Assignment on Virus, Bacteria & Cyanobacteria

1 Microorganism
A microorganism ("small" and "organism") or microbe is a microscopic organism, which may be a single cell or multicellular organism. The study of microorganisms is called microbiology, a subject that began with Antonie van Leeuwenhoek's discovery of microorganisms in 1675, using a microscope of his own design. Microorganisms are very diverse; they include all of the prokaryotes, namely the bacteria and archaea; and various forms of eukaryotes, comprising the protozoa, fungi, algae, microscopic plants (green algae), and animals such as rotifers and planarians. Some microbiologists also classify viruses as microorganisms, but others consider these as nonliving. Most microorganisms are microscopic, but there are some like Thiomargarita namibiensis, which are macroscopic and visible to the naked eye.

2 Viruses 2.1 Viruses

A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types of life forms, from animals and plants to bacteria and archaea. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants, and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898,about 5,000 viruses have been described in detail,although there are millions of different types.Viruses are found in almost every ecosystem on Earth and are the most abundant type of biological entity.The study of viruses is known as virology, a sub-speciality of microbiology. Virus particles (known as virions) consist of two or three parts: i) the genetic material made from either DNA or RNA, long molecules that carry genetic information; ii) a protein coat that protects these genes; and in some cases iii) an envelope of lipids that surrounds the protein coat when they are outside a cell. The shapes of viruses range from simple helical and icosahedral forms to more complex structures. The average virus is about one one-hundredth the size of the average bacterium. Most viruses are too small to be seen directly with an optical microscope.

2.2 Is a Virus Alive?

All living things are made of cells, are able to grow and reproduce, and are guided by information stored in their DNA. Viruses are segments of nucleic acids contained in a protein coat. Viruses are not cells. Viruses are pathogensagents that cause disease. Viruses do not grow, do not have homeostasis, and do not metabolize.

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Assignment on Virus, Bacteria & Cyanobacteria

2.3 Discovery of Viruses

Near the end of the nineteenth century, scientists were trying to find the cause of tobacco mosaic disease, which stunts the growth of tobacco plants. In 1935, biologist Wendell Stanley of the Rockefeller Institute purified tobacco mosaic virus (TMV) and determined that the purified virus is a crystal. Stanley concluded that TMV is a chemical rather than an organism.

Fig: 2.3.1 Wendell Stanley Scientist

Figure 2.3.1 2.4 Structure

Viruses display a wide diversity of shapes and sizes, called morphologies. In general, viruses are much smaller than bacteria. Most viruses that have been studied have a diameter between 20 and 300 nanometres. Some filoviruses have a total length of up to 1400 nm; their diameters are only about 80 nm.Most viruses cannot be seen with an optical microscope so scanning and transmission electron microscopes are used to visualise virions.To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such as tungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only.

Figure 2.4.1

Figure 2.4.2

Fig: 2.4.1 Diagram of how a virus capsid can be constructed using multiple copies of just two protein molecules. Fig: 2.4.2 Structure of icosahedral cowpea mosaic virus. Fig: 2.4.3 Basic Structure of Virus.

Figure 2.4.3

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Assignment on Virus, Bacteria & Cyanobacteria

2.5 Viral Structure

Virions are complete, fully developed viral particles composed of nucleic acid surrounded by a protein coat. Some viruses have an envelope composed of a phospholipid bilayer with viral glycoproteins. 2.5.1. Nucleic acid Viral genomes are either DNA or RNA (not both). Nucleic acid may be single- or double-stranded Nucleic acid may be circular or linear or separate molecules. Nucleic acid: protein ranges from about 1% - 50%.

2.5.2. Capsid Capsid - protein coat Capsomeres are subunits of the capsid Protomeres are capsomere subunits.

2.5.3. Envelope the outer covering of some viruses, the envelope is derived from the host cell plasma membrane when the virus buds out. Some enveloped viruses have spikes, which are viral glycoproteins that project from the envelope. Influenzavirus has two kinds of spikes, H (hemagglutinin) and N (neuraminidase). The H spike allows the virus to attach to host cells (and red blood cells), the N spike is an enzyme that allows the mature viral particles to escape from the host cell

Non-enveloped or naked viruses are protected by their capsid alone.

