General Microbiology

Overview

Microbiology is the science which studies micro-organisms. These are living beings of small size which can not be seen with the naked eye (some unicellular protists are visible to the eye). They can therefore be observed only with a microscope.

Microorganisms are a very diverse group, they exist in the state of cell or group. They are also known as "germs" is a generic term and unscientific for bacteria, yeasts, molds, algae, protozoa and viruses, pathogens or not. Colloquially, the word "microbe" means a micro-organism responsible of disease.

Micro-organisms are encountered in all types of environments found in nature. They are found in soil, water, air, but also most hostile environments such as the poles, deserts, geysers, the ocean floor, etc.. Many micro-organisms associated with plants or animals with which they can maintain symbiotic relationships of commensalism or parasitism. Some micro-organisms can be pathogenic, ie cause disease in plants or animals.

Microorganisms are classified into two groups: prokaryotes and eukaryotes. Bacteria are prokaryotes, while fungi, algae and protozoa are eukaryotes. Viruses that are also micro-organisms are classified in either of these two groups

Procaryotes

Designated by the term "prokaryotes" (Greek pro = before and caryon = nucleus), all micro-organisms whose cell has no nucleus or other nuclear organelles.

The prokaryotes are divided into two taxonomic groups: the archaea and bacteria.

Bacteria

Bacteria (Bacteria) are micro-organisms living unicellular prokaryotes. They measure a few micrometers in length (usually 0.5 to 5 m long) and can present different shapes: spherical forms (cocci), forms or elongated rods (bacilli) and more or less spiral (Spirilla) .

Bacteria are ubiquitous and are present in all types of habitats: soil, water, air, plants and animals. In humans, it was calculated that 1012 bacteria colonize the skin, bacteria colonize the 1010 and 1014 mouth bacteria live in the intestine. Most of these bacteria are harmless or beneficial to the organism. However, many bacterial species are pathogenic and are responsible for infectious diseases such as cholera, syphilis and tuberculosis.

Cell structure of bacteria

Bacteria are relatively simple cells, characterized by the absence of nucleus and organelles such as mitochondria and chloroplasts. Figure 1 below represents the structure of a bacterial cell.

Chromosome:

The bacterial chromosome is shaped filament of DNA. It is generally circular and is the support of heredity. In addition to genomic DNA, bacterial cells often contain circular DNA molecules called extra-chromosomal plasmids

Ribosomes:

A ribosome consists of molecules with a particular type of RNA, ribosomal RNA (rRNA), associated with proteins. It is composed of two subunits, large and small. These two sub-units are called respectively the 50s and 30s (s expressing the speed of sedimentation of these units in the experiences of ultracentrifugation) in prokaryotes (60s and 40s in eukaryotes).

Ribosomes play a key role in protein synthesis (protein translation): These are they who roam the messenger RNA (mRNA) and adding new amino acids, provided by the transfer RNA (tRNA), the chain protein under construction: they are the catalysts of protein synthesis.

Cytoplasm:

In prokaryotes, the cytoplasm is the only compartment of the cell. It is composed of a gel called aqueous cytosol, which are:

1. • Molecules reserve "solution" (proteins, carbohydrates, lipids);
   • genetic material and other cellular components that float freely inside.

Cytoplasmic membrane:

This is the membrane surrounding the cytoplasm. It consists of phospholipids and proteins.

The cytoplasmic membrane acts as a selective filter that passes nutrients. It also allows the passage of light, heat, etc.. As the surface of contact with the outside, it also ensures the transmission of information necessary for the responsiveness of the cell to environmental changes and coordination with other cells. The plasma membrane creates a space in constant exchange with the environment.

Cell wall:

The cell wall is one of the important characteristics of bacteria. It gives the bacterium its shape and protects against burst under the effect of osmotic pressure of cytoplasm.

Depending on their cell wall, bacteria can be divided into two groups: Gram positive (Gram +) and Gram negative (Gram-). This differentiation is based on the structure and chemical composition of the cell wall underscored by the Gram stain. Bacteria on Gram staining + have a thick cell wall, while the bacteria Gram-wall are fine.
Some bacteria do not have a wall: the mycoplasma.

Capsule:

This is the device layer that surrounds the bacterial cell. Composed of polysaccharides and proteins, it allows the attachment of bacteria to surfaces and protects against the adverse effects of external environment (toxic compounds, detergents, desiccation, ...). Some bacteria do not possess a capsule.

Extra-cellular structures (flagella and pilis):

Most bacteria are not automobiles. But others, such as Salmonella, have a structure extracellular form of fine filaments called flagella, which enable them to move. The flagella are also used by the heterotrophic bacteria to go to areas rich in nutrients through a process called chemotaxis (chemical attraction).

Other species are covered with many small "hairs", the pilis, which play no role in locomotion, but are involved in the accession process of the bacteria to a medium or in the phenomenon of conjugation (sexual reproduction).

