Microorganism

A microorganism, or microbe, is an organism (form of life) that is microscopic (too small to be seen by the unaided human eye). Microorganisms can be bacteria, fungi, archaea, or protists, but not viruses and prions, which are generally classified as non-living. Microorganisms are often described as single-celled, or unicellular, organisms; however, some unicellular protists are visible to the human eye, and some multicellular species are microscopic.

Microorganisms live almost everywhere on earth where there is liquid water or even a tiny amount of moisture, including hot springs on the ocean floor, deep inside rocks within the earth's crust, on the human skin, in a cow's stomach, and inside a sponge used for washing dishes. Many microorganisms are critical to nutrient recycling in ecosystems as they act as decomposers, while others living in nodules on the roots of some plants convert nitrogen from the air to a form usable by plants. Microorganisms multiply rapidly under good growth conditions often contributing benefit to the larger plant or animal host organism and existing in healthy dynamic balance with other microorganisms and the host organism. At times, however, pathogenic microbes can invade larger organisms, override that organism's defenses, and cause disease.

As different as microorganisms are from human beings, the unity of life is shown in the numerous features shared between humans and microorganisms, including a carbon-based biochemistry with genetic material based on nucleic acids such as DNA (using a near universal genetic code), the presence of cell membranes, the need for energy and metabolism, and so forth. This commonality allows even microbes and human beings to relate, whether it is the beneficial relationship of E. coli in the human digestive system or the harmful relationship in which humans serve as host for the protozoan Plasmodium, which causes malaria.

The study of microorganisms (and viruses) is called microbiology.

History

Origin and evolution

Single-celled, prokaryotic microorganisms were the first forms of life to develop on earth, approximately 4 billion years ago and for about 3 billion years, all organisms were microscopic (Schopf 1994). Therefore, for most of the time period in which life has existed on earth, microorganisms have been the only form of life. (Delong and Pace 2001). The identification of bacteria, algae, and fungi in amber that is 220 million years old, shows that the morphology of microorganisms has not changed significantly since the Triassic period (Schmidt et al. 2006).

Most microorganisms reproduce rapidly and in great number. Prokaryotes, such as bacteria, reproduce asexually. Mayr (2001) notes that "sexual reproduction is unknown among them." However, they also freely exchange genes laterally by conjugation, transformation, and transduction, including among widely-divergent species (Wolska 2003). Mayr (2001) notes that even the archaebacteria (archaea) exchange genes with other families. This horizontal, or lateral, gene transfer, coupled with a high mutation rate and many other means of genetic variation allows prokaryotes to adapt swiftly (via natural selection on the microevolutionary level) to survive in new environments and respond to environmental stresses. This rapid microevolution coupled with rapid asexual reproduction has led to the recent development of antibiotic resistant "super-bugs"—pathogenic bacteria that are resistant to modern antibiotics (Enright et al. 2002).

Discovery

Prior to Anton van Leeuwenhoek's discovery of microorganisms in 1676, it had been a mystery as to 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 he did establish that there were forms of life that were not visible to the naked eye (Leeuwenhoek 1753a, 1753b). Leeuwenhoek's discovery, along with subsequent observations by Lazzaro Spallanzani and Louis Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.

Lazzarro Spallanzani found that microorganisms could only settle in a broth if the broth was exposed to the air. He also found that boiling the broth would sterilize it and kill the microorganisms. However, this did not settle the issue of spontaneous generation since some felt the boiling of the broth was also eliminating the "vital force" and sealing the flasks prevented air with this vital force to enter and generate life (Towle 1989).

Louis Pasteur 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. Pasteur claimed to have "driven partisans of the doctrine of spontaneous generation into the corner" (Towle 1989). Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported the germ theory of disease. The view that living organisms only came from other living organisms, or biogenesis, became a cornerstone of biology (Towle 1989).

In 1876, Robert Koch established that microbes can cause disease. He did this by finding that the blood of cattle who were infected with anthrax always had large numbers of Bacillus anthracis. Koch also 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, causing the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, inject it into a healthy animal, and cause illness. Based upon these experiments, he devised criteria for establishing a causal link between a microbe and a disease in what are now known as Koch's postulates (Nobel lectures 1967). Though these postulates cannot be applied in all cases, they do retain historical importance in the development of scientific thought and are still used today (O'Brien and Goedert 1996).