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2.6 Host Range

The specific types of cells a virus can infect in its host species represent the host range of the virus. Classification: Animal virus Plant virus Bacterial virus (bacteriophage)

2.7 Viral Reproduction

Viruses must rely on living cells (host cells) for replication. Before a virus can replicate, it must first infect a living cell. An animal virus enters its host cell by endocytosis. A bacterial virus, or bacteriophage, punches a hole in the bacterial cell wall and injects its DNA into the cell.

2.8 Important Viral Diseases

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Assignment on Virus, Bacteria & Cyanobacteria

2.9 Plant virus

Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses are pathogenic to higher plants.

2.9.1 Transmission of plant viruses

Through sap Insects Nematodes Plasmodiophorids Seed and pollen borne viruses Direct plant-to-human transmission

Figure 2.9.1.1
Fig: 2.9.1.1 Pepper mild mottle virus Fig: 2.9.1.2 Leaf curl virus

Figure 2.9.1.2

2.10 Animal virus

Animal viruses are viruses that infect animals. Viruses infect all cellular life and although viruses infect every animal, plant and protist species, each has their own specific range of viruses that often infect only that species.

2.10.1 Vertebrates
The viruses of vertebrates are informally distinguished between those that primarily cause infections of humans and those that infect other animals. The two fields of study are called medical (or clinical) virology and veterinary virology respectively. Although not the first viruses to be discovered and characterised,those that cause infections of humans are the most studied. Different viruses can infect all the organs and tissues of the body and the outcomes range from mild or no symptoms, to life-threatening diseases.Humans cannot be infected by plant or insect viruses, but they are susceptible to infections with viruses from other vertebrates. These are called viral zoonoses or zoonotic infections. Examples include , rabies, yellow fever and pappataci fever.

Figure 2.10.1.1

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Assignment on Virus, Bacteria & Cyanobacteria

2.10.2 Invertebrates
Invertebrates do not produce antibodies by the lymphocyte-based adaptive immune system that is central to vertebrate immunity, but they are capable of effective immune responses. Phagocytosis was first observed in invertebrates, and this and other innate immune responses are important in immunity to viruses and other pathogens. The hemolymph of invertebrates contains many soluble defence molecules, such as hemocyanins, lectins, and proteins, which protect these animals against invaders.

Figure 2.10.2.1
Fig: 2.10.1.1 Rabbits around a waterhole during the myxomatosis trial at the site on Wardang Island in 1938. Fig: 2.10.2.1 Honey bee infected with deformed wing virus.

2.11 Virus Protection and Treatment

Because viruses use vital metabolic pathways within host cells to replicate, they are difficult to eliminate without using drugs that cause toxic effects to host cells in general. The most effective medical approaches to viral diseases are vaccinations to provide immunity to infection, and antiviral drugs that selectively interfere with viral replication.

2.11.1 Vaccines
Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and rubella. Smallpox infections have been eradicated. Vaccines are available to prevent over thirteen viral infections of humans, and more are used to prevent viral infections of animals. Vaccines can consist of live-attenuated or killed viruses, or viral proteins (antigens).

2.11.2 Antiviral drugs

Antiviral drugs are often nucleoside analogues, (fake DNA building-blocks), which viruses mistakenly incorporate into their genomes during replication. The life-cycle of the virus is then halted because the newly synthesised DNA is inactive.

3 Bacteria
Bacteria constitute a large domain or kingdom of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth's crust. Bacteria also live in plants and animals. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 51030 bacteria on Earth, forming a biomass that exceeds that of all plants and animals. Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. Fig: 3.1 Scanning electron micrograph of Escherichia coli bacilli.

Figure 3.1

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Assignment on Virus, Bacteria & Cyanobacteria

3.2 History of bacteriology

Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1683, using a single-lens microscope of his own design. He then published his observations in a series of letters to the Royal Society of London. Bacteria were Leeuwenhoek's most remarkable microscopic discovery. Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828. Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.)