Morphology and association of bacteria

Bacteria have a wide variety of cellular morphologies (Figure 2). This feature is exploited for the identification of cells by microscopic observation. Most bacteria have a spherical form, called shells, or in rod-shaped, called bacilli. Some bacteria have an intermediate form, have the coccobacilles and also have a helical shape, called Spirilla.

The mode of arrangement of cells is also a feature which distinguishes the bacteria (Figure 3). Many bacterial species can be observed in single isolated, while other species are associated with each other. These may associated in pairs (diplococci), such as Neisseria, in the chain as streptococci and staphylococci such as clusters.

Archaea

Archaea or the Archaea (formerly called Archaea) are a major group of prokaryotes, bacteria are distinguished by certain biochemical characteristics, such as formation of cell membranes or the mechanism of DNA replication.

The archaea are anaerobic species and generally live in extreme conditions (saline, very acidic or very alkaline environment at temperatures close to boiling). Some archaea are also more common organisms that live in conditions of ordinary life soil, lakes, sea or the intestines of animals.

The archaea are not considered as micro-organisms harmful to health. In fact, until now, no clear evidence proves the existence of pathogenic archaea.

Eucaryotes

Eukaryotes, from the Greek "true nucleus" means all living beings whose genetic material is enclosed, within the cell, in a structure called the nucleus, as opposed to prokaryotes. Algae, fungi and protozoa are eukaryotes.

The eukaryotic cell is surrounded by a membrane, the plasma membrane. The interior is occupied by liquid water, the cytoplasm, in which swim various organelles responsible for specific cellular activities (mitochondria, Golgi apparatus, etc.).. Finally, the cell contains a nucleus containing the genetic material (in the form of DNA) surrounded by a double membrane.

Figure 4 below represents the different organelles of a eukaryotic cell.

In addition to the structures found in prokaryotic cells, eukaryotes have other organelles that are specific. These include: the nucleus, the mitochondria, the endoplasmic reticulum and the vacuole.

• Kernel:

The nucleus is the structure that contains the genetic information of the cell. It is surrounded by two lipid membranes perforated within which lie the chromosomes. The kernel controls all cellular activities and the maintenance of genetic information from one generation to another cell.

• Mitochondria:

Mitochondria are organelles ovoid ensuring the implementation of cellular respiration, and providing the bulk of the energy (as ATP) necessary to operate the cell.

• Endoplasmic reticulum:

The endoplasmic reticulum is associated with cellular structures responsible for the synthesis of proteins and lipids (the ribosomes in the first case and enzymes in the latter). These newly synthesized molecules are supported by the endoplasmic reticulum, which provide transport to the Golgi apparatus by vesicles.

• Golgi apparatus:

The Golgi apparatus is an organelle, usually located near the nucleus, involved in the maturation of proteins and newly synthesized lipids in the cell to make them functional. This maturation includes in particular the elimination of certain carbohydrate residues and the addition additional carbohydrate molecules (as is the case for membrane proteins and lipids, often associated with sugar molecules). Another role of the Golgi apparatus is the sorting of molecules and their dispersal to different cellular compartments where these molecules are necessary.

• Other organelles:

The phototrophic eukaryotic cells such as algae have chloroplasts that convert light energy from the sun into chemical energy used to manufacture sugars through photosynthesis. The reserves are produced and stored in the vacuoles of these cells.

Some eukaryotic cells can become mobile using cilia or flagella (sperm, for example). Their flagellum is more evolved than that of prokaryotes.

Algae

These microorganisms, uni-or multicellular, are largely answered in fresh or salt water and soil. These are organisms capable of ensuring their nutrition through photosynthesis (autotrophic), thanks to the chlorophyll they contain.

Algae also have pigments such as carotenoids, xanthophylls and the phycocyanin providing coloring and play an important biochemical role.

Mushrooms

Fungi are eukaryotic organisms related to plants, but which stand out in particular by way of non-photosynthetic nutrition.

Mushrooms have forms of life very different. The simplest are unicellular, but most are multicellular. They feed on organic matter in their environment by secreting enzymes that "digest" various organic compounds that surround them and reduce soluble small molecules.

Fungi are present in the soil, plants, plant debris, lichen parasites of humans, animals and plants.

The classification of fungi described four phyla (branch) main: the Oomycetes, the Zygomycetes, Ascomycetes and the Basidiomycetes. Molds and yeasts that have a major interest in food microbiology are fungi.

Mold

We found mold in two major groups of fungi, Zygomycetes (lower fungi) and Ascomycetes (mushrooms). At first, the hyphae (filaments that make up the mycelium) are not segregated, they are in seconds (Figure 5).

We can distinguish, within the Zygomycetes, two major types of morphology of the mycelium, on the basis of criteria such as the branching of hyphae and position of sporocystes (spherical structures containing spores). In the mold of the genus Rhizopus (eg black bread mold, Rhizopus nigricans), the sporangia are arranged in clusters from ramifications of a filament called stolon. They also bear rhizoids which act as "roots" for the fungus to determine its substrate. In species such as Phycomyces, the provision of sporocystes seems anarchic, as occurred at random from the hyphae that form a network.