Types of microorganisms

Microorganisms can be found almost anywhere in the taxonomic organization of life on the planet. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists and a number of fungi. Viruses are generally regarded as not living and therefore strictly speaking are not microbes, although the field of microbiology also encompasses the study of viruses.

Bacteria

The prokaryotic bacteria are the simplest and the most diverse and widespread group of organisms on Earth. Bacteria inhabit practically all environments where some liquid water is available and the temperature is below 140°C. They are found in sea water, soil, the gastrointestinal tract, hot springs, and in food. Practically all surfaces that have not been specially sterilized are covered in bacteria. The number of bacteria in the world is estimated to be around five million trillion trillion, or 5 × 10³⁰ (Coleman and Wiebe 1998).

Bacteria are practically all invisible to the naked eye, with few extremely rare exceptions, such as Thiomargarita namibiensis (Schulz and Jorgensen, 2001). They are unicellular organisms and lack organelles, including a nucleus. Their genome is usually a single string of DNA, although some of them harbor small pieces of DNA called plasmids. Bacteria are surrounded by a cell wall. They reproduce asexually by binary fission. Some species form spores, but for bacteria this is a mechanism for survival, not reproduction. Under optimal conditions, bacteria can grow extremely rapidly and have been reported as doubling as quickly as every ten minutes (Eagon 1962).

Archaea

Archaea are single-celled, microscopic organisms lacking nuclei and are therefore prokaryotes, classified as Monera in the alternative five-kingdom taxonomy, but the domain Archaea in the three-domain system and the kingdom Archaebacteria in the six-kingdom system. They were originally described in extreme environments, but have since been found in all types of habitats (Robertson et al. 2005).

A single organism from this domain has been called an "archaean." Furthermore, this biologic term is also used as an adjective.

Eukaryotes

All living things that are individually visible to the naked eye are eukaryotes (with few exceptions, such as the visible single-celled Thiomargarita namibiensis), including humans. However, a large number of eukaryotes are also microorganisms.

Eukaryotes are characterized by the presence of a nucleus, an organelle that houses the DNA. DNA itself is arranged in complex chromosomes. mitochondria are organelles that are vital in metabolism as they are the site of cellular respiration. Mitochondria are believed to have originated from symbiotic bacteria and have their own DNA, which is considered to be a remnant genome (Dyall et al. 2004). Plant cells also have cell walls and chloroplasts in addition to other organelles. Chloroplasts produce energy from light by photosynthesis. Chloroplasts also are believed to have originated from symbiotic bacteria (Dyall et al. 2004).

Unicellular eukaryotes are those whose members consist of a single cell throughout their life cycle. This qualification is significant since most multicellular eukaryotes consist of a single cell at the beginning of their life cycles. Microbial eukaryotes can be either haploid or diploid, or rarely have multiple cell nuclei. Not all microorganisms are unicellular as some microbial eukaryotes can have multiple cells.

Of the eukaryotic groups, most protists are unicellular, although some are multicellular and colonial. Protists are a heterogeneous group of living organisms, comprising those eukaryotes that are not animals, plants, or fungi. Among the protists, the protozoans (single-celled, microscopic or near-microscopic protists that exhibit some characteristics like animals, such as motility) are generally defined as unicellular and most are microorganisms. These include such microorganisms as amoeba, paramecium, Plasmodium (cause of malaria), and dinoflagellates. Most protozoans are around 0.01–0.05 mm and are too small to be seen with the naked eye, but can easily be found under a microscope. However, forms that are up to 0.5 mm are still fairly common and can be seen with the unaided eye.

Algae, which are generally classified as photosynthetic protists, include many single-celled species that are also microorganisms, such as Chlamydomonas. However, algae also include macroscopic, multicellular forms and some that are very large.

The eukaryotic fungi also have several unicellular species, such as baker's yeast (Saccharomyces cerevisiae). Animals are always multicellular, even if not be visible to the naked eye.

