Bacteria

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Bacteria
Temporal range: Archean or earlier present
EscherichiaColi NIAID.jpg
Scanning electron micrograph of Escherichia coli rods
Scientific classification Red Pencil Icon.png
Domain:Bacteria
Woese, Kandler & Wheelis, 1990 [1]
Phyla
Synonyms
Eubacteria Woese & Fox, 1977 [3]

Bacteria ( /bækˈtɪəriə/ ( Loudspeaker.svg listen ); common noun bacteria, singular bacterium) are a type of biological cell. They constitute a large domain 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 of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, [4] and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory (specifically unculturable phyla, known as candidate phyla, make up 103 out of approximately 142 known phyla). [5] The study of bacteria is known as bacteriology, a branch of microbiology.

Cell (biology) The basic structural and functional unit of all organisms; the smallest unit of life.

The cell is the basic structural, functional, and biological unit of all known organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology, cellular biology, or cytology.

Domain (biology) Taxonomic rank

In biological taxonomy, a domain, also superkingdom or empire, is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese et.al. in 1990.

Microorganism Microscopic living organism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

Contents

Virtually all animal life on earth is dependent on bacteria for their survival as only bacteria and some archea possess the genes and enzymes necessary to synthesize vitamin B12, also known as cobalamin, and provide it through the food chain. Vitamin B12 is a water-soluble vitamin that is involved in the metabolism of every cell of the human body. It is a cofactor in DNA synthesis, and in both fatty acid and amino acid metabolism, It is particularly important in the normal functioning of the nervous system via its role in the synthesis of myelin. [6] [7] [8] [9]

Vitamin B<sub><small>12</small></sub> several chemical forms of vitamin B12

Vitamin B12, also known as cobalamin, is a water-soluble vitamin that is involved in the metabolism of every cell of the human body: it is a cofactor in DNA synthesis, and in both fatty acid and amino acid metabolism. It is particularly important in the normal functioning of the nervous system via its role in the synthesis of myelin, and in the maturation of developing red blood cells in the bone marrow.

Metabolism The set of life-sustaining chemical transformations within the cells of organisms

Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments..

Cofactor (biochemistry) a non-protein chemical compound or metallic ion that is required for a proteins biological activity to happen

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst, a substance that increases the rate of a chemical reaction. Cofactors can be considered "helper molecules" that assist in biochemical transformations. The rates at which these happen are characterized by in an area of study called enzyme kinetics.

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 5×1030 bacteria on Earth, [10] forming a biomass which exceeds that of all plants and animals. [11] Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. [12] In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, which, with a depth of up to 11 kilometres, is the deepest known part of the oceans. [13] [14] Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. [13] [15] According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are." [13]

Fresh water Naturally occurring water with low amounts of dissolved salts

Fresh water is any naturally occurring water except seawater and brackish water. Fresh water includes water in ice sheets, ice caps, glaciers, icebergs, bogs, ponds, lakes, rivers, streams, and even underground water called groundwater. Fresh water is generally characterized by having low concentrations of dissolved salts and other total dissolved solids. Though the term specifically excludes seawater and brackish water, it does include mineral-rich waters such as chalybeate springs.

Biomass (ecology) total mass of living organisms in a given area (all species or selected species)

The biomass is the mass of living biological organisms in a given area or ecosystem at a given time. Biomass can refer to species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It can include microorganisms, plants or animals. The mass can be expressed as the average mass per unit area, or as the total mass in the community.

Nutrient cycle Set of processes exchanging nutrients between parts of a system

A nutrient cycle is the movement and exchange of organic and inorganic matter back into the production of matter. Energy flow is a unidirectional and noncyclic pathway, whereas the movement of mineral nutrients is cyclic. Mineral cycles include the carbon cycle, sulfur cycle, nitrogen cycle, water cycle, phosphorus cycle, oxygen cycle, among others that continually recycle along with other mineral nutrients into productive ecological nutrition.

