Many major lineages, called phyla, of Bacteria are known from the study of laboratory cultures, and many others have been identified from the retrieval and sequencing of ribosomal RNA (rRNA) genes from microbial communities in natural habitats. It clearly shows, the most phylogenetically ancient (least derived) phylum contains the genus Aquifex and relatives, all of which are hyperthermophilic H2
-oxidizing chemolithotrophs. Other “early” phyla such as Thermodesulfobacterium, Thermotoga and the Chloroflexus group (green nonsulfur bacteria) also contain thermophilic species. Continuing past the green nonsulfur bacteria, we see the deinococci and relatives, the morphologically unique spirochetes, the phototrophic green sulfur bacteria, the chemoorganotrophic Flavobacterium and Cytophaga groups, the budding Planctomyces–Pirellula and the Verrucomicrobium groups, the Chlamydia, and the genera Nitrospira and Deferribacter. Other major groups include the gram-positive bacteria and the cyanobacteria. The gram-positive bacteria are a large group of primarily chemoorganotrophic Bacteria. They can be separated into two subgroups called the Firmicutes and the Actinobacteria. The cyanobacteria are oxygenic phototrophic bacteria with evolutionary roots near those of the gram-positive Bacteria. The remaining phylum of cultured Bacteria, the Proteobacteria, is by far the largest and most metabolically diverse of all Bacteria.
Major phyla of Bacteria
Proteobacteria constitute the majority of known bacteria of medical, industrial and agricultural significance. As a group, the Proteobacteria are all gram-negative bacteria. They show an exceptionally wide diversity of energy-generating mechanisms, with chemolithotrophic, chemoorganotrophic, and phototrophic species. They have the great diversity of energy metabolisms used by various representatives of this group. The Proteobacteria are equally diverse in terms of their relationship to oxygen (O2), with anaerobic, microaerophilic, and facultatively aerobic species known. Morphologically, they also exhibit a wide range of cell shapes, including straight and curved rods, cocci, spirilla, filamentous, budding and appendaged forms. Based on 16S rRNA gene sequences, the phylum Proteobacteria can be divided into six classes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, and Zetaproteobacteria, each containing many genera and species. The Zeta class is currently composed of only one organism, the marine iron-oxidizing bacterium Mariprofundus, but other relatives almost certainly exist. Despite the phylogenetic breadth of the Proteobacteria, species in different classes often have similar or even identical metabolisms. For example, phototrophy and methylotrophy occur in species of three different classes of Proteobacteria and ammonia and nitrite-oxidizing (nitrifying) bacteria span four different classes of Proteobacteria plus an additional genus that forms the heart of a separate phylum of Bacteria. The sharing of metabolic traits in the different classes of Proteobacteria is also a good reminder that phenotype and phylogeny often give different views of prokaryotic diversity.
All "Proteobacteria" are gram-negative (though some may stain Gram-positive or Gram-variable in practice), with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are nonmotile or rely on bacterial gliding. The latter include the Myxobacteriales, an order of bacteria that can aggregate to form multicellular fruiting bodies. Also, a wide variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, chemolithoautotrophic, and heterotrophic, but numerous exceptions occur. A variety of genera, which are not closely related to each other, convert energy from light through photosynthesis.
The "Proteobacteria" are divided into six classes with validly published names, referred to by the Greek letters alpha through epsilon, zeta and the Acidithiobacillia and Oligoflexia. These were previously regarded as subclasses of the phylum, but they are now treated as classes. These classes are monophyletic. The genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies. In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales.
Proteobacterial classes with validly published names include some prominent genera: e.g.:
Nitrosomonas and Nitrobacter: Bacteria able to grow hemolithotrophically at the expense of reduced inorganic nitrogen compounds are called nitrifying bacteria. These two are belongs to nitrifying bacteria. Nitrification results from the sequential activities of two physiological groups of organisms, the ammonia-oxidizing bacteria (which oxidize NH3 to nitrite, NO2-) and the nitrite-oxidizing bacteria, the actual nitrate-producing bacteria, which oxidize NO2 - toNO3-. Ammonia-oxidizing bacteria typically have genus names beginning in Nitroso-, whereas genus names ofnitrate producers begin with Nitro-.
Pseudomonas: The cells are straight or slightly curved gram negative, chemoorganotrophic rods with polar flagella. Some major distinguishing characteristics of the pseudomonad group include an obligately respiratory metabolism, the absence of gas formation from glucose and a positive oxidase test, all of which help to distinguish pseudomonads from enteric bacteria. Pseudomonads typically have very simple nutritional requirements and one of their characteristic properties is the ability to use many different organic compounds as carbon and energy sources; some species utilize over 100 different compounds. The pseudomonads are ecologically important in soil and water and are probably responsible for the degradation of many low-molecular-weight compounds derived from the breakdown of plant and animal materials in oxic habitats. They are also capable of catabolizing many xenobiotic (not naturally occurring) compounds, such as pesticides and other toxic chemicals, and are thus important agents of bioremediation in the environment. Pseudomonas fluorescens is a plant-associated rhizobacteria helping the plant growth. Pseudomonas aeruginosa is frequently associated with infections of the urinary and respiratory tracts in humans.