Figure 3.2.1

Fig: 3.2.1 Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

3.3 Bacteria Main Shapes

Spherical (like a ball) These are usually the simplest ones. Bacteria shaped like this are called cocci (singular coccus).

Rod shaped These are known as bacilli (singular bacillus). Some of the rod-shaped bacteria are curved; these are known as vibrio.

Spiral These known are as spirilla (singular spirillus). If their coil is very tight they are known as spirochetes.

Figure 3.3.1
Fig: 3.3.1 Shapes of Bacteria.

3.4 Bacteria are found everywhere

Bacteria can be found in: Soil Radioactive waste Water Plants Animals Deep in the earth's crust Organic material Arctic ice Glaciers Hot springs The stratosphere (between 6 to 30 miles up in the atmosphere) Ocean depths - they have been found deep in ocean canyons and trenches over 32,800 feet (10,000 meters) deep. They live in total darkness by thermal vents at incredible pressure. They make their own food by oxidizing sulfur that oozes from deep inside the earth.

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Assignment on Virus, Bacteria & Cyanobacteria

Scientists who specialize in bacteria - bacteriologists - say bacteria are found absolutely everywhere except for places that humans have sterilized. Even the most unlikely places where temperatures may be extreme, or where there may be a high concentration of toxic chemicals have bacteria - these are known as extremophiles (an extremophile is any organism adapted to living in conditions of extreme temperature, pressure, or/and chemical concentrations) - these bacteria can survive where no other organism can.

3.5 The cells of bacteria

A bacterial cell differs somewhat from the cell of a plant or animal. Bacterial cells have no nucleus and other organelles (sub-units within a cell with a specific function) bound by a membrane, except for ribosomes. Bacteria have pili, flagella, and a cell capsule (most of them), unlike animal or plant cells. An organism without a nucleus is called a prokaryote. A bacterial cell includes:

Figure 3.5.1

Basal body - this anchors the base of the flagellum, allowing it to rotate. Capsule - a layer on the outside of the cell wall. Some bacteria don't have a capsule. Cell wall - a thin layer (membrane) outside the plasma membrane, and within the capsule. DNA (Deoxyribonucleic acid) - contains all the genetic instructions used in the development and functioning of the bacterium. It is inside the cytoplasm. Cytoplasm - a gelatinous substance inside the plasma membrane. Genetic material and ribosomes lie inside. Flagellum - this is used for movement; to propel the cell. Some bacterial cells have more than one. Pili (singular: pilus) - these spikes allow the cell to stick to surfaces and transfer genetic material to other cells. A study revealed that pili are involved in causing traveler's diarrhea. Plasma membrane - it generates energy and transports chemicals. Substances can pass through the membrane (permeable). It is located within the cell wall. Ribosomes - this is where protein is made (synthesized). Ribosomes are small organelles made up of RNA-rich granules.

Fig: 3.5.1 Structure of Bacteria.

3.6 Metabolism - How do bacteria feed themselves?

Bacteria feed themselves in a variety of ways. Heterotrophic bacteria (or just heterotrophs) these eat other organisms. Most of them are saprobes, they absorb dead organic material, such as decomposing flesh. Some of these parasitic bacteria kill their host, while others help them. Autototrophic bacteria (or just autotrophs) - these make their own food. This could be done by photosynthesis - they use sunlight, C02, and water to make their food. Bacteria that use sunlight to synthesize their food are called photoautotrophs. These include the cyanobacteria which probably played a vital role in creating the Earth's oxygen atmosphere. Other photoautotraphs do not produce oxygen, such as heliobacteria, purple non-sulfur bacteria, purple sulfur bacteria, and green sulfur bacteria. Others do it by chemosynthesis - they use C02, water, and such chemicals as ammonia to synthesize their food. We call them nitrogen fixers. They are commonly in legume roots and ocean vents. Examples of legumes are alfalfa, clover, peas, beans, lentils, and peanuts. These bacteria are known as chemoautotrophs. Other chemicals used for nutrition are nitrogen, sulfur, phosphorous, vitamins, and such metallic elements as sodium, potassium, calcium, magnesium, manganese, iron, zinc, and cobalt.