The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are approximately 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body. This means that although they do have the upper hand in actual numbers, it is only by 30%, and not 900%. [16]

The largest number exist in the gut flora, and a large number on the skin. [17] The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial, particularly in the gut flora. However, several species of bacteria are pathogenic and 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 per year, mostly in sub-Saharan Africa. [18] In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector, [19] as well as in biotechnology, and the manufacture of antibiotics and other chemicals. [20]

Skin soft outer covering organ of vertebrates

Skin is the soft outer tissue covering of vertebrates with three main functions: protection, regulation, and sensation.

Immune system A biological system that protects an organism against disease

The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue. In many species, there are two major subsystems of the immune system: the innate immune system and the adaptive immune system. Both subsystems use humoral immunity and cell-mediated immunity to perform their functions. In humans, the blood–brain barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system, which protects the brain.

Probiotic microorganisms said to provide health benefits when consumed

Probiotics are live microorganisms intended to provide health benefits when consumed, generally by improving or restoring the gut flora. Probiotics are considered generally safe to consume, but may cause bacteria-host interactions and unwanted side effects in rare cases.

Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as 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 prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea . [1]

Plant multicellular eukaryote of the kingdom Plantae

Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, plants were treated as one of two kingdoms including all living things that were not animals, and all algae and fungi were treated as plants. However, all current definitions of Plantae exclude the fungi and some algae, as well as the prokaryotes. By one definition, plants form the clade Viridiplantae, a group that includes the flowering plants, conifers and other gymnosperms, ferns and their allies, hornworts, liverworts, mosses and the green algae, but excludes the red and brown algae.

Eukaryote Taxonomic group whose members have complex structures enclosed within membranes

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes, which have no membrane-bound organelles. Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes.

Cell nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.

In cell biology, the nucleus is a membrane-bound organelle found in eukaryotic cells. Eukaryotes usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others including osteoclasts have many.

Etymology

The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (bakterion), [21] the diminutive of βακτηρία (bakteria), meaning "staff, cane", [22] because the first ones to be discovered were rod-shaped. [23] [24]

Origin and early evolution

The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. [25] [26] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the 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. [27] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. [28] [29]

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. [30] [31] This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. [32] [33] This is known as primary endosymbiosis.

In July 2018, scientists reported that the earliest life on land may have been bacteria living on land 3.22 billion years ago. [34]

Morphology

Bacteria display many cell morphologies and arrangements Bacterial morphology diagram.svg
Bacteria display many cell morphologies and arrangements

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0  micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long [35] and Epulopiscium fishelsoni reaches 0.7 mm. [36] Among the smallest bacteria are members of the genus Mycoplasma , which measure only 0.3 micrometres, as small as the largest viruses. [37] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied. [38]

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). [39] Some bacteria, called vibrio , are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla , or tightly coiled, called spirochaetes . A small number of other unusual shapes have been described, such as star-shaped bacteria. [40] 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. [41] [42]

The range of sizes shown by prokaryotes, relative to those of other organisms and biomolecules. Relative scale.svg
The range of sizes shown by prokaryotes, relative to those of other organisms and biomolecules.

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 group to form larger multicellular structures, such as the elongated filaments of Actinobacteria , the aggregates of Myxobacteria , and the complex hyphae of Streptomyces . [43] These multicellular structures are often only seen in certain conditions. 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. [44] In these fruiting bodies, the bacteria perform separate tasks; for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions. [45]

Bacteria often attach to surfaces and form dense aggregations called biofilms, and larger formations known as microbial mats. These biofilms and mats can range from a few micrometres in thickness to up to half a metre 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. [46] [47] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. [48] Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria. [49]

Cellular structure

Structure and contents of a typical gram-positive bacterial cell (seen by the fact that only one cell membrane is present). Prokaryote cell.svg
Structure and contents of a typical gram-positive bacterial cell (seen by the fact that only one cell membrane is present).

