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Introduction to microorganisms

The importance of microorganisms to agriculture cannot be overemphasized. Microorganisms affect man in various negative and positive ways, therefore making it justifiable to study them. Microorganisms are known to cause disease in plants and animals contributing to poor growth and hence poor yield. Some of them however are known to contribute in positive ways such as in biodegradation and fermentation. This course is therefore designed to teach students the importance of microorganisms and to also teach them the basic characteristics of different groups of microbes that are important in crop production.
General Introduction to Microorganisms
The word microorganism uses combining forms of micro- (from the Greek:  mikros, "small") and organism from the Greek:  organismós, "organism"). It is usually styled solid but is sometimes hyphenated (micro-organism), especially in older texts. The word microbe comes from mikrós, "small" and, bíos, "life".
A microorganism or microbe therefore is a microscopic organism, which may be single-celled or multicellular. The study of microorganisms is called microbiology, a subject that began with the discovery of microorganisms in 1674 by Antonie van Leeuwenhoek, using a microscope of his own design.
Microorganisms are very diverse and include all bacteria, archaea and most protozoa. This group also contains some fungi, algae, and some micro-animals such as rotifers. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists classify viruses and viroids as microorganisms, but others consider these as nonliving. In July 2016, scientists identified a set of 355 genes from the last universal common ancestor of all life, including microorganisms, living on Earth.
Microorganisms live in every part of the biosphere, including soil, hot springs, inside rocks at least 19 km (12 mi) deep underground, the deepest parts of the ocean, and at least 64 km (40 mi) high in the atmosphere. Microorganisms, under certain test conditions, have been observed to thrive in the vacuum of outer space. Microorganisms likely far outweigh all other living things combined. The mass of prokaryote microorganisms including the bacteria and archaea may be as much as 0.8 trillion tons of carbon, out of the total biomass of between 1 and 4 trillion tons. Microorganisms appear to thrive in the Mariana Trench, the deepest spot in the Earth's oceans. Other researchers reported related studies that microorganisms thrive inside rocks up to 580 m (1,900 ft; 0.36 mi) below the sea floor under 2,590 m (8,500 ft; 1.61 mi) of ocean off the coast of the northwestern United States, as well as 2,400 m (7,900 ft; 1.5 mi) beneath the seabed off Japan.[14] In August 2014, scientists confirmed the existence of microorganisms living 800 m (2,600 ft; 0.50 mi) below the ice of Antarctica. According to one researcher, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are."
The possible existence of microorganisms was discussed for many centuries before their discovery in the 17th century. The existence of unseen microbial life was postulated by Jainism. In the 6th century BC, Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air and fire. The Jain scriptures also describe nigodas, which are sub-microscopic creatures living in large clusters and having a very short life, which are said to pervade every part of the universe, even the tissues of plants and animal. The earliest known idea to indicate the possibility of diseases spreading by yet unseen organisms was that of the Roman scholar Marcus Terentius Varro in a first century BC book titled On Agriculture in which he warns against locating a homestead near swamps:
Antonie Van Leeuwenhoek (1632–1723) was one of the first people to observe microorganisms, using microscopes of his own design. Robert Hooke, a contemporary of Leeuwenhoek, also used microscopes to observe microbial life; his 1665 book Micrographia describes these observations and coined the term cell.
Before Leeuwenhoek's discovery of microorganisms in 1675, it had been a mystery why grapes could be turned into wine, milk into cheese, or why food would spoil. Leeuwenhoek did not make the connection between these processes and microorganisms, but using a microscope, he did establish that there were signs of life that were not visible to the naked eye. Leeuwenhoek's discovery, along with subsequent observations by Spallanzani and Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.
Lazzaro Spallanzani (1729–1799) found that boiling broth would sterilise it, killing any microorganisms in it. He also found that new microorganisms could only settle in a broth if the broth was exposed to air.
Louis Pasteur (1822–1895) expanded upon Spallanzani's findings by exposing boiled broths to the air, in vessels that contained a filter to prevent all particles from passing through to the growth medium, and also in vessels with no filter at all, with air being admitted via a curved tube that would not allow dust particles to come in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported germ theory.
