classification
•Organization into Groups
•Car
•Truck
•SUV
•Van
Identification
•Distinguishing Features
•Engine Size
•Mileage
•Number of Passengers
•Types of Transmission
Nomenclature
•Providing a Name
•Genus and Species
•Honda City
•Chevy Impala
•Toyota Camry
•Ford Eco Sport
1. Classification is the arrangement of organisms into groups or taxa (s., taxon) based on mutual similarity or
evolutionary relatedness.
2. Nomenclature is concerned with the assignment of names to taxonomic groups in agreement with published
rules.
3. Identification is the practical side of taxonomy, the process of determining that a particular isolate belongs to a
recognized taxon. (So in short Identify-Naming them and classify them)

9. Classification
Arrangement of organisms into groups based on mutual similarity or evolutionary relatedness OR Ordering of
organisms into groups OR Systematic grouping of microorganisms by certain features
Types of Classification:
 Phenetic classification - Grouping organisms together based on the mutual similarity of their phenotypic
characteristics. Groups do not necessarily reflect genetic similarity or evolutionary relatedness. Instead,
groups are based on convenient, observable characteristics. Morphological, physiological, biochemical,
serological features are compared
 This is based on the supposition that overall similarity reflects well enough the relatedness of organisms
 Features or attributes or descriptors – enable to classify the individuals and taxons
 Quantitative – can be measured or counted
 Qualitative – shape, color, etc, some feature present or missing
 Means – Morphology in microscope, morphology of colony, biochemical activity, antibiogram, serotyping,
phagotyping

10. Classification
 Phylogenetic or Genotypic classification- These are systems based on evolutionary
relationships rather than external appearance (the term phylogeny [Greek phylon, tribe
or race, and genesis, generation or origin] refers to the evolutionary development of a
species). It is based on the direct comparison of genetic materials and/or gene product.
 Most precise method of classification
 Started with development of molecular methods and genetic studies
 Genetic taxonomy – nucleotide/nucleoside compositions are used to determine similarity
between species
 Analytic Classification is based upon detection of structural components and metabolic
products using chemical methods
 Cell wall fatty acids, whole cell lipids, whole cell proteins, enzymes
 Methods used – chromatography, mass spectrometry, multilocus enzymeelectrophoresis

11. Taxonomy Pyramid or Ranks
 DOMAIN
 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 Species

12. Nomenclature
 Biologists in the middle ages used to follow polynomial system, i.e naming organisms
with many names
 Later Binomial systems were developed by Swedish biologist Carolus Linnaeus (1707–
1778) based on the anatomical characteristics of plants and animals.
 Nomenclature in microbiology is developed based on the principals established for the plant and
Animal kingdom by Linnaeus.
 The first word in the binomial is the genus name and is always capitalized. The second word is species
name and never capitalized. For example honeybee, Apis mellifera, Escherichia coli, Salmonella typhi,
Bacillus subtilis
 Rules for naming are set by international committees
 International Code of Zoological Nomenclature
 International Code of Biological Nomenclature
 Bacteriological Code and Bergey’s Manual

13. Identification
Methods for Determining Microbial taxonomy
 The Intuitive Method
 Genetic Homology
 DNA/RNA Sequencing
 DNA Chip Technology
 Numerical Taxonomy

14. Techniques for Determining Microbial
Taxonomy and Phylogeny
•Morphological Characteristics
•Physiologic and Metabolic Characteristics
•Ecological Characteristics
•Genetic Analysis
Classical
Charateristics
•Nucleic Acid Base Composition
•Nucleic Acid Hybridization
•Nucleic Acid Sequencing
•Genomic Finger Printing
•Amino Acid Sequence
Molecular
Characterictics

15. Epidemiology
 Epidemiology is the study of the patterns, causes, and effects of health and disease
conditions in defined populations. It is the cornerstone of public health, and
shapes policy decisions and evidence-based practice by identifying risk factors for
disease and targets for preventive healthcare.
 According to WHO, Epidemiology is the study of the distribution and determinants
of health-related states or events (including disease), and the application of this
study to the control of diseases and other health problems. Various methods can
be used to carry out epidemiological investigations: surveillance and descriptive
studies can be used to study distribution; analytical studies are used to study
determinants.

