Bacteria

Bacteria (/bækˈtɪəriə/ (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 portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory.[5] The study of bacteria is known as bacteriology, a branch of microbiology.

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,[6] forming a biomass which exceeds that of all plants and animals.[7] 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.[8] 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.[9][10] 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.[9][11] According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are."[9]

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%.[12]

The largest number exist in the gut flora, and a large number on the skin.[13] 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.[14] 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,[15] as well as in biotechnology, and the manufacture of antibiotics and other chemicals.[16]

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]

Bacteria
Temporal range: Archean or earlier – present
EscherichiaColi NIAID
Scanning electron micrograph of Escherichia coli rods
Scientific classification
Domain: Bacteria
Woese, Kandler & Wheelis, 1990[1]
Phyla

Acidobacteria
Actinobacteria
Aquificae
Armatimonadetes
Bacteroidetes
Caldiserica
Chlamydiae
Chlorobi
Chloroflexi
Chrysiogenetes
Coprothermobacterota[2]
Cyanobacteria
Deferribacteres
Deinococcus-Thermus
Dictyoglomi
Elusimicrobia
Fibrobacteres
Firmicutes
Fusobacteria
Gemmatimonadetes
Lentisphaerae
Nitrospirae
Planctomycetes
Proteobacteria
Spirochaetes
Synergistetes
Tenericutes
Thermodesulfobacteria
Thermotogae
Verrucomicrobia

Synonyms

Eubacteria Woese & Fox, 1977[3]

Etymology

The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (bakterion),[17] the diminutive of βακτηρία (bakteria), meaning "staff, cane",[18] because the first ones to be discovered were rod-shaped.[19][20]

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.[21][22] 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.[23] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.[24][25]

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.[26][27] 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.[28][29] This is known as primary endosymbiosis.

Morphology

Bacterial morphology diagram
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[30] and Epulopiscium fishelsoni reaches 0.7 mm.[31] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.[32] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.[33]

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).[34] 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.[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]

Relative scale
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.[38] 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.[39] 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.[40]

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.[41][42] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[43] 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.[44]

Cellular structure

Prokaryote cell
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.[45] 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.[46] However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism,[47][48] such as the carboxysome.[49] 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.[50][51][52]

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.[53] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.[54] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.[55]

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

Most 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.[56] The nucleoid contains the chromosome with its 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 that of eukaryotes and Archaea.[57]

Some bacteria produce intracellular nutrient storage granules, such as glycogen,[58] polyphosphate,[59] sulfur[60] or polyhydroxyalkanoates.[61] 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.[62]

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.[63] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.[64] 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.[64]

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.[65]

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.[66] 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.[67] 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.[68]

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell.[69] 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.[70]

EMpylori
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.[71]

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.[72] 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).[73] They can also generate movement where they are called type IV pili.[74]

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).[75] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[76]

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.[77]

Endospores

Gram Stain Anthrax
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.[78] Endospores develop within the cytoplasm of the cell; generally a single endospore develops in each cell.[79] 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.[79]

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.[80] In this dormant state, these organisms may remain viable for millions of years,[81][82] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.[83] 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.[84]

Metabolism

Bacteria exhibit an extremely wide variety of metabolic types.[85] 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.[86] 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.[87]

Bacteria either derive energy from light using photosynthesis (called phototrophy), or by breaking down chemical compounds using oxidation (called chemotrophy).[88] 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.[88] 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.[88]

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.[89] In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.[90]

Nutritional types in bacterial metabolism
Nutritional type Source of energy Source of carbon Examples
 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.[91] This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.[92][93] 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.[94] 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

Three cell growth types
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.[95] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.[96] 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.

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.[98]

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.[99] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.[100] In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses.[43] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).[101]

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.[102] 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.[103] The final phase is the death phase where the bacteria run out of nutrients and die.[104]

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,[105] to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum.[106] There are many exceptions to this, for example some Streptomyces and Borrelia species contain a single linear chromosome,[107][108] while some Vibrio species contain more than one chromosome.[109] 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.[110]

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.[111]

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.[112] 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.[113]

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.[114] 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.[115] 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.[116] 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.[117] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,[118] 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.[119][120] 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.[121][122] In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.[123]

Behaviour

Movement

Dvulgaris micrograph
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.[124] The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.[124] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.[125]

Flagella
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.[126] 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.[124]

Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus,[127] 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.[128]

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.[129][130][131] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[40] 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.[132]

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.[133]

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.[134][135]

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.[134] For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.[135]

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.[136]

Classification and identification

Streptococcus mutans Gram
Streptococcus mutans visualised with a Gram stain
EuryarchaeotaNanoarchaeotaCrenarchaeotaProtozoaAlgaePlantaeSlime moldsAnimalFungusGram-positive bacteriaChlamydiaeChloroflexiActinobacteriaPlanctomycetesSpirochaetesFusobacteriaCyanobacteriaThermophilesAcidobacteriaProteobacteria
Phylogenetic tree showing the diversity of bacteria, compared to other organisms.[137] Eukaryotes are coloured red, archaea green and bacteria blue.


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.[98] 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.[138] 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.[139] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[140] and Bergey's Manual of Systematic Bacteriology.[141] 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.[142] 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.[5][143] For example, a few biologists argue that the Archaea and Eukaryotes evolved from gram-positive bacteria.[144]

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.[65] 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.[145] 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.[98][146] 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.[147] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[148] 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;[149] 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.[150][151]

Interactions with other organisms

Bacterial infections and involved species
Overview of bacterial infections and main species involved.[152][153]

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.[154] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.[155] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus,[156] or invade another cell and multiply inside the cytosol, such as Daptobacter.[157] 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.[158]

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.[159] 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.[160] 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.[161][162][163] 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.[164]

Pathogens

SalmonellaNIAID
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, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. 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.[165] 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.[166] 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.[167][168]

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.[169] 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.[170] 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.[171][172]

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.[173] 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.[174] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.[175]

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.[176] 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.[177][178]

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.[179] 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.[180][181] 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.[182][183]

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

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.[184] He then published his observations in a series of letters to the Royal Society of London.[185][186][187] 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.[188] 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.[189] In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,[190] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.[191]

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.[192]

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.[193] 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.[194]

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.[195][196]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[197] 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.[198] 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.[199]

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]