Molds of the best known group of Ascomycetes are those of the genera Penicillium (eg Penicillum notatum, from which penicillin) and Aspergillus (eg mold jams, Aspergillum glaucum). Mycelium Their network covers not sporocystes, but acscopores (structure containing ascus, reproductive cells of Ascomycetes).

Yeast

Yeasts are fungi usually unicellular (some yeasts are able to fly, however, a pseudo multi) able to cause the fermentation of organic materials of animal or plant.

These micro-organisms, usually oval in shape, about 6 to 10 microns and 50 microns, multiply by budding or by scissiparity (cell division). They are often able to accomplish a sporulation or in a dormant but in unfavorable conditions, or in order to spread.

During the term generally refers to the yeast genus Saccharomyces (yeast or yeast bread). There are many other kinds of yeast. In particular with a Candida pathogenicity (in charge of mycosis known as "candida").

Protozoa

Protozoa are unicellular devoid of cell wall (unlike seaweed), some live in colonies.

Most protozoa live in an aquatic environment, ocean, lake, river, pond. Their length varies between 2 and 70 microns. They feed by ingesting bacteria, waste excreted by other organisms, algae or other protozoa.

Most species are mobile, thanks to extensions (the flagella) or to organs like hair (eyelashes) or displacement amiboïde, continuous movement based on the formation of pseudopods (extensions shaped feet).

Other kingdoms

The plant kingdoms (with affinity with algae) and animals (with affinity protozoa) are also classified among eukaryotes. They are not classified as micro-organisms because they are not living and do not occur in the unicellular state.

Virus

Viruses are the smallest of micro-organisms. Their size is of the order of a few nanometers, they may be seen that electron microscope.

They are obligate parasites of all living cells of animals, plants and bacteria. Their growth and proliferation can not be done only within a living cell which, in general, the destruction of the host cell. Viruses are parasites of bacteria called bacteriophages (Figure 6).

Viruses are composed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), a protective shell called the capsid, composed of protein alone or in combination with carbohydrates and sometimes surrounded by a plasma membrane made from a host cell which the virus is released.

The size and appearance of the virus are very varied. Many viruses have a very simple form pseudosphere without any symmetry, whose diameter varies between 60 and 300 nm. Smaller, whose shape is icosahedral (polygons twenty sides), measuring between 18 and 20 nm wide. Some bacteriophages carry, in addition to this structure, a kind of tail that allows them to inject their genome in the bacteria they infect. Longest viruses are viruses stick, some of which can reach several microns in length.

Viruses are often agents of disease, mild or severe. Currently, thousands of viruses have been identified.

Nutrition and growth of micro-organisms

Microbial growth is defined as an increase in cellular constituents, and can result in an increase in size (case of mold, for example) or the number of microorganisms (bacteria, for example).

To grow, microorganisms require water, energy, nitrogen, minerals, possibly of oxygen and / or growth factors (organic substance necessary for growth of micro organism and can not be synthesized by the latter) for their growth. Other factors such as pH, temperature, electromagnetic radiation, have a significant effect on the growth of microorganisms.

In the absence of favorable growth conditions, some microorganisms are transformed into a form of resistance (spores) to continue to survive, but flourish. When the environment becomes favorable, the spores transform into vegetative forms that are performed during biosynthesis of balanced growth for a more or less rapid.

Depending on the source that the microorganism uses for its nutrients, there are several trophic types (Table 1).

 

Table 1: Various nutritional or trophic

Class need	Nature of the requirement	Trophic type
Energy Source	Light radiation	Phototrophic
	Oxidation of organic or inorganic	Chemosynthetic
Electron donor	Mineral	Lithotrophe
	Organic	Organotrophe
Carbon source	Mineral Composition	Autotrophic
	Organic compound	Heterotrophic
Growth factors	Not necessary	PROTOTROPHS
	Necessary	Auxotrophs

Association of microorganisms to other living beings

Association with plants and animals

Many micro-organisms associated with plants and animals with which they have symbiotic relationships, of commensalism or parasitism.

Symbiosis is an association between sustainable living and that everyone benefited. They help each other to feed, protect or breed.

The commensalism is a kind of natural association between two living beings in which the host provides part of its own food to commensal It does, however no obvious contribution of the latter (the relationship is to benefit non-reciprocal) .

Parasitism is a relationship between two beings of different species in which one partner is living at the expense of another (the host). Parasitism is detrimental to the host.

Some microorganisms are pathogenic to plants and animals to which they are associated.

Interaction of microorganisms

The interaction of different micro-organisms can vary:

• The métabiose: Succession on the same environment of micro-organisms, the first preparing the ground for the following, and then stop their multiplication and finally disappear.
• Symbiosis: Development on the same environment and at the same time several microbial species, these species are mutually supporting.
• The Antibiosis: there are several forms:
  • by competition, with the number and virulence of a species, the most combative occupying the middle, it becomes unsafe for development of the species the lowest.
  • inhibition by the antibiotics.
  • by parasitism: bacteriophages, or viruses including the expansion is 25 to 100 times faster than that of bacteria.