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Assignment on Virus, Bacteria & Cyanobacteria

3.7 What kinds of environments do bacteria inhabit?

Aerobes (aerobic bacteria) - these can grow only in the presence of oxygen. Some types may cause serious problems to people's infrastructure as they can cause corrosion, fouling, problems with water clarity, and bad smells. Anaerobes (anaerobic bacteria) - these can only grow if there is no oxygen present. In humans, they are most commonly found in the gastrointestinal tract. They also cause gas gangrene, tetanus, and botulism. Most dental infections are caused by this type of bacterium.

3.8 How do bacteria reproduce?

Binary Fission This is known as an asexual form of reproduction; it does not involve a male and female. The cell continues growing and growing, eventually a new cell wall grows through the center forming two daughter cells, which eventually separate. Each daughter cell has the same genetic material as the parent cell. Bacterial Recombination The problem with binary fission is that every daughter cell is identical to the cell it came from, as well as all its sisters. This makes it harder for bacteria to prevail, especially if we attack them with antibiotics. To get around this, bacteria use a process called recombination.

3.9 The effects of bacteria

Most people tend to imagine negative things when asked about bacteria. It is important to remember that bacteria are so ubiquitous, and have been around so long - since the beginning of life on earth, in fact - that we would not have existed without them. The air we breathe - specifically the oxygen in the air we breathe - was most probably created millions of years ago by the activity of bacteria. Nitrogen fixation Bacteria assimilate atmospheric nitrogen and then release it for plant use when they die. Plants cannot extract nitrogen from the air and place it in the soil - but plants need nitrogen in soil to live - without the bacteria doing this would not be able to carry out a vital part of their metabolism. The relationship between plant and bacteria has become so close in this sense that many plant seeds have a small container of bacteria that will be used when the plant sprouts. Humans need bacteria to survive The human body contains huge amounts of friendly bacteria that are either neutral or help us somehow. Bacteria in the digestive system are crucial for the breakdown of certain types of nutrients, such as complex sugars, into forms the body can use. Friendly bacteria also protect us from dangerous ones by occupying places in the body the pathogenic (disease causing) bacteria want attach to. Some friendly bacteria actually come to the rescue and attack the pathogens. Bacteria and the obesity epidemic According to a study released by the International & American Association for Dental Research, bacteria may be a contributory factor in today's obesity explosion.

3.10 Effect of bacteria as pathogens to humans (causes of diseases)

Some of the most deadly diseases and devastating epidemics in human history have been caused by bacteria. Smallpox and malaria - not caused by bacteria - have killed more humans than bacterial diseases. However, the following bacterial diseases have destroyed hundreds of millions of human lives:

Cholera Diphtheria Dysentery

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Assignment on Virus, Bacteria & Cyanobacteria

Plague Pneumonia Tuberculosis Typhoid Typhus

Figure 3.10.1
Fig: 3.10.1 Diseases caused by Bacteria.

3.11 Significance of bacteria in food technology

Lactic acid bacteria, such as Lactobacillus and Lactococcus together with yeast and molds (fungi) have been used for the preparation of such foods as cheese, soy sauce, vinegar, yoghurt and pickles. Humans have been using these bacteria for preparing fermented foods for thousands of years.

3.12 Significance of bacteria in other technologies

Bacteria can break down organic compounds at remarkable speed and help us in our waste processing and bioremediation activities. Bacteria are frequently used for cleaning up oil spills. They are useful in clearing up toxic waste. The pharmaceutical and chemical industries use bacteria in the production of certain chemicals. They are used in the molecular biology, biochemistry and genetic research because they can grow quickly and are relative easy to manipulate. Scientists can use bacteria to study the functions of genes and enzymes, as well as bacterial metabolic pathways, and then test out their results on more complex organisms. Such bacteria as Bacillus thuringiensis (BT) can be used in agriculture instead of pesticides, without the undesirable environmental consequences that pesticide use may cause

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Assignment on Virus, Bacteria & Cyanobacteria

4 Cyanobacteria
Cyanobacteria, also known as Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria. Although often called blue-green algae, that name is a misnomer as cyanobacteria are prokaryotic and algae are eukaryotic. By producing oxygen as a gas as a by-product of photosynthesis, cyanobacteria are thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the composition of life forms on Earth by stimulating biodiversity and leading to the near-extinction of oxygen-intolerant organisms. Fig: 4 Cyanobacteria Temporal range 3500-0Ma.