16. Classification of Infectious Diseases
Microbiologists classify infectious
diseases according to the characteristics
of the causative organisms.
Clinical Classification
Clinicians tend to classify infectious
diseases according to their most common
or most important clinical manifestation or
by the organ system that are primarily
affected
Microbiological Classification

17. Classification of Infectious Diseases
(Cont’d)
 Epidemiologist usually classify infectious diseases according to two important epidemiological characteristics – their means of transmission
and the reservoir of the organisms
 If one is aware of the reservoir of the agent in addition to means of transmission, it is generally possible to determine a strategy to prevent
transmission even when the microbiological characteristics of the organism are not known. E.g. demonstration of water reservoir of cholera by John Snow in
London in 1853 preceded the identification of Vibrio cholera by Robert Koch in 1884. In more recent times, the epidemic at the American legion Convention in Philadelphia in 1976 demonstrated that
the outbreak of the Legionnaires’ disease was due to airborne spread of microorganisms from a contaminated reservoir, the air conditioning system in the Bellevue Stratford Hotel. The implicated
organism was isolated and characterized in 1978

18. Epidemiological Characteristics of
Infectious Diseases
 Incubation period is the interval between the effective exposure of the susceptible host to an
infectious agent and the appearance of signs and clinical symptoms of the disease in that host (in
the field of non‐infectious diseases the period between exposure to a specific cause and the
appearance of signs and symptoms of the disease is known as the latency or induction
period); latent periodis the time from infection to onset of the ability to infect; prodromic period is
the time between the perception of illness by the host and the appearance of signs and symptoms
based on which a clinical diagnosis of the disease is possible; communicable period (or duration of
infectiousness) is the time interval during which the infected host, ill or not, eliminates an agent to
the environment and new susceptible individuals can become infected.
 For biological characteristics refer to article (page 36)
http://www.jblearning.com/samples/0763728799/28799_ch02_023_060.pdf

19. Air Borne Pathogens - Lifecycle
 Microbes suspended in the air are known as bio aerosols
 There are many factors within the physical environment that
affect the launching, transport and deposition of bioaerosols.
Particles which become suspended in the air column arise
mainly from terrestrial and aquatic environments and are
typically launched by air turbulence. Winds are the primary
means of transport for bioaerosols. Bioaerosols can be
deposited by a number of mechanisms, including gravity pulling
them down, making contact with surfaces, or combining with
rain which pulls the particles back down to earth's surface.
 Droplet Formation - Microbes are often suspended in the air in
droplets, which are large enough to keep the microbes
hydrated and large enough to maintain a virulent amount of
pathogen, but are still small enough to stay suspended in the
air

20. Physical Environment – Impact on
Airborne Microbes
Atmosphere
 Along with water droplets, dust particles and other matter, air contains microbes. Microbes follow a particular pathway in which they
are suspended into the atmosphere. First they are launched into the air. The source of the launching of airborne microbes stems from
humans, animals and vegetation. then they are transported (by various methods including winds, machinery and people) and finally
are deposited somewhere new. The atmosphere can have a variety of physical characteristics, and can be very extreme in terms of the
relative humidity, temperature and radiation. These factors play a huge role in what kinds of microbes will survive in the atmosphere
and how long they will stay alive
Clouds
 Bioaerosols can be found within clouds. Cloud water is a mixture of organic and inorganic compounds suspended within moisture
(contribution of microbial activity to clouds). The conditions in clouds are not conducive to much life, as microbes present there must
withstand freezing temperatures, the threat of desiccation, and extreme UV rays. Clouds are also an acidic environment, with a pH
ranging from 3 to 7. Nevertheless, there are extremophile microbes which can withstand all of these environmental pressures. Clouds
serve as a transport for these microbes, dispersing them over long distances (Amato 2012).
Physical Environment Stresses
 Dessication is the primary stress that aeromicrobes face, and it limits the amount of time that they can survive while suspended in the
air . Humidity within the air is a second factor which can affect the survival of organisms. Certain bacteria, including Gram + bacteria,
are more tolerant of high humidity in the air, while others are more tolerant of dessication and dry conditions, such as Gram + cells.
Temperature must be in an intermediate range, as too hot of temperatures can denature proteins, and too cold of temperatures can
cause ice crystal formation. Finally, radiation poses a potential hazard for aeromicrobes, as it can damage DNA within the cells.

21. Microbial Communities
Many of the microbes that are capable of surviving harsh conditions can readily form endospores, which can withstand extreme conditions
Bacterial
 One such bacterial microorganism that can resist environmental stresses is Bacillus anthracis. It is a gram positive rod shaped bacteria
that utilizes spore formation to resist environmental stresses. The spore is a dehydrated cell with extremely thick cell walls which can
remain inactive for many years. This spore makes Bacillus anthracis a highly resilient bacteria, allowing it can survive extreme
temperatures, chemical contamination, and low nutrient environments. This bacteria is associated with Anthrax, which is a severe
respiratory disease that infects humans.
Fungal
 Another such microorganism that can resist environmental stresses is Aspergillus fumigatus, which is a major airborne fungal
pathogen (McCormick 2010). This pathogen is capable of causing many human diseases when conidia are inhaled into the lungs.
While A. fumigatus lacks virulence traits, it is very adaptable to changing environmental conditions and therefore is still capable of
mass infection.
Viral
 An example of a viral airborne pathogen is the Avian Influenza Virus, which is a single stranded RNA visur that can infect a broad range
of animal species as well as humans and cause the Avian Influenza.