See also

References

  1. ^ a b c d Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–79. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
  2. ^ Pavan ME, et al. (May 2018). "Proposal for a new classification of a deep branching bacterial phylogenetic lineage: transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. nov., within Coprothermobacterales ord. nov., Coprothermobacteria classis nov. and Coprothermobacterota phyl. nov. and emended description of the family Thermodesulfobiaceae". Int. J. Syst. Evol. Microbiol. 68 (5): 1627–32. doi:10.1099/ijsem.0.002720. PMID 29595416.
  3. ^ a b Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
  4. ^ Fredrickson JK, Zachara JM, Balkwill DL, Kennedy D, Li SM, Kostandarithes HM, Daly MJ, Romine MF, Brockman FJ (July 2004). "Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state". Applied and Environmental Microbiology. 70 (7): 4230–41. doi:10.1128/AEM.70.7.4230-4241.2004. PMC 444790. PMID 15240306.
  5. ^ a b Rappé MS, Giovannoni SJ (2003). "The uncultured microbial majority". Annual Review of Microbiology. 57: 369–94. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284.
  6. ^ Whitman WB, Coleman DC, Wiebe WJ (June 1998). "Prokaryotes: the unseen majority". Proceedings of the National Academy of Sciences of the United States of America. 95 (12): 6578–83. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454.
  7. ^ C.Michael Hogan. 2010. Bacteria. Encyclopedia of Earth. eds. Sidney Draggan and C.J.Cleveland, National Council for Science and the Environment, Washington, DC Archived 11 May 2011 at the Wayback Machine
  8. ^ Forbes SL (2008). "Decomposition Chemistry in a Burial Environment". In Tibbett M, Carter DO. Soil Analysis in Forensic Taphonomy. CRC Press. pp. 203–223. ISBN 978-1-4200-6991-4.
  9. ^ a b c Choi CQ (17 March 2013). "Microbes Thrive in Deepest Spot on Earth". LiveScience. Archived from the original on 2 April 2013. Retrieved 17 March 2013.
  10. ^ Glud R, Wenzhöfer F, Middelboe M, Oguri K, Turnewitsch R, Canfield DE, Kitazato H (2013). "High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth". Nature Geoscience. 6 (4): 284–88. Bibcode:2013NatGe...6..284G. doi:10.1038/ngeo1773.
  11. ^ Oskin B (14 March 2013). "Intraterrestrials: Life Thrives in Ocean Floor". LiveScience. Archived from the original on 2 April 2013. Retrieved 17 March 2013.
  12. ^ Sender R, Fuchs S, Milo R (2016). "Revised estimates for the number of human and bacteria cells in the body". bioRxiv 036103.
  13. ^ Sears CL (October 2005). "A dynamic partnership: celebrating our gut flora". Anaerobe. 11 (5): 247–51. doi:10.1016/j.anaerobe.2005.05.001. PMID 16701579.
  14. ^ "2002 WHO mortality data". Archived from the original on 23 October 2013. Retrieved 20 January 2007.
  15. ^ "Metal-Mining Bacteria Are Green Chemists". Science Daily. 2 September 2010. Archived from the original on 31 August 2017.
  16. ^ Ishige T, Honda K, Shimizu S (April 2005). "Whole organism biocatalysis". Current Opinion in Chemical Biology. 9 (2): 174–80. doi:10.1016/j.cbpa.2005.02.001. PMID 15811802.
  17. ^ βακτήριον. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project.
  18. ^ βακτηρία in Liddell and Scott.
  19. ^ bacterium Archived 27 January 2011 at the Wayback Machine, on Oxford Dictionaries.
  20. ^ Harper, Douglas. "bacteria". Online Etymology Dictionary.
  21. ^ Schopf JW (July 1994). "Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic". Proceedings of the National Academy of Sciences of the United States of America. 91 (15): 6735–42. Bibcode:1994PNAS...91.6735S. doi:10.1073/pnas.91.15.6735. PMC 44277. PMID 8041691.
  22. ^ DeLong EF, Pace NR (August 2001). "Environmental diversity of bacteria and archaea". Systematic Biology. 50 (4): 470–78. CiteSeerX 10.1.1.321.8828. doi:10.1080/106351501750435040. PMID 12116647.
  23. ^ Brown JR, Doolittle WF (December 1997). "Archaea and the prokaryote-to-eukaryote transition". Microbiology and Molecular Biology Reviews. 61 (4): 456–502. PMC 232621. PMID 9409149.
  24. ^ Di Giulio M (December 2003). "The universal ancestor and the ancestor of bacteria were hyperthermophiles". Journal of Molecular Evolution. 57 (6): 721–30. Bibcode:2003JMolE..57..721D. doi:10.1007/s00239-003-2522-6. PMID 14745541.
  25. ^ Battistuzzi FU, Feijao A, Hedges SB (November 2004). "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology. 4: 44. doi:10.1186/1471-2148-4-44. PMC 533871. PMID 15535883.
  26. ^ Poole AM, Penny D (January 2007). "Evaluating hypotheses for the origin of eukaryotes". BioEssays. 29 (1): 74–84. doi:10.1002/bies.20516. PMID 17187354.
  27. ^ Dyall SD, Brown MT, Johnson PJ (April 2004). "Ancient invasions: from endosymbionts to organelles". Science. 304 (5668): 253–7. Bibcode:2004Sci...304..253D. doi:10.1126/science.1094884. PMID 15073369.
  28. ^ Lang BF, Gray MW, Burger G (1999). "Mitochondrial genome evolution and the origin of eukaryotes". Annual Review of Genetics. 33: 351–97. doi:10.1146/annurev.genet.33.1.351. PMID 10690412.
  29. ^ McFadden GI (December 1999). "Endosymbiosis and evolution of the plant cell". Current Opinion in Plant Biology. 2 (6): 513–19. doi:10.1016/S1369-5266(99)00025-4. PMID 10607659.
  30. ^ Schulz HN, Jorgensen BB (2001). "Big bacteria". Annual Review of Microbiology. 55: 105–37. doi:10.1146/annurev.micro.55.1.105. PMID 11544351.
  31. ^ Williams C (2011). "Who are you calling simple?". New Scientist. 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0.
  32. ^ Robertson J, Gomersall M, Gill P (November 1975). "Mycoplasma hominis: growth, reproduction, and isolation of small viable cells". Journal of Bacteriology. 124 (2): 1007–18. PMC 235991. PMID 1102522.
  33. ^ Velimirov B (2001). "Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium". Microbes and Environments. 16 (2): 67–77. doi:10.1264/jsme2.2001.67.
  34. ^ Dusenbery, David B (2009). Living at Micro Scale, pp. 20–25. Harvard University Press, Cambridge, Massachusetts ISBN 978-0-674-03116-6.
  35. ^ Yang DC, Blair KM, Salama NR (March 2016). "Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments". Microbiology and Molecular Biology Reviews. 80 (1): 187–203. doi:10.1128/MMBR.00031-15. PMC 4771367. PMID 26864431.
  36. ^ Cabeen MT, Jacobs-Wagner C (August 2005). "Bacterial cell shape". Nature Reviews. Microbiology. 3 (8): 601–10. doi:10.1038/nrmicro1205. PMID 16012516.
  37. ^ Young KD (September 2006). "The selective value of bacterial shape". Microbiology and Molecular Biology Reviews. 70 (3): 660–703. doi:10.1128/MMBR.00001-06. PMC 1594593. PMID 16959965.
  38. ^ Claessen D, Rozen DE, Kuipers OP, Søgaard-Andersen L, van Wezel GP (February 2014). "Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies". Nature Reviews. Microbiology. 12 (2): 115–24. doi:10.1038/nrmicro3178. PMID 24384602.
  39. ^ Shimkets LJ (1999). "Intercellular signaling during fruiting-body development of Myxococcus xanthus". Annual Review of Microbiology. 53: 525–49. doi:10.1146/annurev.micro.53.1.525. PMID 10547700.
  40. ^ a b Kaiser D (2004). "Signaling in myxobacteria". Annual Review of Microbiology. 58: 75–98. doi:10.1146/annurev.micro.58.030603.123620. PMID 15487930.
  41. ^ Donlan RM (September 2002). "Biofilms: microbial life on surfaces". Emerging Infectious Diseases. 8 (9): 881–90. doi:10.3201/eid0809.020063. PMC 2732559. PMID 12194761.
  42. ^ Branda SS, Vik S, Friedman L, Kolter R (January 2005). "Biofilms: the matrix revisited". Trends in Microbiology. 13 (1): 20–26. doi:10.1016/j.tim.2004.11.006. PMID 15639628.
  43. ^ a b Davey ME, O'toole GA (December 2000). "Microbial biofilms: from ecology to molecular genetics". Microbiology and Molecular Biology Reviews. 64 (4): 847–67. doi:10.1128/MMBR.64.4.847-867.2000. PMC 99016. PMID 11104821.
  44. ^ Donlan RM, Costerton JW (April 2002). "Biofilms: survival mechanisms of clinically relevant microorganisms". Clinical Microbiology Reviews. 15 (2): 167–93. doi:10.1128/CMR.15.2.167-193.2002. PMC 118068. PMID 11932229.
  45. ^ Slonczewski JL, Foster JW (2013). Microbiology : an Evolving Science (Third ed.). New York: W W Norton. p. 82. ISBN 9780393123678.
  46. ^ Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Scott MP (2013). Molecular Cell Biology (7th ed.). WH Freeman. p. 13. ISBN 9781429234139.
  47. ^ Bobik TA (May 2006). "Polyhedral organelles compartmenting bacterial metabolic processes". Applied Microbiology and Biotechnology. 70 (5): 517–25. doi:10.1007/s00253-005-0295-0. PMID 16525780.
  48. ^ Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (September 2008). "Protein-based organelles in bacteria: carboxysomes and related microcompartments". Nature Reviews. Microbiology. 6 (9): 681–91. doi:10.1038/nrmicro1913. PMID 18679172.
  49. ^ Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO (August 2005). "Protein structures forming the shell of primitive bacterial organelles". Science. 309 (5736): 936–8. Bibcode:2005Sci...309..936K. CiteSeerX 10.1.1.1026.896. doi:10.1126/science.1113397. PMID 16081736.
  50. ^ Gitai Z (March 2005). "The new bacterial cell biology: moving parts and subcellular architecture". Cell. 120 (5): 577–86. doi:10.1016/j.cell.2005.02.026. PMID 15766522.
  51. ^ Shih YL, Rothfield L (September 2006). "The bacterial cytoskeleton". Microbiology and Molecular Biology Reviews. 70 (3): 729–54. doi:10.1128/MMBR.00017-06. PMC 1594594. PMID 16959967.
  52. ^ Norris V, den Blaauwen T, Cabin-Flaman A, Doi RH, Harshey R, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Saier M, Skarstad K (March 2007). "Functional taxonomy of bacterial hyperstructures". Microbiology and Molecular Biology Reviews. 71 (1): 230–53. doi:10.1128/MMBR.00035-06. PMC 1847379. PMID 17347523.
  53. ^ Harold FM (June 1972). "Conservation and transformation of energy by bacterial membranes". Bacteriological Reviews. 36 (2): 172–230. PMC 408323. PMID 4261111.