In 1876, Robert Koch (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle which were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microorganism and a disease and these are now known as Koch's postulates. Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today.
On 8 November 2013, scientists reported the discovery of what may be the earliest signs of life on Earth—the oldest complete fossils of a microbial mat (associated with sandstone in Western Australia) estimated to be 3.48 billion years old.
Ecology of Microorganisms
Microorganisms are found in almost every habitat present in nature, including hostile environments such as the poles, deserts, geysers, rocks, and the deep sea. Some types of microorganisms have adapted to the extreme conditions and sustained colonies; these organisms are known as extremophiles. Extremophiles have been isolated from rocks as much as 7 kilometres below the Earth's surface, and it has been suggested that the amount of living organisms below the Earth's surface is comparable with the amount of life on or above the surface. Extremophiles have been known to survive for a prolonged time in a vacuum, and can be highly resistant to radiation, which may even allow them to survive in space.[70] Many types of microorganisms have intimate symbiotic relationships with other larger organisms; some of which are mutually beneficial (mutualism), while others can be damaging to the host organism (parasitism). If microorganisms can cause disease in a host they are known as pathogens and then they are sometimes referred to as microbes. Microorganisms play critical roles in Earth's biogeochemical cycles as they are responsible for decomposition and nitrogen fixation.
In soil
The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. This is achieved by a number of diazotrophs. One way this can occur is in the nodules in the roots of legumes that contain symbiotic bacteria of the genera  Rhizobium, Mesorhizobium, Sinorhizobium,
Bradyrhizobium,  and Azorhizobium.

A lichen is a symbiosis of a fungus with microbial algae. The algal partner is photosynthetic, enabling the fungus to live in habitats such as bare rocks where other sources of nutrition are not available.
Other fungi, including some edible mushrooms such as the cep, form mycorrhizal symbioses with trees. The fungi increase the supply of nutrients to the tree in return for a supply of energy.
Microbes in human culture
Microorganisms are vital to humans and the environment, as they participate in the carbon and nitrogen cycles, as well as fulfilling other vital roles in virtually all ecosystems, such as recycling other organisms' dead remains and waste products through decomposition. Microorganisms also have an important place in most higher-order multicellular organisms as symbionts.
Uses of Microorganisms in Food production
Fermentation in food processing
Microorganisms are used to make yoghurt, cheese, curd, kefir, ayran, xynogala, and other types of food. They are used to leaven bread, and to convert sugars to alcohol in wine and beer. Microorganisms are used in brewing, wine making, baking, pickling and other food-making processes.
They are also used to control the fermentation process in the production of cultured dairy products such as yogurt and cheese. The cultures also provide flavor and aroma, and inhibit undesirable organisms. The role of microorganism in assuring hygiene in food preparations
Hygiene is the avoidance of infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms, in particular bacteria, are found virtually everywhere, the levels of harmful microorganisms can be reduced to acceptable levels. However, in some cases, it is required that an object or substance be completely sterile, i.e. devoid of all living entities and viruses. A good example of this is a hypodermic needle.
There are several methods for investigating the level of hygiene in a sample of food, drinking water, equipment, etc. Water samples can be filtrated through an extremely fine filter. This filter is then placed in a nutrient medium. Microorganisms on the filter then grow to form a visible colony. Harmful microorganisms can be detected in food by placing a sample in a nutrient broth designed to enrich the organisms in question. Various methods, such as selective media or polymerase chain reaction, can then be used for detection. The hygiene of hard surfaces, such as cooking pots, can be tested by touching them with a solid piece of nutrient medium and then allowing the microorganisms to grow on it.
There are no conditions where all microorganisms would grow, and therefore often several methods are needed. For example, a food sample might be analyzed on three different nutrient mediums designed to indicate the presence of "total" bacteria (conditions where many, but not all, bacteria grow), molds (conditions where the growth of bacteria is prevented by, e.g., antibiotics) and coliform bacteria (these indicate a sewage contamination).
Uses in Water and sewage treatment
The majority of all oxidative sewage treatment processes rely on a large range of microorganisms to oxidize organic constituents which are not amenable to sedimentation or flotation. Anaerobic microorganisms are also used to reduce sludge solids producing methane gas (amongst other gases) and a sterile mineralised residue. In potable water treatment, one method, the slow sand filter, employs a complex gelatinous layer composed of a wide range of microorganisms to remove both dissolved and particulate material from raw water.