Intracellular structures

The bacterial cell is surrounded by a cell membrane which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. [50] Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells. [51] However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism, [52] [53] such as the carboxysome. [54] Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division. [55] [56] [57]

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm. [58] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. [59] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria. [60]

An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm. Carboxysomes EM ptA.jpg
An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid. [61] The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and Archaea. [62]

Some bacteria produce intracellular nutrient storage granules, such as glycogen, [63] polyphosphate, [64] sulfur [65] or polyhydroxyalkanoates. [66] Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vacuoles which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels. [67]

Extracellular structures

Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids. [68] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively. [69] 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 ( produced by fungal species penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan. [69]

There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into gram-positive bacteria and gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species. [70]

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. [71] 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 . [72] Some bacteria have cell wall structures that are neither classically gram-positive or gram-negative. This includes clinically important bacteria such as Mycobacteria which have a thick peptidoglycan cell wall like a gram-positive bacterium, but also a second outer layer of lipids. [73]

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell. [74] 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 . [75]

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface EMpylori.jpg
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

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. [76]

Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres 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. [77] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below). [78] They can also generate movement where they are called type IV pili. [79]

Glycocalyx is produced by many bacteria to surround their cells, and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system). [80] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms. [81]

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. [82]

Endospores

Bacillus anthracis (stained purple) growing in cerebrospinal fluid Gram Stain Anthrax.jpg
Bacillus anthracis (stained purple) growing in cerebrospinal fluid

Certain genera of gram-positive bacteria, such as Bacillus , Clostridium , Sporohalobacter , Anaerobacter , and Heliobacterium , can form highly resistant, dormant structures called endospores . [83] Endospores develop within the cytoplasm of the cell; generally a single endospore develops in each cell. [84] Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins. [84]

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, freezing, pressure, and desiccation. [85] In this dormant state, these organisms may remain viable for millions of years, [86] [87] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space. [88] 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. [89]

Metabolism

Bacteria exhibit an extremely wide variety of metabolic types. [90] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications. [91] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth. [92]

Bacteria either derive energy from light using photosynthesis (called phototrophy), or by breaking down chemical compounds using oxidation (called chemotrophy). [93] Chemotrophs use chemical compounds as a source of energy by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to drive metabolism. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that use inorganic compounds such as hydrogren, carbon monoxide, or ammonia as sources of electrons are called lithotrophs, while those that use organic compounds are called organotrophs. [93] The compounds used to receive electrons are also used to classify bacteria: aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide. [93]

Many bacteria get their carbon from other organic carbon, called heterotrophy. Others such as cyanobacteria and some purple bacteria are autotrophic, meaning that they obtain cellular carbon by fixing carbon dioxide. [94] In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. [95]

Nutritional types in bacterial metabolism
Nutritional typeSource of energySource of carbonExamples
  Phototrophs  Sunlight Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)  Cyanobacteria, Green sulfur bacteria, Chloroflexi, or Purple bacteria  
  Lithotrophs Inorganic compounds Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)  Thermodesulfobacteria, Hydrogenophilaceae , or Nitrospirae  
  Organotrophs Organic compounds Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)    Bacillus , Clostridium or Enterobacteriaceae  

In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. One example is that some bacteria have the ability to fix nitrogen gas using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of most metabolic types listed above. [96] This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively. [97] [98] Bacterial metabolic processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. [99] Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.

Growth and reproduction

Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image. Three cell growth types.svg
Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.

Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. [100] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. [101] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces , or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

A colony of Escherichia coli E.-coli-growth.gif
A colony of Escherichia coli

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms. [103]

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. [104] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. [105] In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. [48] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy). [106]

Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. [107] [108] The second phase of growth is the logarithmic phase, also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. [109] The final phase is the death phase where the bacteria run out of nutrients and die. [110]

Genetics

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii , [111] to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum . [112] There are many exceptions to this, for example some Streptomyces and Borrelia species contain a single linear chromosome, [113] [114] while some Vibrio species contain more than one chromosome. [115] Bacteria can also contain plasmids, small extra-chromosomal DNAs that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors. [116]

Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes. [117]

Bacteria, as asexual organisms, inherit an identical copy of the parent's genomes and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. [118] Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate. [119]

Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation. [120] Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA. [121] The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells. [122] The second way bacteria transfer genetic material is by transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. [123] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA, [124] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference. [125] [126] The third method of gene transfer is conjugation, whereby DNA is transferred through direct cell contact. In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance. [127] [128] In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions. [129]

Behaviour

Movement

Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long. Dvulgaris micrograph.JPG
Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.

Many bacteria are motile and can move using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement. [130] The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. [130] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power. [131]

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous Flagella.png
The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous

Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli ) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk. [132] Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum ( monotrichous ), a flagellum at each end ( amphitrichous ), clusters of flagella at the poles of the cell ( lophotrichous ), while others have flagella distributed over the entire surface of the cell ( peritrichous ). The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves. [130]

Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus, [133] and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward. [134]

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes : these include chemotaxis, phototaxis, energy taxis, and magnetotaxis. [135] [136] [137] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. [45] The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.

Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm. [138]

Communication

A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals. [139]

Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behaviour. [140] [141]

The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. [140] For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species. [141]

One type of inter-cellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light.

Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population. [142]

Classification and identification

Streptococcus mutans visualised with a Gram stain Streptococcus mutans Gram.jpg
Streptococcus mutans visualised with a Gram stain
EuryarchaeotaNanoarchaeotaCrenarchaeotaProtozoaAlgaePlantaeSlime moldsAnimalFungusGram-positive bacteriaChlamydiaeChloroflexiActinobacteriaPlanctomycetesSpirochaetesFusobacteriaCyanobacteriaThermophilesAcidobacteriaProteobacteriaBacteria
Phylogenetic tree showing the diversity of bacteria, compared to other organisms. [1] Eukaryotes are coloured red, archaea green and bacteria blue.
  1. ^ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (March 2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–87. Bibcode:2006Sci...311.1283C. CiteSeerX  10.1.1.381.9514 . doi:10.1126/science.1123061. PMID 16513982.

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. [103] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. [143] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. [144] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, [145] and Bergey's Manual of Systematic Bacteriology. [146] The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria.

The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. [1] The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology. [147] However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. [148] [149] For example, a few biologists argue that the Archaea and Eukaryotes evolved from gram-positive bacteria. [150]

The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria.

The Gram stain , developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. [70] The thick layers of peptidoglycan in the "gram-positive" cell wall stain purple, while the thin "gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (gram-positive cocci, gram-positive bacilli, gram-negative cocci and gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. [151] Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.

Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms. [103] [152] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining.

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. [153] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. [154] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea; [155] but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species—and even these diverse estimates may be off by many orders of magnitude. [156] [157]

Interactions with other organisms

Overview of bacterial infections and main species involved. Bacterial infections and involved species.png
Overview of bacterial infections and main species involved.

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odour.

Predators

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria. [160] These include organisms such as Myxococcus xanthus , which forms swarms of cells that kill and digest any bacteria they encounter. [161] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus , [162] or invade another cell and multiply inside the cytosol, such as Daptobacter. [163] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms. [164]

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen. [165] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.

In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds. [166] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus ), as well as fermenting complex undigestible carbohydrates. [167] [168] [169] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements. [170]

Pathogens

Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells SalmonellaNIAID.jpg
Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus (Caused by Clostridium tetani), typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy (caused by Micobacterium leprae) and tuberculosis (Caused by Mycobacterium tubeculosis). A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.

Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus , can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. [171] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia , another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease. [172] Finally, some species, such as Pseudomonas aeruginosa , Burkholderia cenocepacia , and Mycobacterium avium , are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis. [173] [174]

Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome. [175] Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations. [176] Infections can be prevented by antiseptic measures such as sterilising the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

Significance in technology and industry

Bacteria, often lactic acid bacteria, such as Lactobacillus and Lactococcus , in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yogurt. [177] [178]

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. [179] Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes. [180] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals. [181]

Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide. [182] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects. [183] [184]

Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms. [185] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. [186] [187] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies. [188] [189]

Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centers. This ensures the availability of the strain to scientists worldwide.

History of bacteriology

Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope. Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. [190] He then published his observations in a series of letters to the Royal Society of London. [191] [192] [193] Bacteria were Leeuwenhoek's most remarkable microscopic discovery. They were just at the limit of what his simple lenses could make out and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. [194] His observations had also included protozoans which he called animalcules, and his findings were looked at again in the light of the more recent findings of cell theory.

Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828. [195] In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria, [196] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835. [197]

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 moulds, 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. [198]

Robert Koch, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis Koch finally proved the germ theory, for which he received a Nobel Prize in 1905. [199] In Koch's postulates , he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today. [200]

Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology. [201] [202]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. [203] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum —the spirochaete that causes syphilis—into compounds that selectively killed the pathogen. [204] 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. [205]

A major step forward in the study of bacteria came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria. [3] This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system. [1]

Computer-made form

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0 , made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist. [206] [207]

See also

Related Research Articles

Gram-positive bacteria Bacteria that give a positive result in the Gram stain test

Gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall.

Biofilm any group of microorganisms in which cells stick to each other and often also to a surface (adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances)

A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPS). The cells within the biofilm produce the EPS components, which are typically a polymeric conglomeration of extracellular polysaccharides, proteins, lipids and DNA. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes".

Human microbiome Microorganisms in or on human tissues and biofluids

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Types of human microbiota include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.

Unicellular organism Organism that consists of only one cell

A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Unicellular organisms fall into two general categories: prokaryotic organisms and eukaryotic organisms. Prokaryotes include bacteria and archaea. Many eukaryotes are multicellular, but the group includes the protozoa, unicellular algae, and unicellular fungi. Unicellular organisms are thought to be the oldest form of life, with early protocells possibly emerging 3.8–4 billion years ago.

<i>Bacillus subtilis</i> species of bacterium

Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans. A member of the genus Bacillus, B. subtilis is rod-shaped, and can form a tough, protective endospore, allowing it to tolerate extreme environmental conditions. B. subtilis has historically been classified as an obligate aerobe, though evidence exists that it is a facultative anaerobe. B. subtilis is considered the best studied Gram-positive bacterium and a model organism to study bacterial chromosome replication and cell differentiation. It is one of the bacterial champions in secreted enzyme production and used on an industrial scale by biotechnology companies.

<i>Staphylococcus epidermidis</i> species of bacterium

Staphylococcus epidermidis is a Gram-positive bacterium, and one of over 40 species belonging to the genus Staphylococcus. It is part of the normal human flora, typically the skin flora, and less commonly the mucosal flora. It is a facultative anaerobic bacteria. Although S. epidermidis is not usually pathogenic, patients with compromised immune systems are at risk of developing infection. These infections are generally hospital-acquired. S. epidermidis is a particular concern for people with catheters or other surgical implants because it is known to form biofilms that grow on these devices. Being part of the normal skin flora, S. epidermidis is a frequent contaminant of specimens sent to the diagnostic laboratory.

Microbial intelligence is the intelligence shown by microorganisms. The concept encompasses complex adaptive behavior shown by single cells, and altruistic or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.

The bacterium, despite its simplicity, contains a well-developed cell structure which is responsible for some of its unique biological structures and pathogenicity. Many structural features are unique to bacteria and are not found among archaea or eukaryotes. Because of the simplarger organisms and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.

Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria, and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.