  54. ^ Bryant DA, Frigaard NU (November 2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends in Microbiology. 14 (11): 488–96. doi:10.1016/j.tim.2006.09.001. PMID 16997562.
  55. ^ Psencík J, Ikonen TP, Laurinmäki P, Merckel MC, Butcher SJ, Serimaa RE, Tuma R (August 2004). "Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria". Biophysical Journal. 87 (2): 1165–72. Bibcode:2004BpJ....87.1165P. doi:10.1529/biophysj.104.040956. PMC 1304455. PMID 15298919.
  56. ^ Thanbichler M, Wang SC, Shapiro L (October 2005). "The bacterial nucleoid: a highly organized and dynamic structure". Journal of Cellular Biochemistry. 96 (3): 506–21. doi:10.1002/jcb.20519. PMID 15988757.
  57. ^ Poehlsgaard J, Douthwaite S (November 2005). "The bacterial ribosome as a target for antibiotics". Nature Reviews. Microbiology. 3 (11): 870–81. doi:10.1038/nrmicro1265. PMID 16261170.
  58. ^ Yeo M, Chater K (March 2005). "The interplay of glycogen metabolism and differentiation provides an insight into the developmental biology of Streptomyces coelicolor". Microbiology. 151 (Pt 3): 855–61. doi:10.1099/mic.0.27428-0. PMID 15758231. Archived from the original on 29 September 2007.
  59. ^ Shiba T, Tsutsumi K, Ishige K, Noguchi T (March 2000). "Inorganic polyphosphate and polyphosphate kinase: their novel biological functions and applications". Biochemistry. Biokhimiia. 65 (3): 315–23. PMID 10739474. Archived from the original on 25 September 2006.
  60. ^ Brune DC (June 1995). "Isolation and characterization of sulfur globule proteins from Chromatium vinosum and Thiocapsa roseopersicina". Archives of Microbiology. 163 (6): 391–99. doi:10.1007/BF00272127. PMID 7575095.
  61. ^ Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S (2005). "Ecological and agricultural significance of bacterial polyhydroxyalkanoates". Critical Reviews in Microbiology. 31 (2): 55–67. doi:10.1080/10408410590899228. PMID 15986831.
  62. ^ Walsby AE (March 1994). "Gas vesicles". Microbiological Reviews. 58 (1): 94–144. PMC 372955. PMID 8177173.
  63. ^ van Heijenoort J (March 2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan". Glycobiology. 11 (3): 25R–36R. doi:10.1093/glycob/11.3.25R. PMID 11320055.
  64. ^ a b Koch AL (October 2003). "Bacterial wall as target for attack: past, present, and future research". Clinical Microbiology Reviews. 16 (4): 673–87. doi:10.1128/CMR.16.4.673-687.2003. PMC 207114. PMID 14557293.
  65. ^ a b Gram, HC (1884). "Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten". Fortschr. Med. 2: 185–189.
  66. ^ Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.
  67. ^ Walsh FM, Amyes SG (October 2004). "Microbiology and drug resistance mechanisms of fully resistant pathogens". Current Opinion in Microbiology. 7 (5): 439–44. doi:10.1016/j.mib.2004.08.007. PMID 15451497.
  68. ^ Alderwick LJ, Harrison J, Lloyd GS, Birch HL (March 2015). "The Mycobacterial Cell Wall—Peptidoglycan and Arabinogalactan". Cold Spring Harbor Perspectives in Medicine. 5 (8): a021113. doi:10.1101/cshperspect.a021113. PMC 4526729. PMID 25818664.
  69. ^ Engelhardt H, Peters J (December 1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions". Journal of Structural Biology. 124 (2–3): 276–302. doi:10.1006/jsbi.1998.4070. PMID 10049812.
  70. ^ Beveridge TJ, Pouwels PH, Sára M, Kotiranta A, Lounatmaa K, Kari K, Kerosuo E, Haapasalo M, Egelseer EM, Schocher I, Sleytr UB, Morelli L, Callegari ML, Nomellini JF, Bingle WH, Smit J, Leibovitz E, Lemaire M, Miras I, Salamitou S, Béguin P, Ohayon H, Gounon P, Matuschek M, Koval SF (June 1997). "Functions of S-layers". FEMS Microbiology Reviews. 20 (1–2): 99–149. doi:10.1016/S0168-6445(97)00043-0. PMID 9276929.
  71. ^ Kojima S, Blair DF (2004). The bacterial flagellar motor: structure and function of a complex molecular machine. International Review of Cytology. 233. pp. 93–134. doi:10.1016/S0074-7696(04)33003-2. ISBN 978-0-12-364637-8. PMID 15037363.
  72. ^ Beachey EH (March 1981). "Bacterial adherence: adhesin-receptor interactions mediating the attachment of bacteria to mucosal surface". The Journal of Infectious Diseases. 143 (3): 325–45. doi:10.1093/infdis/143.3.325. PMID 7014727.
  73. ^ Silverman PM (February 1997). "Towards a structural biology of bacterial conjugation". Molecular Microbiology. 23 (3): 423–29. doi:10.1046/j.1365-2958.1997.2411604.x. PMID 9044277.
  74. ^ Costa TR, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M, Waksman G (June 2015). "Secretion systems in Gram-negative bacteria: structural and mechanistic insights". Nature Reviews. Microbiology. 13 (6): 343–59. doi:10.1038/nrmicro3456. PMID 25978706.
  75. ^ Stokes RW, Norris-Jones R, Brooks DE, Beveridge TJ, Doxsee D, Thorson LM (October 2004). "The glycan-rich outer layer of the cell wall of Mycobacterium tuberculosis acts as an antiphagocytic capsule limiting the association of the bacterium with macrophages". Infection and Immunity. 72 (10): 5676–86. doi:10.1128/IAI.72.10.5676-5686.2004. PMC 517526. PMID 15385466.
  76. ^ Daffé M, Etienne G (1999). "The capsule of Mycobacterium tuberculosis and its implications for pathogenicity". Tubercle and Lung Disease. 79 (3): 153–69. doi:10.1054/tuld.1998.0200. PMID 10656114.
  77. ^ Finlay BB, Falkow S (June 1997). "Common themes in microbial pathogenicity revisited". Microbiology and Molecular Biology Reviews. 61 (2): 136–69. PMC 232605. PMID 9184008.
  78. ^ Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P (September 2000). "Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments". Microbiology and Molecular Biology Reviews. 64 (3): 548–72. doi:10.1128/MMBR.64.3.548-572.2000. PMC 99004. PMID 10974126.
  79. ^ a b McKenney PT, Driks A, Eichenberger P (January 2013). "The Bacillus subtilis endospore: assembly and functions of the multilayered coat". Nature Reviews. Microbiology. 11 (1): 33–44. doi:10.1038/nrmicro2921. PMID 23202530.
  80. ^ Nicholson WL, Fajardo-Cavazos P, Rebeil R, Slieman TA, Riesenman PJ, Law JF, Xue Y (August 2002). "Bacterial endospores and their significance in stress resistance". Antonie van Leeuwenhoek. 81 (1–4): 27–32. doi:10.1023/A:1020561122764. PMID 12448702.
  81. ^ Vreeland RH, Rosenzweig WD, Powers DW (October 2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal". Nature. 407 (6806): 897–900. Bibcode:2000Natur.407..897V. doi:10.1038/35038060. PMID 11057666.
  82. ^ Cano RJ, Borucki MK (May 1995). "Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber". Science. 268 (5213): 1060–64. Bibcode:1995Sci...268.1060C. doi:10.1126/science.7538699. PMID 7538699.
  83. ^ Nicholson WL, Schuerger AC, Setlow P (April 2005). "The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight". Mutation Research. 571 (1–2): 249–64. doi:10.1016/j.mrfmmm.2004.10.012. PMID 15748651.
  84. ^ Hatheway CL (January 1990). "Toxigenic clostridia". Clinical Microbiology Reviews. 3 (1): 66–98. doi:10.1128/CMR.3.1.66. PMC 358141. PMID 2404569.
  85. ^ Nealson KH (January 1999). "Post-Viking microbiology: new approaches, new data, new insights". Origins of Life and Evolution of the Biosphere. 29 (1): 73–93. doi:10.1023/A:1006515817767. PMID 11536899.
  86. ^ Xu J (June 2006). "Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances". Molecular Ecology. 15 (7): 1713–31. doi:10.1111/j.1365-294X.2006.02882.x. PMID 16689892.
  87. ^ Zillig W (December 1991). "Comparative biochemistry of Archaea and Bacteria". Current Opinion in Genetics & Development. 1 (4): 544–51. doi:10.1016/S0959-437X(05)80206-0. PMID 1822288.
  88. ^ a b c Slonczewski JL, Foster JW. Microbiology: An Evolving Science (3 ed.). WW Norton & Company. pp. 491–44.
  89. ^ Hellingwerf KJ, Crielaard W, Hoff WD, Matthijs HC, Mur LR, van Rotterdam BJ (1994). "Photobiology of bacteria". Antonie van Leeuwenhoek (Submitted manuscript). 65 (4): 331–47. doi:10.1007/BF00872217. PMID 7832590.
  90. ^ Dalton H (June 2005). "The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360 (1458): 1207–22. doi:10.1098/rstb.2005.1657. PMC 1569495. PMID 16147517.
  91. ^ Zehr JP, Jenkins BD, Short SM, Steward GF (July 2003). "Nitrogenase gene diversity and microbial community structure: a cross-system comparison". Environmental Microbiology. 5 (7): 539–54. doi:10.1046/j.1462-2920.2003.00451.x. PMID 12823187.
  92. ^ Zumft WG (December 1997). "Cell biology and molecular basis of denitrification". Microbiology and Molecular Biology Reviews. 61 (4): 533–616. PMC 232623. PMID 9409151.
  93. ^ Drake HL, Daniel SL, Küsel K, Matthies C, Kuhner C, Braus-Stromeyer S (1997). "Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?". BioFactors. 6 (1): 13–24. doi:10.1002/biof.5520060103. PMID 9233536.
  94. ^ Morel FM, Kraepiel AM, Amyot M (1998). "The chemical cycle and bioaccumulation of mercury". Annual Review of Ecology and Systematics. 29: 543–66. doi:10.1146/annurev.ecolsys.29.1.543.
  95. ^ Koch AL (2002). "Control of the bacterial cell cycle by cytoplasmic growth". Critical Reviews in Microbiology. 28 (1): 61–77. doi:10.1080/1040-840291046696. PMID 12003041.
  96. ^ Eagon RG (April 1962). "Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes". Journal of Bacteriology. 83 (4): 736–37. PMC 279347. PMID 13888946.
  97. ^ Stewart EJ, Madden R, Paul G, Taddei F (February 2005). "Aging and death in an organism that reproduces by morphologically symmetric division". PLoS Biology. 3 (2): e45. doi:10.1371/journal.pbio.0030045. PMC 546039. PMID 15685293.
  98. ^ a b c Thomson RB, Bertram H (December 2001). "Laboratory diagnosis of central nervous system infections". Infectious Disease Clinics of North America. 15 (4): 1047–71. doi:10.1016/S0891-5520(05)70186-0. PMID 11780267.
  99. ^ Paerl HW, Fulton RS, Moisander PH, Dyble J (April 2001). "Harmful freshwater algal blooms, with an emphasis on cyanobacteria". TheScientificWorldJournal. 1: 76–113. doi:10.1100/tsw.2001.16. PMC 6083932. PMID 12805693.
