bacteria

 

[pl. of bacterium], microscopic unicellular prokaryotic organisms characterized by the lack of a membrane-bound nucleus and membrane-bound organelles. Once considered a part of the plant kingdom, bacteria were eventually placed in a separate kingdom, Monera. Bacteria fall into one of two groups, Archaebacteria (ancient forms thought to have evolved separately from other bacteria) and Eubacteria. A recently proposed system classifies the Archaebacteria, or archaea, and the Eubacteria as major groupings (sometimes called domains) above the kingdom level.

Bacteria were the only form of life on earth for 2 billion years. They were first observed by Antony van Leeuwenhoek in the 17th cent.; bacteriology as an applied science began to develop in the late 19th cent. as a result of research in medicine and in fermentation processes, especially by Louis Pasteur and Robert Koch.

Bacteria are remarkably adaptable to diverse environmental conditions: they are found in the bodies of all living organisms and on all parts of the earth—in land terrains and ocean depths, in arctic ice and glaciers, in hot springs, and even in the stratosphere. Our understanding of bacteria and their metabolic processes has been expanded by the discovery of species that can live only deep below the earth's surface and by species that thrive without sunlight in the high temperature and pressure near hydrothermal vents on the ocean floor. There are more bacteria, as separate individuals, than any other type of organism; there can be as many as 2.5 billion bacteria in one gram of fertile soil.

Characteristics

Bacteria are grouped in a number of different ways. Most bacteria are of one of three typical shapes—rod-shaped (bacillus), round (coccus, e.g., streptococcus), and spiral (spirillum). An additional group, vibrios, appear as incomplete spirals. The cytoplasm and plasma membrane of most bacterial cells are surrounded by a cell wall; further classification of bacteria is based on cell wall characteristics (see Gram's stain). They can also be characterized by their patterns of growth, such as the chains formed by streptococci. Many bacteria, chiefly the bacillus and spirillum forms, are motile, swimming about by whiplike movements of flagella; other bacteria have rigid rodlike protuberances called pili that serve as tethers.

Some bacteria (those known as aerobic forms) can function metabolically only in the presence of free or atmospheric oxygen; others (anaerobic bacteria) cannot grow in the presence of free oxygen but obtain oxygen from compounds. Facultative anaerobes can grow with or without free oxygen; obligate anaerobes are poisoned by oxygen.

Reproduction

In bacteria the genetic material is organized in a continuous strand of DNA. This circle of DNA is localized in an area called the nucleoid, but there is no membrane surrounding a defined nucleus as there is in the eukaryotic cells of protists, fungi, plants, and animals (see eukaryote). In addition to the nucleoid, the bacterial cell may include one or more plasmids, separate circular strands of DNA that can replicate independently, and that are not responsible for the reproduction of the organism. Drug resistance is often conveyed via plasmid genes.

Reproduction is chiefly by binary fission, cell division yielding identical daughter cells. Some bacteria reproduce by budding or fragmentation. Despite the fact that these processes should produce identical generations, the rapid rate of mutation possible in bacteria makes them very adaptable. Some bacteria are capable of specialized types of genetic recombination, which involves the transfer of nucleic acid by individual contact (conjugation), by exposure to nucleic acid remnants of dead bacteria (transformation), by exchange of plasmid genes, or by a viral agent, the bacteriophage (transduction). Under unfavorable conditions some bacteria form highly resistant spores with thickened coverings, within which the living material remains dormant in altered form until conditions improve. Others, such as the radioactivity-resistant Deinococcus radiodurans, can withstand serious damage by repairing their own DNA.

Nutrition

Most bacteria are heterotrophic, living off other organisms. Most of these are saprobes, bacteria that live off dead organic matter. The bacteria that cause disease are heterotrophic parasites. There are also many non-disease-causing bacterial parasites, many of which are helpful to their hosts. These include the “normal flora” of the human body.

Autotrophic bacteria manufacture their own food by the processes of photosynthesis and chemosynthesis (see autotroph). The photosynthetic bacteria include the green and purple bacteria and the cyanobacteria. Many of the thermophilic archaebacteria are chemosynthetic autotrophs.

