8.5D: Nongenetic Categories for Medicine and Ecology

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In medicine, microorganisms are identified by morphology, physiology, and other attributes; in ecology by habitat, energy, and carbon source.

Learning Objectives

Outline the traits used to classify: bacteria, viruses and microrganisms in ecology

Key Points

A pathogen causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.
When identifying bacteria in the laboratory, the following characteristics are used: Gram staining, shape, presence of a capsule, bonding tendency, motility, respiration, growth medium, and whether it is intra- or extracellular.
Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause.
In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.
Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms; these are called extremophiles and many kinds exist.
Different species of microorganisms use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them.

Key Terms

obligate: Able to exist or survive only in a particular environment or by assuming a particular role: an obligate parasite; an obligate anaerobe.
pathogen: Any organism or substance, especially a microorganism, capable of causing disease, such as bacteria, viruses, protozoa, or fungi. Microorganisms are not considered to be pathogenic until they have reached a population size that is large enough to cause disease.
extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.

Classifying microorganisms in medicine

A pathogen (colloquially known as a germ) is an infectious agent that causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.

BACTERIA

Although most bacteria are harmless, even beneficial, quite a few are pathogenic. Each pathogenic species has a characteristic spectrum of interactions with its human hosts.

Conditionally, pathogenic bacteria are only pathogenic under certain conditions; such as a wound that allows for entry into the blood, or a decrease in immune function. Bacterial infections can also be classified by location in the body, for example, the vagina, lungs, skin, spinal cord and brain, and urinary tract.

When identifying bacteria in the laboratory, the following chatacteristics are used: Gram staining, shape, presence of a capsule, bonding tendency (singly or in pairs), motility, respiration, growth medium, and whether it is intra- or extracellular.

Culture techniques are designed to grow and identify particular bacteria, while restricting the growth of the others in the sample. Often these techniques are designed for specific specimens: for example, a sputum sample will be treated to identify organisms that cause pneumonia. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (aerobic or anaerobic), patterns of hemolysis, and staining.

VIRUSES

Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate due to their pseudo-living nature. Essentially, they are non-living particles with some chemical characteristics similar to those of life; thus, they do not fit neatly into an established biological classification system.

Viruses are mainly classified by phenotypic characteristics,such as:

morphology
nucleic acid type
mode of replication
host organisms
type of disease they cause

Currently there are two main schemes used for the classification of viruses: (1) the International Committee on Taxonomy of Viruses (ICTV) system; and (2) the Baltimore classification system, which places viruses into one of seven groups. To date, six orders have been established by the ICTV:

Caudovirales
Herpesvirales
Mononegavirales
Nidovirales
Picornavirales
Tymovirales

These orders span viruses with varying host ranges, only some of which infect human hosts.

Baltimore classification is a system that places viruses into one of seven groups depending on a combination of:

their nucleic acid (DNA or RNA)
strandedness (single or double)
sense
method of replication

Other classifications are determined by the disease caused by the virus or its morphology, neither of which is satisfactory as different viruses can either cause the same disease or look very similar. In addition, viral structures are often difficult to determine under the microscope. Classifying viruses according to their genome means that those in a given category will all behave in a similar fashion, offering some indication of how to proceed with further research.

Other organisms invariably cause disease in humans, such as obligate intracellular parasites that are able to grow and reproduce only within the cells of other organisms.

CATEGORIES OF MICROORGANISMS IN ECOLOGY

In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.

Habitat Type

Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms. Some even concluded that life may have begun on Earth in hydrothermal vents far under the ocean’s surface.

An extremophile is an organism that thrives in physically or geochemically extreme conditions, detrimental to most life on Earth. Most known extremophiles are microbes. The domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of both bacteria and archaeans. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles.

There are many different classes of extremophiles, each corresponding to the way its environmental niche differs from mesophilic conditions. Many extremophiles fall under multiple categories and are termed polyextremophiles. Some examples of types of extremophiles:

Acidophile: an organism with optimal growth at levels of pH 3 or below
Xerophile: an organism that can grow in extremely dry, desiccating conditions; exemplified by the soil microbes of the Atacama Desert
Halophile: an organism requiring at least 0.2M concentrations of salt (NaCl) for growth
Thermophile: an organism that can thrive at temperatures between 45–122 °C

Trophic level, energy source and carbon source

Figure: **The nutritional modes of an organism**: A flowchart to determine if a species is autotroph, heterotroph, or a subtype.

Phototrophs: carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. They are not obligatorily photosynthetic. Most of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and can fix carbon.
Photoheterotrophs: produce ATP through photophosphorylation but use environmentally-obtained organic compounds to build structures and other bio- molecules.
Photolithoautotroph: an autotrophic organism that uses light energy, and an inorganic electron donor (e.g., H₂O, H₂, H₂S), and CO₂ as its carbon source.
Chemotrophs: obtain their energy by the oxidation of electron donors in their environments.
Chemoorganotrophs: organisms which oxidize the chemical bonds in organic compounds as their energy source and attain the carbon molecules they need for cellular function. These oxidized organic compounds include sugars, fats and proteins.
Chemoorganoheterotrophs (or organotrophs) exploit reduced-carbon compounds as energy sources, such as carbohydrates, fats, and proteins from plants and animals. Chemolithoheterotrophs (or lithotrophic heterotrophs) utilize inorganic substances to produce ATP, including hydrogen sulfide and elemental sulfur.
Lithoautotroph: derives energy from reduced compounds of mineral origin. May also be referred to as chemolithoautotrophs, reflecting their autotrophic metabolic pathways. Lithoautotrophs are exclusively microbes and most are bacteria. For lithoautotrophic bacteria, only inorganic molecules can be used as energy sources.
Mixotroph: Can use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them. Can be either eukaryotic or prokaryotic.

Figure: **Differing morphology in different Herpes viruses**: Various viruses from the Herpesviridae family seen using an electron micrograph. Amongst these members is varicella-zoster (Chickenpox), and herpes simplex type 1 and 2 (HSV-1, HSV-2).