  100. ^ Challis GL, Hopwood DA (November 2003). "Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species". Proceedings of the National Academy of Sciences of the United States of America. 100 Suppl 2 (90002): 14555–61. Bibcode:2003PNAS..10014555C. doi:10.1073/pnas.1934677100. PMC 304118. PMID 12970466.
  101. ^ Kooijman SA, Auger P, Poggiale JC, Kooi BW (August 2003). "Quantitative steps in symbiogenesis and the evolution of homeostasis". Biological Reviews of the Cambridge Philosophical Society. 78 (3): 435–63. doi:10.1017/S1464793102006127. PMID 14558592.
  102. ^ Prats C, López D, Giró A, Ferrer J, Valls J (August 2006). "Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase". Journal of Theoretical Biology. 241 (4): 939–53. doi:10.1016/j.jtbi.2006.01.029. PMID 16524598.
  103. ^ Hecker M, Völker U (2001). General stress response of Bacillus subtilis and other bacteria. Advances in Microbial Physiology. 44. pp. 35–91. doi:10.1016/S0065-2911(01)44011-2. ISBN 978-0-12-027744-5. PMID 11407115.
  104. ^ Slonczewski JL, Foster JW. Microbiology: An Evolving Science (3 ed.). WW Norton & Company. p. 143.
  105. ^ Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M (October 2006). "The 160-kilobase genome of the bacterial endosymbiont Carsonella". Science. 314 (5797): 267. doi:10.1126/science.1134196. PMID 17038615.
  106. ^ Pradella S, Hans A, Spröer C, Reichenbach H, Gerth K, Beyer S (December 2002). "Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56". Archives of Microbiology. 178 (6): 484–92. doi:10.1007/s00203-002-0479-2. PMID 12420170.
  107. ^ Hinnebusch J, Tilly K (December 1993). "Linear plasmids and chromosomes in bacteria". Molecular Microbiology. 10 (5): 917–22. doi:10.1111/j.1365-2958.1993.tb00963.x. PMID 7934868.
  108. ^ Lin YS, Kieser HM, Hopwood DA, Chen CW (December 1993). "The chromosomal DNA of Streptomyces lividans 66 is linear". Molecular Microbiology. 10 (5): 923–33. doi:10.1111/j.1365-2958.1993.tb00964.x. PMID 7934869.
  109. ^ Val ME, Soler-Bistué A, Bland MJ, Mazel D (December 2014). "Management of multipartite genomes: the Vibrio cholerae model". Current Opinion in Microbiology. 22: 120–26. doi:10.1016/j.mib.2014.10.003. PMID 25460805.
  110. ^ Kado CI (October 2014). Historical Events That Spawned the Field of Plasmid Biology. Microbiology Spectrum. 2. p. 3. doi:10.1128/microbiolspec.PLAS-0019-2013. ISBN 9781555818975. PMID 26104369.
  111. ^ Belfort M, Reaban ME, Coetzee T, Dalgaard JZ (July 1995). "Prokaryotic introns and inteins: a panoply of form and function". Journal of Bacteriology. 177 (14): 3897–903. doi:10.1128/jb.177.14.3897-3903.1995. PMC 177115. PMID 7608058.
  112. ^ Denamur E, Matic I (May 2006). "Evolution of mutation rates in bacteria". Molecular Microbiology. 60 (4): 820–7. doi:10.1111/j.1365-2958.2006.05150.x. PMID 16677295.
  113. ^ Wright BE (May 2004). "Stress-directed adaptive mutations and evolution". Molecular Microbiology. 52 (3): 643–50. doi:10.1111/j.1365-2958.2004.04012.x. PMID 15101972.
  114. ^ Chen I, Dubnau D (March 2004). "DNA uptake during bacterial transformation". Nature Reviews. Microbiology. 2 (3): 241–9. doi:10.1038/nrmicro844. PMID 15083159.
  115. ^ Johnsborg O, Eldholm V, Håvarstein LS (December 2007). "Natural genetic transformation: prevalence, mechanisms and function". Research in Microbiology. 158 (10): 767–78. doi:10.1016/j.resmic.2007.09.004. PMID 17997281.
  116. ^ Bernstein H, Bernstein C, Michod RE (2012). "DNA repair as the primary adaptive function of sex in bacteria and eukaryotes". Chapter 1: pp. 1–49 in: DNA Repair: New Research, Sakura Kimura and Sora Shimizu (eds.). Nova Sci. Publ., Hauppauge, NY ISBN 978-1-62100-808-8.
  117. ^ Brüssow H, Canchaya C, Hardt WD (September 2004). "Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion". Microbiology and Molecular Biology Reviews. 68 (3): 560–602, table of contents. doi:10.1128/MMBR.68.3.560-602.2004. PMC 515249. PMID 15353570.
  118. ^ Bickle TA, Krüger DH (June 1993). "Biology of DNA restriction". Microbiological Reviews. 57 (2): 434–50. PMC 372918. PMID 8336674.
  119. ^ Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (March 2007). "CRISPR provides acquired resistance against viruses in prokaryotes". Science. 315 (5819): 1709–12. Bibcode:2007Sci...315.1709B. doi:10.1126/science.1138140. PMID 17379808.
  120. ^ Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (August 2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes". Science. 321 (5891): 960–64. Bibcode:2008Sci...321..960B. doi:10.1126/science.1159689. PMC 5898235. PMID 18703739.
  121. ^ Michod RE, Bernstein H, Nedelcu AM (May 2008). "Adaptive value of sex in microbial pathogens" (PDF). Infection, Genetics and Evolution. 8 (3): 267–85. doi:10.1016/j.meegid.2008.01.002. PMID 18295550. Archived (PDF) from the original on 30 December 2016.
  122. ^ Hastings PJ, Rosenberg SM, Slack A (September 2004). "Antibiotic-induced lateral transfer of antibiotic resistance". Trends in Microbiology. 12 (9): 401–14. doi:10.1016/j.tim.2004.07.003. PMID 15337159.
  123. ^ Davison J (September 1999). "Genetic exchange between bacteria in the environment". Plasmid. 42 (2): 73–91. doi:10.1006/plas.1999.1421. PMID 10489325.
  124. ^ a b c Bardy SL, Ng SY, Jarrell KF (February 2003). "Prokaryotic motility structures". Microbiology. 149 (Pt 2): 295–304. doi:10.1099/mic.0.25948-0. PMID 12624192.
  125. ^ Macnab RM (December 1999). "The bacterial flagellum: reversible rotary propellor and type III export apparatus". Journal of Bacteriology. 181 (23): 7149–53. PMC 103673. PMID 10572114.
  126. ^ Wu M, Roberts JW, Kim S, Koch DL, DeLisa MP (July 2006). "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique". Applied and Environmental Microbiology. 72 (7): 4987–94. doi:10.1128/AEM.00158-06. PMC 1489374. PMID 16820497.
  127. ^ Mattick, John S (2002). "Type IV Pili and Twitching Motility". Annual Review of Microbiology. 56: 289–314. doi:10.1146/annurev.micro.56.012302.160938. PMID 12142488.
  128. ^ Merz AJ, So M, Sheetz MP (September 2000). "Pilus retraction powers bacterial twitching motility". Nature. 407 (6800): 98–102. Bibcode:2000Natur.407...98M. doi:10.1038/35024105. PMID 10993081.
  129. ^ Lux R, Shi W (July 2004). "Chemotaxis-guided movements in bacteria". Critical Reviews in Oral Biology and Medicine. 15 (4): 207–20. doi:10.1177/154411130401500404. PMID 15284186.
  130. ^ Schweinitzer T, Josenhans C (July 2010). "Bacterial energy taxis: a global strategy?". Archives of Microbiology. 192 (7): 507–20. doi:10.1007/s00203-010-0575-7. PMC 2886117. PMID 20411245.
  131. ^ Frankel RB, Bazylinski DA, Johnson MS, Taylor BL (August 1997). "Magneto-aerotaxis in marine coccoid bacteria". Biophysical Journal. 73 (2): 994–1000. Bibcode:1997BpJ....73..994F. doi:10.1016/S0006-3495(97)78132-3. PMC 1180996. PMID 9251816.
  132. ^ Goldberg MB (December 2001). "Actin-based motility of intracellular microbial pathogens". Microbiology and Molecular Biology Reviews. 65 (4): 595–626, table of contents. doi:10.1128/MMBR.65.4.595-626.2001. PMC 99042. PMID 11729265.
  133. ^ Dusenbery, David B (1996). Life at Small Scale. Scientific American Library. ISBN 0-7167-5060-0.
  134. ^ a b Shapiro JA (1998). "Thinking about bacterial populations as multicellular organisms" (PDF). Annual Review of Microbiology. 52: 81–104. doi:10.1146/annurev.micro.52.1.81. PMID 9891794. Archived from the original (PDF) on 17 July 2011.
  135. ^ a b Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995). "Microbial biofilms". Annual Review of Microbiology. 49: 711–45. doi:10.1146/annurev.mi.49.100195.003431. PMID 8561477.
  136. ^ Miller MB, Bassler BL (2001). "Quorum sensing in bacteria". Annual Review of Microbiology. 55: 165–99. doi:10.1146/annurev.micro.55.1.165. PMID 11544353.
  137. ^ 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.
  138. ^ Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbø CL, Case RJ, Doolittle WF (2003). "Lateral gene transfer and the origins of prokaryotic groups". Annual Review of Genetics. 37: 283–328. doi:10.1146/annurev.genet.37.050503.084247. PMID 14616063.
  139. ^ Olsen GJ, Woese CR, Overbeek R (January 1994). "The winds of (evolutionary) change: breathing new life into microbiology". Journal of Bacteriology. 176 (1): 1–6. doi:10.2172/205047. PMC 205007. PMID 8282683.
  140. ^ "IJSEM Home". Ijs.sgmjournals.org. 28 October 2011. Archived from the original on 19 October 2011. Retrieved 4 November 2011.
  141. ^ "Bergey's Manual Trust". Bergeys.org. Archived from the original on 7 November 2011. Retrieved 4 November 2011.
  142. ^ Gupta RS (2000). "The natural evolutionary relationships among prokaryotes". Critical Reviews in Microbiology. 26 (2): 111–31. CiteSeerX 10.1.1.496.1356. doi:10.1080/10408410091154219. PMID 10890353.
  143. ^ Doolittle RF (June 2005). "Evolutionary aspects of whole-genome biology". Current Opinion in Structural Biology. 15 (3): 248–53. doi:10.1016/j.sbi.2005.04.001. PMID 15963888.
  144. ^ Cavalier-Smith T (January 2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318.
  145. ^ Woods GL, Walker DH (July 1996). "Detection of infection or infectious agents by use of cytologic and histologic stains". Clinical Microbiology Reviews. 9 (3): 382–404. doi:10.1128/CMR.9.3.382. PMC 172900. PMID 8809467.
  146. ^ Weinstein MP (March 1994). "Clinical importance of blood cultures". Clinics in Laboratory Medicine. 14 (1): 9–16. doi:10.1016/S0272-2712(18)30390-1. PMID 8181237.
  147. ^ Louie M, Louie L, Simor AE (August 2000). "The role of DNA amplification technology in the diagnosis of infectious diseases". CMAJ. 163 (3): 301–09. PMC 80298. PMID 10951731. Archived from the original on 14 June 2006.
  148. ^ Oliver JD (February 2005). "The viable but nonculturable state in bacteria". Journal of Microbiology. 43 Spec No: 93–100. PMID 15765062. Archived from the original on 28 September 2007.
