Bacteria and Viruses

Bacteria are a diverse group and all of them have unicellular prokaryotic organization, which lack membrane-bounded organelles, including a well-defined nucleus. They have the simplest cellular organization.

A generalized bacterium (Figure 2.1) shows these parts: Capsule (outer slimy layer), Cell wall (rigid support), Cell membrane (plasma membrane), DNA in the Nucleoid (irregular dense area, not a true nucleus), Pilus (thin attachment fibre), Cytoplasm (inner fluid), Ribosome (protein-making granules), Mesosome (folded membrane), Plasmid (small extra DNA ring) and Flagellum (long movement thread).

Cell Wall: It is a rigid wall around the plasma membrane of the bacterial cell. The major component of the bacterial cell wall is a unique macromolecule, called peptidoglycan or murein. It is composed of long glycan (polysaccharide) chains, cross-linked by short peptide fragments (Figure 2.2: the molecular model of peptidoglycan). Its amount differs in different bacteria. The cell wall also contains lipids, which are linked to peptidoglycan.

Gram's staining: Sir Hans Christian Gram devised the technique of Gram's staining. Gram-positive bacteria stain purple because they retain the violet dye. Gram-negative bacteria do not retain the violet dye and so they appear in their original colour.

The composition of the cell wall is quite different in Gram-positive and Gram-negative bacteria. The cell wall of Gram-positive bacteria contains a thick layer of peptidoglycan and has less lipid content. While the cell wall of Gram-negative bacteria has a thin layer of peptidoglycan.

The cell wall of Gram-negative bacteria has an outer membrane made of lipopolysaccharides and lipoproteins. The outer membrane makes Gram-negative bacteria resistant to many antibiotics. It contains a protein called porin, which acts like a pore for specific molecules. The cell wall of Gram-negative bacteria has more periplasmic space (space between the peptidoglycan layer and the cell membrane) than Gram-positive.

Capsule: Some bacteria produce a capsule outside their cell walls. It is a gelatinous layer and gives sticky character to bacterial colonies.

Cell Membrane: The cell membrane or plasma membrane is present just beneath the cell wall. It lies at the outermost in bacteria that lack a cell wall (e.g., Mycoplasma). The cell membrane of bacteria does not have sterols (e.g., cholesterol) in its chemical makeup. At some points, the cell membrane invaginates and forms vesicles, tubules or lamellae in the cytoplasm. These structures are known as mesosomes. These are involved in DNA replication and cell division and also serve as respiratory centres.

Cytoplasm and Genetic Material: Cytoplasm contains dissolved substances and large structures such as nucleoid, ribosomes, and mesosomes. It lacks a cytoskeleton and membrane-bounded organelles. Many ribosomes are freely dispersed in the cytoplasmic matrix and some are loosely attached to the plasma membrane. Bacterial ribosomes are smaller than eukaryotic ribosomes. Each ribosome sediments at 70S (larger subunit at 50S and smaller subunit at 30S). Near the centre of the cytoplasm, there is an irregular-shaped dense area i.e., nucleoid. It contains DNA. A bacterium possesses a single, circular, double-stranded DNA. Bacterial DNA does not have attached histones. It is sometimes called the chromosome of the bacterium.

Plasmids: Some bacteria have circular, double-stranded extra-chromosomal DNA molecules, called plasmids. They are self-replicating and can replicate before or after division. They contain genes that enable bacteria for resistance against unfavourable conditions (e.g., antibiotics). Plasmids also serve as important vectors in genetic engineering. They are used to carry selected genes to bacteria for cloning or for the synthesis of specific proteins.

Many bacteria can survive extended periods of harsh conditions by forming specialized "resting" cells, called endospores (Figure 2.4). Endospores are thick-walled and metabolically inactive (dormant). The process by which bacteria make endospores is called sporulation. It happens in the following way:

1. When a bacterium faces unfavourable conditions, it replicates its DNA. The cell membrane makes a septum to isolate the new DNA and a small portion of cytoplasm.
2. The cell membrane again grows around the new DNA, cytoplasm, and septum. In this way, the new DNA is surrounded by two membranes.
3. The DNA of the vegetative cell disintegrates and the whole cell begins to dehydrate. A new peptidoglycan layer forms between the membranes around the separated DNA and cytoplasm.
4. A spore coat also forms around it. The structure matures into an endospore.
5. The vegetative cell breaks and the endospore is released.
6. The endospore remains dormant unless favourable conditions return. Under favourable conditions, the endospore germinates to give rise to a new vegetative cell.

Why it matters: Endospores are the toughest survival form in biology — they resist heat, drying, chemicals and lack of food, which is why they are the key to bacterial survival in harsh conditions (and why sterilization must be so thorough).

Bacteria use different motility patterns to navigate and explore natural habitats (Figure 2.5).