Habitats and ecology

Microorganisms are found in almost every habitat present in nature. Even in 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. Some can be found in extremely salty bodies of water, such as the Dead Sea. Extremophiles have been isolated from rocks as much as 7 kilometres below the earth's surface (Szewzyk et al. 1994), and it has been suggested that the amount of living organisms below the earth's surface may be comparable with the amount of life on or above the surface (Gold 1992). Extremophiles have been known to survive for a prolonged time in a vacuum, and can be highly resistant to ultraviolet radiation, which may even allow them to survive in space (Horneck 1981).

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.

The nitrogen cycle depends on the fixation of atmospheric nitrogen. 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 (Barea et al. 2005).

Importance

Microorganisms are vital to humans and the environment, as they participate in the Earth's element cycles, such as the carbon cycle and nitrogen cycle, as well as fulfilling other vital roles in virtually all ecosystems, such as in food chains and in decomposition. Nitrogen fixation is performed naturally by a number of different prokaryotes, including bacteria. Microbes also make up a large part of the Earth's biomass and thus are critical to food chains. Microscopic algae provide oxygen, and microbes are vital in decomposing dead plants and animals, releasing their nutrients for reuse.

Microbes also have an important place in many higher-order multicellular organisms as symbionts. Most species of legumes, for example, provide a habitat for nitrogen-fixing bacteria, and receive a usable form of nitrogen as a benefit. Bacteria and protists living symbiotically in the gut of such even-toed ungulates as cattle, deer, goats, and sheep, break down cellulose into a digestible form of carbohydrate, thereby permitting the host animals to consume and digest the most abundant organic compound on earth. Both sides receive some benefit from this relationship. The microorganisms get food and a secure place to live and the ungulate gets help with its digestion. The microorganisms themselves are also digested, providing proteins and other nutrients, but not before the community of microorganisms has had a chance to reproduce and give rise to a new generation so the relationship can continue (Lott 2003). The process also generates heat, which can help to keep the ungulate warm, and breaks down plant toxins, which permits ungulates to eat plants that are poisonous to other animals (Voelker 1986). One byproduct of the microbial digestion is large quantities of methane gas, which is expelled by the ungulates and becomes a not-insignificant contribution to the accumulation of greenhouse gases in the atmosphere.

Microorganisms are also important in food production by humans, being used in brewing, baking, and other food-making processes.

The lactobacilli and yeasts in sourdough bread are especially useful. To make bread, one uses a small amount (20-25 percent) of "starter" dough that has the yeast culture, and mixes it with flour and water. Some of this resulting dough is then saved to be used as the starter for subsequent batches. The culture can be kept at room temperature and continue yielding bread for years as long as it remains supplied with new flour and water. This technique was often used when "on the trail" in the American Old West.

Microorganisms 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.

In science and technology, microbes are also essential tools in biotechnology and the study of biochemistry, genetics, and molecular biology. On the negative side, microorganisms can also be used in the production of devastating biological weapons for warfare.

Microorganisms and human health

Microorganisms can form an endosymbiotic relationship with other, larger, organisms, including humans. For example, 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 (O'Hara and Shanahan 2006).

Microorganisms also are well-known as the cause of many infectious diseases. The organisms involved include bacteria, causing diseases such as plague, tuberculosis, and anthrax; [protozoa]], causing diseases such as malaria, sleeping sickness, 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 viruses, which are not considered microorganisms. No clear examples of archaean pathogens are known (Eckburg 2003), although a relationship has been proposed between the presence of some methanogens and human periodontal disease (Lepp et al. 2004).

Hygiene

Hygiene involves the avoidance of infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms, particularly bacteria, are found practically everywhere, this means in most cases the reduction of harmful microorganisms to acceptable levels. However, in some cases, it is required that an object or substance is completely sterile; that is, devoid of all living entities and viruses. A good example of this is use of a hypodermic needle.

In food preparation, microorganisms are reduced by preservation methods (such as the addition of vinegar), clean utensils used in preparation, short storage periods, or by cool temperatures. If complete sterility is needed, the two most common methods are irradiation and the use of an autoclave, which resembles a pressure cooker.

There are several methods for investigating the level of hygiene in a sample of food, drinking water, equipment, and so forth. 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 PCR, 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 in which all microorganisms would grow, and therefore often several different 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, for example, antibiotics), and coliform bacteria (these indicate a sewage contamination).

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