Beneficial Bacteria

Harmless and beneficial bacteria far outnumber harmful varieties. Because they are capable of producing so many enzymes necessary for the building up and breaking down of organic compounds, bacteria are employed extensively by humans—for soil enrichment with leguminous crops (see nitrogen cycle), for preservation by pickling, for fermentation (as in the manufacture of alcoholic beverages, vinegar, and certain cheeses), for decomposition of organic wastes (in septic tanks, in some sewage disposal plants, and in agriculture for soil enrichment) and toxic wastes, and for curing tobacco, retting flax, and many other specialized processes. Bacteria frequently make good objects for genetic study: large populations grown in a short period of time facilitate detection of mutations, or rare variations.

Pathogenic Bacteria

Bacterial parasites that cause disease are called pathogens. Among bacterial plant diseases are leaf spot, fire blight, and wilts; animal diseases caused by bacteria include tuberculosis, cholera, syphilis, typhoid fever, and tetanus. Some bacteria attack the tissues directly; others produce poisonous substances called toxins. Natural defense against harmful bacteria is provided by antibodies (see immunity). Certain bacterial diseases, e.g., tetanus, can be prevented by injection of antitoxin or of serum containing antibodies against specific bacterial antigens; immunity to some can be induced by vaccination; and certain specific bacterial parasites are killed by antibiotics.

New strains of more virulent bacterial pathogens, many of them resistant to antibiotics, have emerged in recent years. Many believe this to be due to the overuse of antibiotics, both in prescriptions for minor, self-limiting ailments and as growth enhancers in livestock; such overuse increases the likelihood of bacterial mutations. For example, a variant of the normally harmless Escherichia coli has caused serious illness and death in victims of food poisoning. See also drug resistance.

Bibliography

See P. Singleton, Introduction to Bacteria (1992); W. Biddle, A Field Guide to Germs (1995).

Bacteria Fossil range: Archean or earlier - Recent
Escherichia coli cells magnified 25,000 times
Scientific classification
Domain: Bacteria
Phyla
Actinobacteria Aquificae Chlamydiae Bacteroidetes/Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia

Bacteria (singular: bacterium) are unicellular microorganisms. Typically a few micrometres in length, individual bacteria have a wide-range of shapes, ranging from spheres to rods to spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste,^[1] seawater, and deep in the Earth's crust. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5×10³⁰) bacteria in the world.^[2] Bacteria are vital in recycling nutrients, and many important steps in nutrient cycles depend on bacteria, such as the fixation of nitrogen from the atmosphere. However, most of these bacteria have not been characterised, and only about half of the phyla of bacteria have species that can be cultured in the laboratory.^[3] The study of bacteria is known as bacteriology, a branch of microbiology.

There are approximately 10 times as many bacterial cells as human cells in the human body, with large numbers of bacteria on the skin and in the digestive tract.^[4] Although the vast majority of these bacteria are rendered harmless or beneficial by the protective effects of the immune system, a few pathogenic bacteria cause infectious diseases, including cholera, syphilis, anthrax, leprosy and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa.^[5] In developed countries, antibiotics are used to treat bacterial infections and in various agricultural processes, so antibiotic resistance is becoming common. In industry, bacteria are important in processes such as wastewater treatment, the production of cheese and yoghurt, and the manufacture of antibiotics and other chemicals.^[6]

Bacteria are prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotic life consists of two very different groups of organisms that evolved independently from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.^[7]

History of bacteriology

Further information: Microbiology

The existence of microorganisms was hypothesized during the late Middle Ages. In The Canon of Medicine (1020), Abū Alī ibn Sīnā (Avicenna) stated that bodily secretions are contaminated by "foul foreign earthly bodies" before a person becomes infected, but he did not view these bodies as primary causes of disease. When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib wrote of infectious diseases being caused by contagious entities that enter the human body.^[8][9] These ideas about the contagious nature of some diseases became more popular in Europe during the Renaissance, particularly through the writing of Girolamo Fracastoro.^[10]