Medical microbiology medical specialty

Medical microbiology, the large subset of microbiology that is applied to medicine, is a branch of medical science concerned with the prevention, diagnosis and treatment of infectious diseases. In addition, this field of science studies various clinical applications of microbes for the improvement of health. There are four kinds of microorganisms that cause infectious disease: bacteria, fungi, parasites and viruses, and one type of infectious protein called prion.

Extracellular polymeric substance natural polymers secreted by microorganisms

Extracellular polymeric substances (EPSs) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPSs establish the functional and structural integrity of biofilms, and are considered the fundamental component that determines the physiochemical properties of a biofilm.

Ultramicrobacteria are bacteria that are smaller than 0.1 μm3 under all growth conditions. This term was coined in 1981, describing cocci in seawater that were less than 0.3 μm in diameter. Ultramicrobacteria have also been recovered from soil and appear to be a mixture of Gram-positive, Gram-negative and cell-wall-lacking species. Ultramicrobacteria possess a relatively high surface-area-to-volume ratio due to their small size, which aids in growth under oligotrophic conditions. The relatively small size of ultramicrobacteria also enables parasitism of larger organisms; some ultramicrobacteria have been observed to be obligate or facultative parasites of various eukaryotes and prokaryotes. One factor allowing ultramicrobacteria to achieve their small size seems to be genome minimization such as in the case of the ultramicrobacterium P. ubique whose small 1.3 Mb genome is seemingly devoid of extraneous genetic elements like nonworking genes, transposons, extrachromosomal elements etc. However, genomic data from ultramicrobacteria is lacking since the study of ultramicrobacteria, like many other prokaryotes, is hindered by difficulties in cultivating them.

Prokaryote Group of organisms whose cells lack a cell nucleus

A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό (pro) "before" and κάρυον (karyon) "nut" or "kernel". Prokaryotes are divided into two domains, Archaea and Bacteria. Species with nuclei and organelles are placed in the third domain, Eukaryota. Prokaryotes reproduce without fusion of gametes. The first living organisms are thought to have been prokaryotes.

Archaea A domain of single-celled prokaryotic microorganisms

Archaea constitute a domain of single-celled organisms. These microorganisms are prokaryotes, and have no cell nucleus. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outmoded.

Microbiology Study of microscopic organisms

Microbiology is the study of microorganisms, those being unicellular, multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, parasitology, mycology and bacteriology.

Vampirococcus is an informally described genus of ovoid Gram-negative bacteria, but the exact phylogeny remains to be determined. This predatory prokaryote was first described in 1983 by Esteve et al. as small, anaerobic microbe about 0.6 μm wide before being given the name of Vampirococcus in 1986 by Guerrero et al. This prokaryote is a freshwater obligate predator that preys specifically on various species of the photosynthetic purple sulfur bacterium, Chromatium. As an epibiont, Vampirococcus attaches to the cell surface of their prey and "sucks" out the cytoplasm using a specialized cytoplasmic bridge. They are commonly mentioned as an example of epibionts when discussing strategies employed by bacterial predators. This microbe still has yet to be classified based on genomic sequencing or 16S rRNA because it cannot be sustained long enough outside its natural environment to isolate a pure culture.

Roberto Kolter is Professor of Microbiology, Emeritus at Harvard Medical School, an author, and past president of the American Society for Microbiology. Kolter has been a professor at Harvard Medical School since 1983 and was Co-director of Harvard's Microbial Sciences Initiative from 2003-2018. During the 35-year term of the Kolter laboratory from 1983 to 2018, more than 130 graduate student and postdoctoral trainees explored an eclectic mix of topics gravitating around the study of microbes. Kolter is a fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology.

Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.

An archaellum is a unique whip-like structure on the cell surface of many archaea. The name was proposed in 2012 following studies that showed it to be evolutionarily and structurally different from the bacterial and eukaryotic flagella. The archaellum is functionally the same – it can be rotated and is used to swim in liquid environments. The archaellum was found to be structurally similar to the type IV pilus.

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