  149. ^ Euzéby JP (8 December 2011). "Number of published names". List of Prokaryotic names with Standing in Nomenclature. Archived from the original on 19 January 2012. Retrieved 10 December 2011.
  150. ^ Curtis TP, Sloan WT, Scannell JW (August 2002). "Estimating prokaryotic diversity and its limits". Proceedings of the National Academy of Sciences of the United States of America. 99 (16): 10494–9. Bibcode:2002PNAS...9910494C. doi:10.1073/pnas.142680199. PMC 124953. PMID 12097644.
  151. ^ Schloss PD, Handelsman J (December 2004). "Status of the microbial census". Microbiology and Molecular Biology Reviews. 68 (4): 686–91. doi:10.1128/MMBR.68.4.686-691.2004. PMC 539005. PMID 15590780.
  152. ^ Fisher B, Harvey RP, Champe PC (2007). "Chapter 33". Lippincott's Illustrated Reviews: Microbiology (Lippincott's Illustrated Reviews Series). Hagerstwon, MD: Lippincott Williams & Wilkins. pp. 367–92. ISBN 978-0-7817-8215-9.
  153. ^ LEF.org > Bacterial Infections Updated: 19 January 2006. Retrieved on 11 April 2009
  154. ^ Martin MO (September 2002). "Predatory prokaryotes: an emerging research opportunity". Journal of Molecular Microbiology and Biotechnology. 4 (5): 467–77. PMID 12432957.
  155. ^ Velicer GJ, Stredwick KL (August 2002). "Experimental social evolution with Myxococcus xanthus". Antonie van Leeuwenhoek. 81 (1–4): 155–64. doi:10.1023/A:1020546130033. PMID 12448714.
  156. ^ Gromov BV (1972). "Electron Microscope Study of Parasitism by Bdellovibrio Chorellavorus Bacteria on Cells of the Green Alga Chorella Vulgaris". Tsitologiya. 14 (2): 256–60.
  157. ^ Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L (April 1986). "Predatory prokaryotes: predation and primary consumption evolved in bacteria". Proceedings of the National Academy of Sciences of the United States of America. 83 (7): 2138–42. Bibcode:1986PNAS...83.2138G. doi:10.1073/pnas.83.7.2138. PMC 323246. PMID 11542073.
  158. ^ Velicer GJ, Mendes-Soares H (January 2009). "Bacterial predators". Current Biology. 19 (2): R55–56. doi:10.1016/j.cub.2008.10.043. PMID 19174136.
  159. ^ Stams AJ, de Bok FA, Plugge CM, van Eekert MH, Dolfing J, Schraa G (March 2006). "Exocellular electron transfer in anaerobic microbial communities". Environmental Microbiology. 8 (3): 371–82. doi:10.1111/j.1462-2920.2006.00989.x. PMID 16478444.
  160. ^ Barea JM, Pozo MJ, Azcón R, Azcón-Aguilar C (July 2005). "Microbial co-operation in the rhizosphere". Journal of Experimental Botany. 56 (417): 1761–78. doi:10.1093/jxb/eri197. PMID 15911555.
  161. ^ O'Hara AM, Shanahan F (July 2006). "The gut flora as a forgotten organ". EMBO Reports. 7 (7): 688–93. doi:10.1038/sj.embor.7400731. PMC 1500832. PMID 16819463.
  162. ^ Zoetendal EG, Vaughan EE, de Vos WM (March 2006). "A microbial world within us". Molecular Microbiology. 59 (6): 1639–50. doi:10.1111/j.1365-2958.2006.05056.x. PMID 16553872.
  163. ^ Gorbach SL (February 1990). "Lactic acid bacteria and human health". Annals of Medicine. 22 (1): 37–41. doi:10.3109/07853899009147239. PMID 2109988.
  164. ^ Salminen SJ, Gueimonde M, Isolauri E (May 2005). "Probiotics that modify disease risk". The Journal of Nutrition. 135 (5): 1294–98. doi:10.1093/jn/135.5.1294. PMID 15867327.
  165. ^ Fish DN (February 2002). "Optimal antimicrobial therapy for sepsis". American Journal of Health-System Pharmacy. 59 Suppl 1: S13–19. doi:10.1093/ajhp/59.suppl_1.S13. PMID 11885408.
  166. ^ Belland RJ, Ouellette SP, Gieffers J, Byrne GI (February 2004). "Chlamydia pneumoniae and atherosclerosis". Cellular Microbiology. 6 (2): 117–27. doi:10.1046/j.1462-5822.2003.00352.x. PMID 14706098.
  167. ^ Heise ER (February 1982). "Diseases associated with immunosuppression". Environmental Health Perspectives. 43: 9–19. doi:10.2307/3429162. JSTOR 3429162. PMC 1568899. PMID 7037390.
  168. ^ Saiman L (2004). "Microbiology of early CF lung disease". Paediatric Respiratory Reviews. 5 Suppl A: S367–69. doi:10.1016/S1526-0542(04)90065-6. PMID 14980298.
  169. ^ Yonath A, Bashan A (2004). "Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics". Annual Review of Microbiology. 58: 233–51. doi:10.1146/annurev.micro.58.030603.123822. PMID 15487937.
  170. ^ Khachatourians GG (November 1998). "Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria". CMAJ. 159 (9): 1129–36. PMC 1229782. PMID 9835883.
  171. ^ Johnson ME, Lucey JA (April 2006). "Major technological advances and trends in cheese". Journal of Dairy Science. 89 (4): 1174–8. doi:10.3168/jds.S0022-0302(06)72186-5. PMID 16537950.
  172. ^ Hagedorn S, Kaphammer B (1994). "Microbial biocatalysis in the generation of flavor and fragrance chemicals". Annual Review of Microbiology. 48: 773–800. doi:10.1146/annurev.mi.48.100194.004013. PMID 7826026.
  173. ^ Cohen Y (December 2002). "Bioremediation of oil by marine microbial mats". International Microbiology. 5 (4): 189–93. doi:10.1007/s10123-002-0089-5. PMID 12497184.
  174. ^ Neves LC, Miyamura TT, Moraes DA, Penna TC, Converti A (2006). "Biofiltration methods for the removal of phenolic residues". Applied Biochemistry and Biotechnology. 129–132 (1–3): 130–52. doi:10.1385/ABAB:129:1:130. PMID 16915636.
  175. ^ Liese A, Filho MV (December 1999). "Production of fine chemicals using biocatalysis". Current Opinion in Biotechnology. 10 (6): 595–603. doi:10.1016/S0958-1669(99)00040-3. PMID 10600695.
  176. ^ Aronson AI, Shai Y (February 2001). "Why Bacillus thuringiensis insecticidal toxins are so effective: unique features of their mode of action". FEMS Microbiology Letters. 195 (1): 1–8. doi:10.1111/j.1574-6968.2001.tb10489.x. PMID 11166987.
  177. ^ Bozsik A (July 2006). "Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action". Pest Management Science. 62 (7): 651–54. doi:10.1002/ps.1221. PMID 16649191.
  178. ^ Chattopadhyay A, Bhatnagar NB, Bhatnagar R (2004). "Bacterial insecticidal toxins". Critical Reviews in Microbiology. 30 (1): 33–54. doi:10.1080/10408410490270712. PMID 15116762.
  179. ^ Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome". Genome Biology. 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9-research0035. PMC 56896. PMID 11574054.
  180. ^ Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási AL (February 2004). "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature. 427 (6977): 839–43. arXiv:q-bio/0403001. Bibcode:2004Natur.427..839A. doi:10.1038/nature02289. PMID 14985762.
  181. ^ Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biology. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMC 193654. PMID 12952533.
  182. ^ Walsh G (April 2005). "Therapeutic insulins and their large-scale manufacture". Applied Microbiology and Biotechnology. 67 (2): 151–59. doi:10.1007/s00253-004-1809-x. PMID 15580495.
  183. ^ Graumann K, Premstaller A (February 2006). "Manufacturing of recombinant therapeutic proteins in microbial systems". Biotechnology Journal. 1 (2): 164–86. doi:10.1002/biot.200500051. PMID 16892246.
  184. ^ Porter JR (June 1976). "Antony van Leeuwenhoek: tercentenary of his discovery of bacteria". Bacteriological Reviews. 40 (2): 260–69. PMC 413956. PMID 786250.
  185. ^ van Leeuwenhoek A (1684). "An abstract of a letter from Mr. Anthony Leevvenhoek at Delft, dated Sep. 17, 1683, Containing Some Microscopical Observations, about Animals in the Scurf of the Teeth, the Substance Call'd Worms in the Nose, the Cuticula Consisting of Scales". Philosophical Transactions. 14 (155–166): 568–74. doi:10.1098/rstl.1684.0030.
  186. ^ van Leeuwenhoek A (1700). "Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs". Philosophical Transactions. 22 (260–276): 509–518. doi:10.1098/rstl.1700.0013.
  187. ^ van Leeuwenhoek A (1702). "Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them". Philosophical Transactions. 23 (277–288): 1304–11. doi:10.1098/rstl.1702.0042.
  188. ^ Asimov I (1982). Asimov's Biographical Encyclopedia of Science and Technology (2nd ed.). Garden City, NY: Doubleday and Company. p. 143.
  189. ^ Ehrenberg CG (1828). Symbolae Physioe. Animalia evertebrata. Berlin: Decas prima.
  190. ^ Breed RS, Conn HJ (May 1936). "The Status of the Generic Term Bacterium Ehrenberg 1828". Journal of Bacteriology. 31 (5): 517–18. PMC 543738. PMID 16559906.
  191. ^ Ehrenberg CG (1835). Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes [Third contribution to the knowledge of great organization in the direction of the smallest space] (in German). Berlin: Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften. pp. 143–336.
  192. ^ "Pasteur's Papers on the Germ Theory". LSU Law Center's Medical and Public Health Law Site, Historic Public Health Articles. Archived from the original on 18 December 2006. Retrieved 23 November 2006.
  193. ^ "The Nobel Prize in Physiology or Medicine 1905". Nobelprize.org. Archived from the original on 10 December 2006. Retrieved 22 November 2006.
  194. ^ O'Brien SJ, Goedert JJ (October 1996). "HIV causes AIDS: Koch's postulates fulfilled". Current Opinion in Immunology. 8 (5): 613–8. doi:10.1016/S0952-7915(96)80075-6. PMID 8902385.
  195. ^ Chung K. "Ferdinand Julius Cohn (1828–1898): Pioneer of Bacteriology" (PDF). Department of Microbiology and Molecular Cell Sciences, The University of Memphis. Archived (PDF) from the original on 27 July 2011.
  196. ^ Drews, Gerhart (1999). "Ferdinand Cohn, a founder of modern microbiology" (PDF). ASM News. 65 (8): 547–52. Archived from the original (PDF) on 13 July 2017.
  197. ^ Thurston AJ (December 2000). "Of blood, inflammation and gunshot wounds: the history of the control of sepsis". The Australian and New Zealand Journal of Surgery. 70 (12): 855–61. doi:10.1046/j.1440-1622.2000.01983.x. PMID 11167573.
  198. ^ Schwartz RS (March 2004). "Paul Ehrlich's magic bullets". The New England Journal of Medicine. 350 (11): 1079–80. doi:10.1056/NEJMp048021. PMID 15014180.
  199. ^ "Biography of Paul Ehrlich". Nobelprize.org. Archived from the original on 28 November 2006. Retrieved 26 November 2006.