Bacteria were first observed by Anton van Leeuwenhoek in 1676, using a single-lens microscope of his own design.^[11] He called them "animalcules" and published his observations in a series of letters to the Royal Society.^[12][13][14] The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828, and is derived from the Greek word βακτήριον -α , bacterion -a , meaning "small staff".^[15]

Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease.^[16] Robert Koch was a pioneer in medical microbiology and worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905.^[17] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease; these postulates are still used today.^[18]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.^[19] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochete that causes syphilis—into compounds that selectively killed the pathogen.^[20] Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.^[21]

A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria.^[22] This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains as part of the three-domain system.^[23]

Origin and early evolution

Further information: Timeline of evolution

The ancestors of modern bacteria were single-celled microorganisms that were the first forms of life to develop on earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life.^[24][25] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the past history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.^[26] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.^[27][28]

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.^[29][30] This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e. g. in ancient "amitochondrial" protozoa). Later on, an independent second engulfment by some mitochondria-containing eukaryotes of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants. There are even some algal groups known that clearly originated from subsequent events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic algae that developed into "second-generation" plastids.^[31][32]

Morphology

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about 10 times smaller than eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species–for example Thiomargarita namibiensis and Epulopiscium fishelsoni–are up to half a millimetre long and are visible to the unaided eye.^[33] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.^[34]

Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed) or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called spirilla, or tightly coiled, called spirochetes. A small number of species even have tetrahedral or cuboidal shapes.^[35] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.^[36][37]

Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells; certain types, such as species of the genus Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia.^[38]

Bacteria often attach to surfaces and form dense aggregations called biofilms or microbial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.^[39][40] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.^[41] Biofilms are also important for chronic bacterial infections and infections of implanted medical devices, as bacteria protected within these structures are much harder to kill than individual bacteria.^[42]

Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.^[43] In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of multicellular organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and differentiate into a specialised dormant state called myxospores, which are more resistant to desiccation and other adverse environmental conditions than are ordinary cells.^[44]

Cellular structure

Further information: Bacterial cell structure

Intracellular structures

The bacterial cell is surrounded by a lipid membrane, or cell membrane, which encompasses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are prokaryotes, bacteria do not have membrane-bound organelles in their cytoplasm and thus contain few intracellular structures. They consequently lack a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum.^[45]

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The absence of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane, between the cytoplasm and the periplasmic space.^[46] Additionally, while some transporter proteins consume chemical energy, others harness concentration gradients to import nutrients across the cell membrane or to expel undesired molecules from the cytoplasm.

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid.^[47] The nucleoid contains the chromosome with associated proteins and RNA. Like all living organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and Archaea.^[48] The order Planctomycetes are an exception to the general absence of internal membranes in bacteria, because they have a membrane around their nucleoid and contain other membrane-bound cellular structures.^[49]

Some bacteria produce intracellular nutrient storage granules, such as glycogen,^[50] polyphosphate,^[51] sulfur^[52] or polyhydroxyalkanoates.^[53] These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy - allowing them to move up or down into water layers with different light intensities and nutrient levels.^[54]

Extracellular structures

Further information: Cell envelope

Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell walls are made of peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids.^[55] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.^[56] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.^[56]

There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.^[57]

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.^[58] These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.^[59]

In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell.^[60] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.^[61]

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.^[62]

Fimbriae are fine filaments of protein, just 2–10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells and are essential for the virulence of some bacterial pathogens.^[63] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation (see bacterial genetics, below).^[64]

Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular polymer, to a highly structured capsule or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages.^[65] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.^[66]

The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.^[67]

Endospores

Further information: Endospores

Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.^[68] In almost all cases, one endospore is formed and this is not a reproductive process, although Anaerobacter can make up to seven endospores in a single cell.^[69] Endospores have a central core of cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat.

Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, pressure and desiccation.^[70] In this dormant state, these organisms may remain viable for millions of years,^[71][72] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.^[73] Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.^[74]

Metabolism

Further information: Microbial metabolism