Uses in bio Energy production
Algae fuel, Cellulosic ethanol, and Ethanol fermentation
Microorganisms are used in fermentation to produce ethanol, and in biogas reactors to produce methane. Scientists are researching the use of algae to produce liquid fuels, and bacteria to convert various forms of agricultural and urban waste into usable fuels.
Uses in Chemicals and enzymes production
Microorganisms are used for many commercial and industrial production of chemicals, enzymes and other bioactive molecules.
Organic acids produced by microbial fermentation include
Acetic acid produced by the bacterium Acetobacter aceti and other acetic acid bacteria (AAB)
Butyric acid (butanoic acid) produced by the bacterium Clostridium butyricum
Lactic acid: Lactobacillus and other lactic acid bacteria (LAB)
Citric acid: produced by the mould fungus Aspergillus niger
Microorganisms are used for preparation of bioactive molecules and enzymes, including:
Streptokinase produced by the bacterium Streptococcus and modified by genetic engineering is used as a clot buster for removing clots from the blood vessels of patients who have undergone myocardial infarctions leading to heart attack.
Cyclosporin A, a bioactive molecule used as an immunosuppressive agent in organ transplantation
Statins produced by the yeast Monascus purpureus are commercialized as blood cholesterol lowering agents which act by competitively inhibiting the enzyme responsible for synthesis of cholesterol.
Uses in science
Microorganisms are essential tools in biotechnology, biochemistry, genetics, and molecular biology. The yeasts (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are important model organisms in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated. They are particularly valuable in genetics, genomics and proteomics. Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living fuel cells, and as a solution for pollution.
Uses in Warfare
Biological warfare
In the Middle Ages, as an early example of biological warfare, diseased corpses were thrown into castles during sieges using catapults or other siege engines. Individuals near the corpses were exposed to the pathogen and were likely to spread that pathogen to others.
Soil microbiology
Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse soil microbiome results in fewer plant diseases and higher yield.[94]
Human health
Human bacterial flora
Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The bacteria that live within the human digestive system contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates.
Microorganisms can cause Diseases In both animals and plants
Pathogen and Germ theory of disease
Microorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoa, causing diseases such as malaria, sleeping sickness, dysentery and toxoplasmosis; and also fungi causing diseases such as ringworm, candidiasis or histoplasmosis.
However, other diseases such as influenza, yellow fever or AIDS are caused by pathogenic viruses, which are not usually classified as living organisms and are not, therefore, microorganisms by the strict definition. No clear examples of archaean pathogens are known, although a relationship has been proposed between the presence of some archaean methanogens and human periodontal disease.

A virus is a nucleoprotein that multiplies only in living cells and has the ability to cause disease. It is too small to be seen individually with a light microscope. All viruses parasitize cells and cause a multitude of diseases in all forms of living organisms. Some viruses attack humans, animals, or both and cause such diseases as influenza, polio, rabies, smallpox, acquired immunodeficiency syndrome (AIDS), and warts; others attack higher plants; and still others attack microorganisms, such as fungi and bacteria. The total number of viruses known to date exceeds 2,000, and new viruses are described almost every month. Nearly half of all known viruses attack and cause diseases in plants. One virus may infect one or dozens of different species of plants, and each species of plant is usually attacked by many different kinds of viruses. A plant may sometimes be infected by more than one kind of virus at the same time.
Although viruses behave like microorganisms in that they have genetic functions, are able to reproduce (replicate), and cause disease, they also behave as chemical molecules. At their simplest, viruses consist of nucleic acid and protein, with the protein forming a protective coat around the nucleic acid. Although viruses can take any of several forms, they are mostly rod shaped, polyhedral, or variants of these two basic structures. In each virus, there is always only RNA or only DNA and, in most plant viruses, there is only one kind of protein. Some viruses, however, may have two or more different proteins.