• Flagellar movements: Most bacilli and spirilla bacteria move by means of flagella. They swim by using their flagella. When a bacterial population moves together by means of flagella, the movement is called swarming. Flagellar movement allows bacteria to travel in liquid media. Counterclockwise rotation of the flagellum pushes the cell forward with the flagellum trailing behind.
• Twitching or crawling: It is used to move over surfaces. It is mediated by pili, which bind to the surrounding solid surface and retract. Thus, the bacterial cell is pulled forward.
• Gliding: It is similar to twitching. In gliding, bacteria secrete a slimy substance, which helps them for smooth gliding over solid surfaces.
• Sliding: It is due to the expansion created by the pushing force of dividing cells.
• Brownian movement: Some bacteria (e.g., Streptococcus) that do not have flagella or pili, move due to the random and uncontrolled movements of the particles present in fluid.
• Movement by axial filament: Some bacteria (e.g., spirochaetes) have a modified flagellum, known as axial filament. It is anchored at one end and runs length-wise in the periplasmic space (between the cell membrane and the outer membrane). It consists of two sets of flagella-like fibrils anchored at the two poles of the cell. It helps spirochaetes for flexing, swimming, creeping and spinning movements (Figure 2.6).

Many kinds of bacteria have flagella, which enable them to move. The secondary function of flagella is to detect and respond to chemical signals. The bacteria which do not possess flagella are called atrichous. The bacteria with a single polar flagellum are called monotrichous. The bacteria with a tuft of flagella at one pole are called lophotrichous. The bacteria with flagella at each of two poles are called amphitrichous. The bacteria with flagella surrounding the whole cell are called peritrichous (Figure 2.7).

Structure: The flagellum of bacteria is entirely different in structure from the flagellum of eukaryotes. They are not built on the 9+2 pattern of microtubules, but are composed of flagellin protein. The bacterial flagellum consists of a basal body, a hook and a filament. The basal body is present just beneath the cell membrane. It consists of rotating rings (one pair in Gram-positive bacteria and two pairs in Gram-negative bacteria). The rings anchor the flagellum in the cell membrane and cell wall. The hook is a curved structure that connects the basal body with the filament (Figure 2.8: parts of the flagellum in Gram-positive vs Gram-negative bacteria).

Pili: Some bacteria have pili (singular: pilus). These are non-helical, filamentous appendages and are smaller and thinner than flagella. Pili are used for attachment of bacteria to various surfaces. They are also involved in the mating process (conjugation) between cells.

The fossil record shows that prokaryotes i.e., archaea and bacteria were abundant 3.5 billion years ago. They evolved and remained all alone on Earth for the next 2 billion years. Today, prokaryotes (archaea and bacteria) are found wherever there is life. Bacteria are found in water, air, soil, food and in the bodies of animals and plants. They outnumber all eukaryotes. They can survive in extreme habitats.

Diversity in Bacteria and their Ecology: Margulis and Schwartz proposed a useful classification system for all prokaryotes. They classified them into 16 phyla. The following discussion deals with the important groups of the domain bacteria (Figure 2.9).

1. Omnibacteria: These are rigid, rod-shaped, heterotrophic, Gram-negative bacteria. Many important pathogens are included in this group. Most of these bacteria have flagella. They do not produce spores. They are usually aerobic. Escherichia coli is an example of such bacteria. This group also includes vibrios.
2. Cyanobacteria: These are photosynthetic bacteria. They played the most important role in the history of the Earth for increasing free oxygen in the atmosphere. They contain chlorophyll-a and accessory pigments like carotenoids, and blue and red phycobilins. Many cyanobacteria fix atmospheric nitrogen in their special cells called heterocysts. They are common in soil in the form of mats. Cyanobacteria-containing lichens are found on rock surfaces. The mats on the sediments in the sea are dominated by cyanobacteria. Colourful blooms may occur in polluted water as a result of the rampant growth of cyanobacteria. The colours of such blooms result from the photosynthetic pigments of cyanobacteria. Perhaps most interesting of all is the recent discovery that the bulk of our modern petroleum deposits were formed by masses of decayed cyanobacteria.
3. Mycoplasmas and Spiroplasmas: These groups differ from all other bacteria in that they lack cell walls. As they lack cell walls, they are resistant to penicillin and other antibiotics that work by inhibiting cell wall growth. Some mycoplasmas cause diseases in mammals e.g., certain types of pneumonia in humans. Spiroplasmas cause significant plant diseases e.g., the lethal yellowing disease of coconuts.
4. Spirochaetes: These are long spirilla with Gram-negative cell walls. They may have 2 to more than 100 flagella. Treponema are important spirochaetes. They cause syphilis (a fatal sexually transmitted disease).
5. Pseudomonads: These are straight or curved Gram-negative rods with one or many flagella at one end. They are found in soil and water. They can easily break down organic compounds. Some of them are autotrophic but many are plant pathogens. Some of them play a role in denitrification. Pseudomonas aeruginosa occurs in soil, water and raw vegetables. Although it is usually harmless, it can form serious infections in weak people.
6. Actinomycetes: These have filamentous growth forms. They produce spores that are resistant to unfavourable conditions. Some actinomycetes are nitrogen fixers and are found in the root nodules of many flowering plants. Some actinomycetes are responsible for dental plaque, in which the enamel of teeth is destroyed. A member of this group i.e., Mycobacterium leprae causes leprosy. Another member i.e., Mycobacterium tuberculosis causes tuberculosis. Many antibiotics e.g., tetracycline, chloramphenicol, erythromycin, and neomycin were originally derived from actinomycetes. About 150 new antibiotics from actinomycetes are being discovered each year.
7. Nitrogen-fixing aerobic bacteria: This group includes economically important bacteria. They are Gram-negative and most are flagellated. Azotobacter is a member of this group. It is found in soil and water and converts atmospheric nitrogen into nitrates.
8. Chemosynthetic bacteria: These bacteria derive energy from the oxidation of inorganic compounds of nitrogen, sulphur and iron. They use this energy for the synthesis of their food. Nitrosomonas and Nitrobacter are included in this group. They oxidize nitrogen compounds (NH₃) to gain energy. The NH₃ is in turn converted to nitrite and nitrate. Thus, they play a vital role in the nitrogen cycle.