Figure 4

4.1 Ecology
Cyanobacteria can be found in almost every terrestrial and aquatic habitatoceans, fresh water, damp soil, temporarily moistened rocks in deserts, bare rock and soil, and even Antarctic rocks. They can occur as planktonic cells or form phototrophic biofilms. They are found in almost every endolithic ecosystem. A few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Some live in the fur of sloths, providing a form of camouflage. Aquatic cyanobacteria are known for their extensive and highly visible blooms that can form in both freshwater and marine environments. The blooms can have the appearance of blue-green paint or scum. These blooms can be toxic, and frequently lead to the closure of recreational waters when spotted. Marine bacteriophages are significant parasites of unicellular marine cyanobacteria.

Figure 4.1
Fig: 4.1 A cyanobacteria bloom near Fiji.

4.2 Characteristics 4.2.1 Nitrogen fixation

Cyanobacteria include unicellular and colonial species. Colonies may form filaments, sheets or even hollow balls. Some filamentous colonies show the ability to differentiate into several different cell types: vegetative cells, the normal, photosynthetic cells that are formed under favorable growing conditions; akinetes, the climate-resistant spores that may form when environmental conditions become harsh; and thick-walled heterocysts, which contain the enzyme nitrogenase, vital for nitrogen fixation. Heterocysts may also form under the appropriate environmental conditions (anoxic) when fixed nitrogen is scarce. Heterocyst-forming species are specialized for nitrogen fixation and are able to fix nitrogen gas into ammonia (NH3), nitrites (NO2) or nitrates (NO3), which can be absorbed by plants and converted to protein and nucleic acids (atmospheric nitrogen is not bioavailable to plants). Fig: 4.2.1 Colonies of Nostoc pruniforme.

Figure 4.2.1

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Assignment on Virus, Bacteria & Cyanobacteria

4.3 Photosynthesis 4.3.1 Carbon fixation

Cyanobacteria use the energy of sunlight to drive photosynthesis, a process where the energy of light is used to split water molecules into oxygen, protons, and electrons. While most of the high-energy electrons derived from water are used by the cyanobacterial cells for their own needs, a fraction of these electrons are donated to the external environment via electrogenic activity. Cyanobacterial electrogenic activity is an important microbiological conduit of solar energy into the biosphere.

4.4 Biotechnology and applications

Some cyanobacteria are sold as food, notably Aphanizomenon flos-aquae and Arthrospira platensis (Spirulina). Recent research has suggested the potential application of cyanobacteria to the generation of renewable energy via converting sunlight into electricity. Internal photosynthetic pathways can be coupled to chemical mediators that transfer electrons to external electrodes. Currently efforts are underway to commercialize algae-based fuels such as diesel, gasoline and jet fuel. Cyanobacteria may possess the ability to produce substances that could one day serve as anti-inflammatory agents and combat bacterial infections in humans. Spirulina's extracted blue color is used as a natural food coloring in gum and candy. Fig: 4.4.1 Cyanobacteria cultured in specific media. Cyanobacteria can be helpful in agriculture as they have the capability to fix atmospheric nitrogen to soil. Fig: 4.4.2 Spirulina tablets.

Figure 4.4.1

Figure 4.4.2 References

Following websites are used for composing this assignment. http://en.wikipedia.org/wiki/Microorganism http://en.wikipedia.org/wiki/Virus#Structure http://www.sparknotes.com/biology/microorganisms/viruses/section1.rhtml http://en.wikipedia.org/wiki/Animal_virus http://en.wikipedia.org/wiki/Plant_virus http://www.medicalnewstoday.com/articles/157973.php http://en.wikipedia.org/wiki/Bacteria http://www.ucmp.berkeley.edu/bacteria/cyanolh.html http://en.wikipedia.org/wiki/Cyanobacteria

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