How viruses cause diseases
Viruses do not divide and do not produce any kind of specialized reproductive structures such as spores. Instead, they multiply by inducing host cells to make more virus. Viruses cause disease not by consuming cells or killing them with toxins, but by utilizing cellular substances during multiplication, taking up space in cells, and disrupting cellular processes. These in turn upset the cellular metabolism and lead to the development of abnormal substances and conditions injurious to the functions and the life of the cell or the organism.

Plant viruses differ greatly from all other plant pathogens not only in size and shape, but also in the simplicity of their chemical constitution and physical structure, methods of infection, multiplication, translocation within the host, dissemination, and the symptoms they produce on the host. Because of their small size and the fact that they are transparent, viruses generally cannot be viewed and detected by the methods used for other pathogens. Cell inclusions consisting of virus particles, however, are visible by light microscopy. Viruses are not cells nor do they consist of cells.
Detection of viruses
The present methods of detecting plant viruses involve primarily the transmission of the virus from a diseased to a healthy plant by budding or grafting, or by rubbing leaves of healthy plants with sap from an infected plant.
Certain other methods of transmission, such as by dodder or insect vectors, are also used to demonstrate the presence of a virus. Most of these methods, however, cannot distinguish whether the pathogen is a virus, a mollicute, or a fastidious vascular bacterium; only transmission through bacteria- and fungi-free plant sap is currently considered as proof of the viral nature of the pathogen.
The most definitive proof of the presence of a virus in a plant is provided by purification, electron microscopy, and, most commonly, serology. In the past 5 to 10 years, the use of DNA or RNA probes and amplification of segments of viral nucleic acid through polymerase chain reaction (PCR) techniques have gained popularity as sensitive methods for the detection and identification of many viruses.
Morphology of viruses
Plant viruses come in different shapes and sizes. Nearly half of them are elongate (rigid rods or flexuous threads), and almost as many are spherical (isometric or polyhedral), with the remaining being cylindrical bacillus-like rods. Some elongated viruses are rigid rods about 15 by 300 nanometers, but most appear as long, thin, flexible threads that are usually 10 to 13 nanometers wide and range in length from 480 to 2,000 nanometers. Rhabdoviruses are short, bacilluslike, cylindrical rods, approximately three to five times as long as they are wide (52–75 by 300– 380nm). Most spherical viruses are actually polyhedral, ranging in diameter from about 17 nanometers (tobacco necrosis satellite virus) to 60 nanometers (wound tumor virus). Tomato spotted wilt virus is surrounded by a membrane and has a flexible, spherical shape about 100 nanometers in diameter.
Many plant viruses have split genomes, i.e., they consist of two or more distinct nucleic acid strands encapsidated in different-sized particles made of the same protein subunits. Thus, some, like tobacco rattle virus, consist of two rods, a long one (195 by 25nm) and a shorter one (43 by 25 nm), whereas others, like alfalfa mosaic virus, consist of four components of different sizes. Also, many isometric viruses have two or three different components of the same size but containing nucleic acid strands of different lengths. In multi component viruses, all of the nucleic acid strand components must be present in the plant for the virus to multiply and perform in its usual manner.
Satellite Viruses and Satellite RNAs
Typical viruses consist of one or more rather large strands of nucleic acid contained in a capsid composed of one or more kinds of protein molecules that can multiply and cause infection by themselves. In addition to typical viruses, however, two other types of virus-like pathogens are associated with plant diseases. Satellite viruses are viruses but cannot cause infection by themselves. Instead, they must always be associated with certain typical viruses (helper viruses) because they depend on the latter for multiplication and plant infection. Satellite viruses often reduce the ability of the helper viruses to multiply and cause disease; i.e., satellite viruses act like parasites of the associated helper virus.
 There are also satellite RNAs, i.e., small, linear or circular RNAs found inside virions ( complete viral particle) of certain multi component viruses. Satellite RNAs are not related, or are only partially related, to the RNA of the virus; satellite RNAs may increase or decrease the severity of viral infections.
Generalized Outline of replication in a single stranded RNA Virus
In a simplified replication of an RNA virus,
- the nucleic acid (RNA) of the virus is first freed from the protein coat.
-It then induces the cell to form the viral RNA polymerase.