Further reading

  • Alcamo IE (2001). Fundamentals of microbiology. Boston: Jones and Bartlett. ISBN 978-0-7637-1067-5.
  • Atlas RM (1995). Principles of microbiology. St. Louis: Mosby. ISBN 978-0-8016-7790-8.
  • Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood Cliffs, N.J: Prentice Hall. ISBN 978-0-13-144329-7.
  • Holt JC, Bergey DH (1994). Bergey's manual of determinative bacteriology (9th ed.). Baltimore: Williams & Wilkins. ISBN 978-0-683-00603-2.
  • Hugenholtz P, Goebel BM, Pace NR (September 1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". Journal of Bacteriology. 180 (18): 4765–74. PMC 107498. PMID 9733676.
  • Funke BR, Tortora GJ, Case CL (2004). Microbiology: an introduction (8th ed.). San Francisco: Benjamin Cummings. ISBN 978-0-8053-7614-2.
  • Ogunseitan OA (2005). Microbial Diversity: Form and Function in Prokaryotes. Wiley-Blackwell. ISBN 978-1-4051-4448-3.
  • Shively JM (2006). Complex Intracellular Structures in Prokaryotes (Microbiology Monographs). Berlin: Springer. ISBN 978-3-540-32524-6.

External links

Actinobacteria

The Actinobacteria are a phylum of Gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil, they behave much like fungi, helping to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales (the actinomycetes), reflects that they were long believed to be fungi. Some soil actinobacteria (such as Frankia) live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of Mycobacterium are important pathogens.