Key — Form: R, rods (bacilli); C, cocci; S, spirilla; M, regular chains or aggregations. Motility: F, flagellated; N, nonmotile; G, gliding. Nutrition: H, heterotrophic; C, chemosynthetic; P, photosynthetic.

Bacteria are very important organisms not only for the environment but also for all other organisms. They have beneficial as well as harmful effects on life on Earth.

Beneficial Bacteria: Among the great diversity of bacteria, many bacteria are beneficial ecologically as well as economically.

Recyclers of nature: Bacteria are involved in almost all biogeochemical cycles in which different essential elements move to and fro between organisms and the environment. Nitrifying bacteria (Nitrosomonas, Nitrobacter and Azotobacter) and denitrifying bacteria (Pseudomonas) play a significant role in the completion of the nitrogen cycle. Decomposer bacteria decompose dead organic matter and play a key role in the carbon-hydrogen-oxygen cycle. The activities of photosynthetic bacteria e.g., cyanobacteria play a role in the increase of free oxygen in the Earth's atmosphere.

Makers of useful products: Many bacteria e.g., Lactobacillus in combination with yeasts and molds, have been used for thousands of years in the preparation of fermented foods such as cheese, pickles, soy sauce, vinegar, wine and yogurt. In the pharmaceutical and agrochemical industry, bacteria are most important in the production of important chemicals. Some bacteria are used for the production of antibiotics. Commercial preparation of animals' skin for making leather goods involves the use of bacteria.

Environmental cleaners: Many bacteria can degrade organic compounds very easily. Such bacteria have been used for the removal or degradation of pollutants (bioremediation) from the environment. For example, bacteria are used to decompose city sewage into harmless products. Some bacteria can digest the hydrocarbons present in petroleum. These bacteria are used to clean up oil spills. Bacteria are also used for the bioremediation of industrial toxic wastes.

Biopesticides: Bacteria are used in the place of pesticides in biological pest control. This commonly involves Bacillus thuringiensis, a Gram-positive, soil-dwelling bacterium. These biopesticides are environmentally friendly and have little or no effect on humans, wildlife, pollinators and most other beneficial insects.

Research and technology tools: Bacteria can grow quickly and scientists can manipulate them very easily. Due to these reasons, bacteria are used in the fields of molecular biology, genetics and biochemistry. Scientists make mutations in bacterial DNA and examine the changes in characteristics. In this way, they determine the function of genes and enzymes in bacteria. This knowledge is then applied to study the same genes and enzymes in more complex organisms. Scientists also insert human genes in bacteria and produce therapeutic proteins e.g., insulin, growth hormones, or antibodies.

In a healthy animal, the internal tissues, e.g., blood, brain, muscle, etc., are normally free of microorganisms. On the other hand, the surface tissues, e.g., skin and mucous membranes, are constantly in contact with the environment and are colonized by certain microbial species. The mixture of organisms regularly found at any anatomical site is referred to as the normal flora.

The normal flora of humans consists of bacteria, a few fungi and protists, and some methanogenic archaea. Bacteria are the most numerous and obvious microbial components of normal flora.