-This enzyme utilizes the viral RNA as a template and forms complementary RNA.
The first new RNA produced is not the viral RNA but a mirror image (complementary copy) of that RNA.
-As the complementary RNA is formed, it is temporarily connected to the viral strand.
- Thus, the two form a double-stranded RNA that soon separates to produce the original virus RNA and the mirror image (-) strand,
- the latter then serve as a template for more virus (+strand) RNA synthesis.
When a virus infects a plant, it moves from one cell to another and multiplies in most, if not all, such cells.
Viruses move from cell to cell through the plasmodesmata connecting adjacent cells. Viruses multiply in each parenchyma cell they infect. In leaf parenchyma cells the virus moves approximately 1 millimeter, or 8 to 10 cells, per day.
In all economically important viral infections, viruses reach the phloem and through it are transported rapidly over long distances within the plant. Most viruses, however, require 2 to 5 days or more to move out of an inoculated leaf. Once the virus has entered the phloem, it moves rapidly in it toward growing regions (apical meristems) or other food-utilizing parts of the plant, such as tubers and rhizomes. In the phloem, the virus spreads systemically throughout the plant and reenters the parenchyma cells adjacent to the phloem through plasmodesmata.
Almost all viral diseases seem to cause some degree of dwarfing or stunting of the entire plant and reduction in total yield.
Viruses usually shorten the length of life of virus-infected plants, although they rarely kill plants on infection.
These effects may be severe and striking in appearance or they may be very slight and easily overlooked.
The most obvious symptoms of virus-infected plants are usually those appearing on the leaves, but some viruses may cause striking symptoms on the stem, fruit, and roots while they may or may not cause any symptom development on the leaves.

Plant viruses are transmitted from plant to plant in a number of ways. Modes of transmission include vegetative propagation, mechanically through sap, through seed, pollen, dodder, and by specific insects, mites, nematodes, and fungi.
Many plant viruses are named after the most conspicuous symptom they cause on the first host in which they have been studied. Thus, a virus causing a mosaic on tobacco is called tobacco mosaic virus, whereas the disease itself is called tobacco mosaic; another virus causing spotted wilt symptoms on tomato is called tomato spotted wilt virus and the disease is called tomato spotted wilt, and so forth.
Considering, however, the variability of symptoms caused by the same virus on the same host plant under different environmental conditions, by different strains of a virus on the same host, or by the same virus on different hosts, it becomes apparent that this system of nomenclature leaves much to be desired.
All viruses belong to the kingdom Viruses. Within the kingdom, viruses are distinguished as RNA viruses and DNA viruses, depending on whether the nucleic acid of the virus is RNA or DNA. Viruses are further subdivided depending on whether they possess one or two strands of RNA or DNA of either positive or negative sense, either filamentous or isometric morphology.
The best way to control a virus disease is by keeping it out of an area through systems of quarantine, inspection, and certification.
The existence of symptomless hosts, the incubation period after inoculation, and the absence of obvious symptoms in seeds, tubers, bulbs, and nursery stock make quarantine difficult and sometimes ineffective.
Eradication of diseased plants to eliminate inoculum from the field may, in some cases, help control the disease.
Plants may be protected against certain viruses by protecting them against the virus vectors. Controlling the insect vectors and removing weeds that serve as hosts may help some to control diseases. Generally, however, insect control is virtually useless for controlling insect-borne, especially aphid transmitted, plant viruses.
Losses caused by nematode transmitted viruses can be reduced considerably by soil fumigation to control the nematodes.
The use of virus-free seed, tubers, budwood, and so on is the single most important measure for avoiding virus diseases of many crops, especially those lacking insect vectors.
Periodic indexing of the mother plants producing such propagative organs is necessary to ascertain their continuous freedom from viruses.
Several types of inspection and certification programs are now in effect in various states producing seeds, tubers, and nursery stock used for propagation.
 Serological testing of mother plants, seeds, and nursery stock for virus by the ELISA technique and, more recently, by nucleic acid techniques has helped greatly in reducing the frequency of viruses in the propagating stock of crop plants.
Introduction to microorganisms Introduction to microorganisms Reviewed by DailyGgist_Official on August 19, 2018 Rating: 5

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