Beyond the great interest in Actinobacteria for their soil role, much is yet to be learned about them. Although currently understood primarily as soil bacteria, they might be more abundant in fresh waters. Actinobacteria is one of the dominant bacterial phyla and contains one of the largest of bacterial genera, Streptomyces. Streptomyces and other actinobacteria are major contributors to biological buffering of soils. They are also the source of many antibiotics.

Although some of the largest and most complex bacterial cells belong to the Actinobacteria, the group of marine Actinomarinales has been described as possessing the smallest free-living prokaryotic cells.A Siberian example is said to be the oldest living organism on Earth, at around half a million years old.

Aerobic organism

An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. In contrast, an anaerobic organism (anaerobe) is any organism that does not require oxygen for growth. Some anaerobes react negatively or even die if oxygen is present.

Anaerobic organism

An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if free oxygen is present. (In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment.)

An anaerobic organism may be unicellular (e.g. protozoans, bacteria) or multicellular. For practical purposes, there are three categories of anaerobe: obligate anaerobes, which are harmed by the presence of oxygen; aerotolerant organisms, which cannot use oxygen for growth but tolerate its presence; and facultative anaerobes, which can grow without oxygen but use oxygen if it is present.

Antibiotic

An antibiotic is a type of antimicrobial substance active against bacteria and is the most important type of antibacterial agent for fighting bacterial infections. Antibiotic medications are widely used in the treatment and prevention of such infections. They may either kill or inhibit the growth of bacteria. A limited number of antibiotics also possess antiprotozoal activity. Antibiotics are not effective against viruses such as the common cold or influenza; drugs which inhibit viruses are termed antiviral drugs or antivirals rather than antibiotics.

Sometimes, the term antibiotic which means "opposing life", based on Greek roots, (ἀντι-) anti: "against" and (βίος-) biotic: "life", is broadly used to refer to any substance used against microbes, but in the usual medical usage, antibiotics (such as penicillin) are those produced naturally (by one microorganism fighting another), whereas nonantibiotic antibacterials (such as sulfonamides and antiseptics) are fully synthetic. However, both classes have the same goal of killing or preventing the growth of microorganisms, and both are included in antimicrobial chemotherapy. "Antibacterials" include antiseptic drugs, antibacterial soaps, and chemical disinfectants, whereas antibiotics are an important class of antibacterials used more specifically in medicine and sometimes in livestock feed.

There's evidence of antibiotic use since ancient times. Many civilizations used topical application of mouldy bread, with many references to its beneficial effects arising from ancient Egypt, China, Serbia, Greece and Rome. The first person to directly document the use of moulds to treat infections was John Parkinson (1567–1650). Antibiotics truly revolutionized medicine in the 20th century. Alexander Fleming (1881–1955) discovered modern day penicillin in 1928. After realizing the great potential there was in penicillin, Fleming pursued the challenge of how to market it and translate it to commercial use. With help from other biochemists, penicillin was finally available for widespread use. This was significantly beneficial during wartime. Unfortunately, it didn't take long for resistance to begin. Effectiveness and easy access have also led to their overuse and some bacteria have developed resistance. This has led to widespread problems, and the World Health Organization have classified antimicrobial resistance as a "serious threat [that] is no longer a prediction for the future, it is happening right now in every region of the world and has the potential to affect anyone, of any age, in any country".

Antimicrobial resistance

Antimicrobial resistance (AMR or AR) is the ability of a microbe to resist the effects of medication that once could successfully treat the microbe. The term antibiotic resistance (AR or ABR) is a subset of AMR, as it applies only to bacteria becoming resistant to antibiotics. Resistant microbes are more difficult to treat, requiring alternative medications or higher doses of antimicrobials. These approaches may be more expensive, more toxic or both. Microbes resistant to multiple antimicrobials are called multidrug resistant (MDR). Those considered extensively drug resistant (XDR) or totally drug resistant (TDR) are sometimes called "superbugs".Resistance arises through one of three mechanisms: natural resistance in certain types of bacteria, genetic mutation, or by one species acquiring resistance from another. All classes of microbes can develop resistance. Fungi develop antifungal resistance. Viruses develop antiviral resistance. Protozoa develop antiprotozoal resistance, and bacteria develop antibiotic resistance. Resistance can appear spontaneously because of random mutations. However, extended use of antimicrobials appears to encourage selection for mutations which can render antimicrobials ineffective.Preventive measures include only using antibiotics when needed, thereby stopping misuse of antibiotics or antimicrobials. Narrow-spectrum antibiotics are preferred over broad-spectrum antibiotics when possible, as effectively and accurately targeting specific organisms is less likely to cause resistance, as well as side effects. For people who take these medications at home, education about proper use is essential. Health care providers can minimize spread of resistant infections by use of proper sanitation and hygiene, including handwashing and disinfecting between patients, and should encourage the same of the patient, visitors, and family members.Rising drug resistance is caused mainly by use of antimicrobials in humans and other animals, and spread of resistant strains between the two. Growing resistance has also been linked to dumping of inadequately treated effluents from the pharmaceutical industry, especially in countries where bulk drugs are manufactured. Antibiotics increase selective pressure in bacterial populations, causing vulnerable bacteria to die; this increases the percentage of resistant bacteria which continue growing. Even at very low levels of antibiotic, resistant bacteria can have a growth advantage and grow faster than vulnerable bacteria. With resistance to antibiotics becoming more common there is greater need for alternative treatments. Calls for new antibiotic therapies have been issued, but new drug development is becoming rarer.Antimicrobial resistance is increasing globally because of greater access to antibiotic drugs in developing countries. Estimates are that 700,000 to several million deaths result per year. Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die as a result. There are public calls for global collective action to address the threat that include proposals for international treaties on antimicrobial resistance. Worldwide antibiotic resistance is not completely identified, but poorer countries with weaker healthcare systems are more affected.

Bacillus (shape)

A bacillus (plural bacilli) or bacilliform bacterium is a rod-shaped bacterium or archaeon. Bacilli are found in many different taxonomic groups of bacteria. However, the name Bacillus, capitalized and italicized, refers to a specific genus of bacteria. The name Bacilli, capitalized but not italicized, can also refer to a less specific taxonomic group of bacteria that includes two orders, one of which contains the genus Bacillus. When the word is formatted with lowercase and not italicized, 'bacillus', it will most likely be referring to shape and not to the genus at all. Bacilliform bacteria are also often simply called rods when the bacteriologic context is clear.

Sea

Bacilli usually divide in the same plane and are solitary, but can combine to form diplobacilli, streptobacilli, and palisades.

Diplobacilli: Two bacilli arranged side by side with each other.

Streptobacilli: Bacilli arranged in chains.

Coccobacillus: Oval and similar to coccus (circular shaped bacterium).There is no connection between the shape of a bacterium and its color in the Gram staining. MacConkey agar can be used to distinguish among Gram negative bacilli such as E. coli and salmonella.

Bacteriophage

A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν (phagein), "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined.Phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. One of the densest natural sources for phages and other viruses is seawater, where up to 9x108 virions per millilitre have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages. They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe as well as in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy). Nevertheless, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection.

Cyanobacteria

Cyanobacteria , also known as Cyanophyta, are a phylum of bacteria that obtain their energy through photosynthesis and are the only photosynthetic prokaryotes able to produce oxygen. The name cyanobacteria comes from the color of the bacteria (Greek: κυανός, translit. kyanós, lit. 'blue'). Cyanobacteria, which are prokaryotes, are also called "blue-green algae", though the term algae in modern usage is restricted to eukaryotes.Unlike heterotrophic prokaryotes, cyanobacteria have internal membranes. These are flattened sacs called thylakoids where photosynthesis is performed.Phototrophic eukaryotes perform photosynthesis by plastids that may have their ancestry in cyanobacteria, acquired long ago via a process called endosymbiosis. These endosymbiotic cyanobacteria in eukaryotes may have evolved or differentiated into specialized organelles such as chloroplasts, etioplasts and leucoplasts.

By producing and releasing oxygen (as a byproduct of photosynthesis), cyanobacteria are thought to have converted the early oxygen-poor, reducing atmosphere into an oxidizing one, causing the Great Oxygenation Event and the "rusting of the Earth", which dramatically changed the composition of the Earth's life forms and led to the near-extinction of anaerobic organisms.

Domain (biology)

In biological taxonomy, a domain [/də(ʊ)ˈmeɪn/] (Latin: regio), 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.

According to this system, the tree of life consists of three domains: Archaea, Bacteria, and Eukarya. The first two are all prokaryotic microorganisms, or single-celled organisms whose cells have no nucleus. All life that has a nucleus and membrane-bound organelles, and multicellular organisms, is included in the Eukarya.

Gram-negative bacteria

Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the gram-staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane.