Benefits of Bacterial Flora of Humans: The associations between humans and their normal flora are mutualistic. In the human body, normal flora gets nutrients, a stable environment and constant temperature, protection, and transport. Similarly, the body also gets many benefits from normal bacteria; for example:

1. Synthesis of vitamins: Bacteria in the alimentary canal produce vitamins. They excrete vitamins which are in excess of their needs. From the alimentary canal, these vitamins are absorbed and distributed in the body. For example, enteric bacteria secrete Vitamin K and Vitamin B₁₂, and lactic acid bacteria produce certain B-vitamins.
2. Prevent colonization by pathogens: The bacteria of normal flora compete with pathogens for attachment sites and nutrients. So, pathogens have less chance of entering body tissues.
3. Inhibit or kill pathogens: The intestinal bacteria produce a variety of substances, which inhibit or kill pathogen bacteria.
4. Stimulates the production of cross reactive antibodies: Since the normal flora behaves as antigens, they induce immunological response. Low levels of antibodies produced against the normal flora are known to cross-react with certain pathogens, and thereby prevent infection or invasion.

You are familiar with the five kingdoms of living organisms. You also know that there are some creatures that do not possess cellular organization yet show some characteristics of livings. Viruses are the representatives of such organisms.

Structure of Virus: Viruses are extremely small infectious agents and can only be seen under an electron microscope. They range in size from 20 nm (parvovirus) to 250 nm (pox viruses). They are 10 to 1000 times smaller than most bacteria. That is why, they can pass through the pores of filter paper.

The central core of a virus is its genome. It is made up of nucleic acid (either DNA or RNA). The core is surrounded by a protein coat, called capsid. It gives a definite shape to the virus. The capsid is made up of protein subunits called capsomeres. The number and kind of capsomeres is characteristic of a particular virus. The central core and capsid are collectively called nucleocapsid.

Herpes virus (causes cold sores, chickenpox etc.) contains 162 capsomeres in its capsid. Adenovirus (causes common cold) contains 252 capsomeres in its capsid.

In some animal viruses only, the nucleocapsid is covered by another membrane called the envelope. It is a lipid-rich membrane and is derived from the host cell. Non-enveloped viruses are known as naked-viruses. There is a great diversity in the general appearance of viruses (Figure 2.10). The animal and plant viruses may be polyhedron (having many sides) or helical. The bacterial viruses (bacteriophages) may be cubical, icosahedral (having 20 faces), helical, or complex (polyhedral head and rod-shaped tail).

Structure of Bacteriophage: Bacteriophages are a diverse group of viruses that attack bacteria. They are among the most complex viruses. The best known phages of Escherichia coli are T-phages. A T4 phage consists of a head and a tail (Figure 2.11). The head is an elongated pyramidal (with two triangles having a common base), hexagonal (six-sided), prism-shaped structure. Its capsid is made of proteins while the core contains a long double-stranded DNA. A straight tail is attached with the head. The tail is also made of inner core and outer sheath, both of which are made of different proteins. A neck attaches the sheath with the head and an end plate is present on the other side of the sheath. Six tail fibres are attached with the end plate. They help the phage to attach with the bacterial wall. These structures are also made of proteins.

Bacteriophages are used as carriers in genetic engineering. The gene of interest is inserted into the DNA of a bacteriophage, which carries it to the target bacterial cell. When the virus incorporates its DNA into the bacterial chromosome, the gene of interest also becomes a part of the bacterial DNA. Such transgenic bacteria (whose genome has DNA of some other organism) can be grown to get copies of the gene of interest and to get the required protein.

Structure of HIV: Human Immunodeficiency Virus (HIV) belongs to the group called retroviruses. It is a special group of animal viruses. Retroviruses contain RNA and their capsids. These structures are surrounded by lipid-rich envelopes. The envelope also comprises glycoprotein spikes, which help the virus identify and bind to its target. They are spherical in form and are about 100 nm in diameter. The most distinguishing character of retroviruses is the presence of a specific enzyme, reverse transcriptase. This enzyme catalyses the process of reverse transcription in which a single-stranded RNA is reversely transcribed into a strand of DNA. The enzyme then uses the DNA strand to complete a double helix of DNA (Figure 2.12: Structure of HIV — Glycoprotein, Viral envelope, Capsid, RNA, Reverse transcriptase).

Experts have concluded that HIV originated in the jungles of Africa among wild chimps. Evidence suggests that a form of this virus entered the human species and became HIV by way of monkey bites or ingesting monkey meat and brains.

HIV is responsible for the disease AIDS (acquired immunodeficiency syndrome). AIDS weakens the immune system of the patient. The disease is fatal because no one can survive without an immune system to defend against other viral and bacterial infections. The disease was first reported in 1981 and the patients were found homosexual. Later on, AIDS was discovered in non-homosexual patients too who had received blood or blood products from other AIDS patients. In 1984, it was discovered that the agent causing AIDS was a virus. In 1986, the AIDS-causing virus was given the name Human Immunodeficiency Virus (HIV). It is a host-specific virus. It can multiply in monkeys but does not cause AIDS in them.