Gram-negative bacteria are found everywhere, in virtually all environments on Earth that support life. The gram-negative bacteria include the model organism Escherichia coli, as well as many pathogenic bacteria, such as Pseudomonas aeruginosa, Neisseria gonorrhoeae, Chlamydia trachomatis, and Yersinia pestis. They are an important medical challenge, as their outer membrane protects them from many antibiotics (including penicillin); detergents that would normally damage the peptidoglycans of the (inner) cell membrane; and lysozyme, an antimicrobial enzyme produced by animals that forms part of the innate immune system. Additionally, the outer leaflet of this membrane comprises a complex lipopolysaccharide (LPS) whose lipid A component can cause a toxic reaction when these bacteria are lysed by immune cells. This toxic reaction can include fever, an increased respiratory rate, and low blood pressure — a life-threatening condition known as septic shock.Several classes of antibiotics have been designed to target gram-negative bacteria, including aminopenicillins, ureidopenicillins, cephalosporins, beta-lactam-betalactamase combinations (e.g. pipercillin-tazobactam), Folate antagonists, quinolones, and carbapenems. Many of these antibiotics also cover gram positive organisms. The drugs that specifically target gram negative organisms include aminoglycosides, monobactams (aztreonam) and Ciprofloxacin.

Gram-positive bacteria

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.

Gram-positive bacteria take up the crystal violet stain used in the test, and then appear to be purple-coloured when seen through a microscope. This is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test.

Gram-negative bacteria cannot retain the violet stain after the decolorization step; alcohol used in this stage degrades the outer membrane of gram-negative cells, making the cell wall more porous and incapable of retaining the crystal violet stain. Their peptidoglycan layer is much thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain (safranin or fuchsine) and appear red or pink.

Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to certain cell wall targeting antibiotics than gram-negative bacteria, due to the absence of the outer membrane.

Microorganism

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

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.

Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.

They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

Necrotizing fasciitis

Necrotizing fasciitis (NF), commonly known as flesh-eating disease, is an infection that results in the death of parts of the body's soft tissue. It is a severe disease of sudden onset that spreads rapidly. Symptoms include red or purple skin in the affected area, severe pain, fever, and vomiting. The most commonly affected areas are the limbs and perineum.Typically, the infection enters the body through a break in the skin such as a cut or burn. Risk factors include poor immune function such as from diabetes or cancer, obesity, alcoholism, intravenous drug use, and peripheral artery disease. It is not typically spread between people. The disease is classified into four types, depending on the infecting organism. Between 55 and 80% of cases involve more than one type of bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) is involved in up to a third of cases. Medical imaging is helpful to confirm the diagnosis.Necrotizing fasciitis may be prevented with proper wound care and handwashing. It is usually treated with surgery to remove the infected tissue, and intravenous antibiotics. Often, a combination of antibiotics is used, such as penicillin G, clindamycin, vancomycin, and gentamicin. Delays in surgery are associated with a much higher risk of death. Even with high-quality treatment, the risk of death is between 25 and 35%.Necrotizing fasciitis occurs in about 0.4 people per 100,000 per year in the US, and about 1 per 100,000 in Western Europe. Both sexes are affected equally. It becomes more common among older people and is rare in children. It has been described at least since the time of Hippocrates. The term "necrotizing fasciitis" first came into use in 1952.

Pathogen

In biology, a pathogen (Greek: πάθος pathos "suffering, passion" and -γενής -genēs "producer of"), in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

The term pathogen came into use in the 1880s. Typically, the term is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as certain kinds of worms and insect larvae, can also produce disease. However, these animals are usually, in common parlance, referred to as parasites rather than pathogens. The scientific study of microscopic, pathogenic organisms is called microbiology, while the study of disease that may include these pathogens is called pathology. Parasitology, meanwhile, is the scientific study of parasites and the organisms that host them.

There are several pathways through which pathogens can invade a host. The principal pathways have different episodic time frames, but soil has the longest or most persistent potential for harboring a pathogen. Diseases in humans that are caused by infectious agents are known as pathogenic diseases, though not all diseases are caused by pathogens. Some diseases, such as Huntington's disease, are caused by inheritance of abnormal genes.

Pathogenic bacteria

Pathogenic bacteria are bacteria that can cause disease. This article deals with human pathogenic bacteria. Although most bacteria are harmless or often beneficial, some are pathogenic, with the number of species estimated as fewer than a hundred that are seen to cause infectious diseases in humans. By contrast, several thousand species exist in the human digestive system.

One of the bacterial diseases with the highest disease burden is tuberculosis, caused by Mycobacterium tuberculosis bacteria, which kills about 2 million people a year, mostly in sub-Saharan Africa. Pathogenic bacteria contribute to other globally important diseases, such as pneumonia, which can be caused by bacteria such as Streptococcus and Pseudomonas, and foodborne illnesses, which can be caused by bacteria such as Shigella, Campylobacter, and Salmonella. Pathogenic bacteria also cause infections such as tetanus, typhoid fever, diphtheria, syphilis, and leprosy. Pathogenic bacteria are also the cause of high infant mortality rates in developing countries.Koch's postulates are the standard to establish a causative relationship between a microbe and a disease.

Pneumonia

Pneumonia is an inflammatory condition of the lung affecting primarily the small air sacs known as alveoli. Typically symptoms include some combination of productive or dry cough, chest pain, fever, and trouble breathing. Severity is variable.Pneumonia is usually caused by infection with viruses or bacteria and less commonly by other microorganisms, certain medications and conditions such as autoimmune diseases. Risk factors include other lung diseases such as cystic fibrosis, COPD, and asthma, diabetes, heart failure, a history of smoking, a poor ability to cough such as following a stroke, or a weak immune system. Diagnosis is often based on the symptoms and physical examination. Chest X-ray, blood tests, and culture of the sputum may help confirm the diagnosis. The disease may be classified by where it was acquired with community, hospital, or health care associated pneumonia.Vaccines to prevent certain types of pneumonia are available. Other methods of prevention include handwashing and not smoking. Treatment depends on the underlying cause. Pneumonia believed to be due to bacteria is treated with antibiotics. If the pneumonia is severe, the affected person is generally hospitalized. Oxygen therapy may be used if oxygen levels are low.Pneumonia affects approximately 450 million people globally (7% of the population) and results in about 4 million deaths per year. Pneumonia was regarded by William Osler in the 19th century as "the captain of the men of death". With the introduction of antibiotics and vaccines in the 20th century, survival improved. Nevertheless, in developing countries, and among the very old, the very young, and the chronically ill, pneumonia remains a leading cause of death. Pneumonia often shortens suffering among those already close to death and has thus been called "the old man's friend".

Prokaryote

A prokaryote is usually a unicellular organism, sometimes a multi-cellular 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. In contrast, 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.

In the prokaryotes, all the intracellular water-soluble components (proteins, DNA and metabolites) are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells. Some prokaryotes, such as cyanobacteria, may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles.Molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species. Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus (containing chromosomal DNA) and organelles. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens; these are common in some extreme environments.

Proteobacteria

Proteobacteria is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, Legionellales and many other notable genera. Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.

Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives". Because of the great diversity of forms found in this group, it was named after Proteus, a Greek god of the sea capable of assuming many different shapes and is not named after the Proteobacteria genus Proteus.Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology such as stalks and buds. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter.

The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs, photoautotrophs, and generalist heterotrophs. The type order is the Burkholderiales, comprising an enormous range of metabolic diversity, including opportunistic pathogens.

The Hydrogenophilalia are obligate thermophiles and include heterotrophs and autotrophs. The type order is the Hydrogenophilales.

The Gammaproteobacteria are the largest class in terms of species with validly published names. The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter.

The Acidithiobacillia contain only sulfur, iron and uranium-oxidising autotrophs. The type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp.

The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the anaerobic side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp.

The Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp.

The Oligoflexia are filamentous aerobes. The type order is the Oligoflexales, which contains the genus Oligoflexus.

Streptococcus

Streptococcus is a genus of gram-positive coccus (plural cocci) or spherical bacteria that belongs to the family Streptococcaceae, within the order Lactobacillales (lactic acid bacteria), in the phylum Firmicutes. Cell division in streptococci occurs along a single axis, so as they grow, they tend to form pairs or chains that may appear bent or twisted. (Contrast with that of staphylococci, which divide along multiple axes, thereby generating irregular, grape-like clusters of cells.)

The term was coined in 1877 by Viennese surgeon Albert Theodor Billroth (1829–1894), by combining the prefix "strepto-" (from Ancient Greek: στρεπτός, translit. streptós, lit. 'easily twisted, pliant'), together with the suffix "-coccus" (from Modern Latin: coccus, from Ancient Greek: κόκκος, translit. kókkos, lit. 'grain, seed, berry'.)

Most streptococci are oxidase-negative and catalase-negative, and many are facultative anaerobes (capable of growth both aerobically and anaerobically).

In 1984, many bacteria formerly grouped in the genus Streptococcus were separated out into the genera Enterococcus and Lactococcus. Currently, over 50 species are recognised in this genus. This genus has been found to be part of the salivary microbiome.

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