Azotobacter: Azotobacter is a free-living chemoorganotrophic bacteria inhabit soil and is capable of aerobic nitrogen (N2) fixation. When they are growing on N2 as a nitrogen source, extensive capsules or slime layers. Azotobacter can form resting structures called cysts. Like bacterial endospores, Azotobacter cysts show negligible endogenous respiration and are resistant to desiccation, mechanical disintegration, and ultraviolet and ionizing radiation. Cysts are not very heat resistant, and they are not completely dormant because they rapidly oxidize carbon sources if supplied.
Enteric bacteria (Escherichia): The enteric bacteria comprise a relatively homogeneous phylogenetic group within the Gammaproteobacteria and consist of facultatively aerobic, gram-negative, nonsporulating rods that are either nonmotile or motile by peritrichous flagella. Among the enteric bacteria are many species pathogenic to humans, other animals, or plants, as well as other species of industrial importance. Escherichia coli, the best known of all microorganisms, is the classic example of an enteric bacterium. Escherichia, Salmonella, Proteus, Enterobacter are the key genera belongs to this group.
Spirilla: The spirilla are gram-negative, motile, spiral-shaped bacteria that show a wide variety of physiological attributes. Some key taxonomic criteria used are cell shape, size, and number of flagella, relation to oxygen (obligately aerobic, microaerophilic), relationship to higher organisms, and certain other physiological characteristics, such as nitrogen fixation and halophilism. Azospirillum lipoferum is a nitrogen-fixing organism and of considerable interest because it enters into a symbiotic relationship with tropical grasses and grain crops such as corn. Spirillum, Aquaspirillum, Oceanospirillum, and Azospirillum are the key genera belong to this group.
Vibrio: The Vibrio group contains gram-negative, facultatively aerobic rods and curved rods that employ a fermentative metabolism. Most species of Vibrio are polarly flagellated, although some are peritrichously flagellated. One key difference between the Vibrio group and enteric bacteria is that members of the former are oxidase-positive, a test for the presence of cytochrome c, whereas members of the latter are oxidase-negative. The best-known genera in this group are Vibrio, Aliivibrio, and Photobacterium. Most vibrios and related bacteria are aquatic, found in marine, brackish, or freshwater habitats. Vibrio cholerae is the specific cause of the disease cholera in humans. Cholera is one of the most common human infectious diseases in developing countries and is transmitted almost exclusively via water.
Rhizobium: Rhizobia are species of Alpha- or Betaproteobacteria that can grow freely in soil or can infect leguminous plants and establish a symbiotic relationship. The same genus (or even species) can contain both rhizobial and nonrhizobial strains. Infection of legume roots by rhizobia leads to the formation of root nodules in which the bacteria fix gaseous nitrogen. Nitrogen fixation in root nodules accounts for a fourth of the N2 fixed annually on Earth and is of enormous agricultural importance, as it increases the fixed nitrogen content of soil. Nodulated legumes can grow well on unfertilized bare soils that are nitrogen deficient, while other plants grow only poorly on them.
This is an ecologically and industrially important group of microorganisms. The group name refers to a phylum of Bacteria, also known as the Low G+C Gram Positive Bacteria, its members share a common evolutionary history. Many have certain distinct cellular characteristics. Gram-positive organisms stain purple with a differential staining procedure developed in 1884 by Christian Gram. This procedure identifies cells that have a thick cell wall of peptidoglycan. While many Firmicutes stain Gram-positive, some do not. In fact, some Firmicutes have no cell wall at all! They are called "low G+C" because their DNA typically has fewer G and C DNA bases than A and T bases as compared to other bacteria. Exceptions have been identified and some Firmicutes have G+C content as high as 55% (e.g. Geobacillus thermocatenulatus). Certain Firmicutes make resistant progeny called endospores, while others can only reproduce through binary fission. It is evident that Firmicutes are as diverse as they are important.
The typical Firmicutes cell envelope consists of a layer of peptidoglycan, which is a polymer of protein and carbohydrate that gives structure and shape to the cell and protects the bacterium from osmotic stress. Underneath the peptidoglycan there is a phospholipid bilayer and its associated proteins that act as a selective barrier. Many members of the Firmicutes have an outermost envelope layer of protein called the S layer. The function of the S layer is not known but it is believed to prevent predation in the environment.
Groups of Firmicutes have been classified based on characteristics like type of cell envelope, endospore formation and aerotolerance (how well they live and grow in oxygen). Currently, there are seven recognized Classes of Firmicutes: the Erysipelotrichia, the Negativicutes, the Limnochordia, the Tissierellia, the Thermolithobacteria, the Clostridia and the Bacilli.
Most Firmicutes have cell walls, and these bacteria can be found in a great variety of habitats. They are grouped in the Class Bacilli or Class Clostridia. Diverse Firmicutes include Staphylococcus, Micrococcus, Streptococcus and Lactobacillus. Some staphylococci and micrococci are commonly found on human skin and mucosal surfaces. Streptococcus is most famous for causing "strep throat" but many benign streptococci are normally found in the mouth and throat. Lactobacillus is common in the making of yogurt and cheese products. Some Lactobacillus species are associated with mucosal surfaces of humans. These resident Lactobacillus species help maintain our health by preventing colonization by disease-associated bacteria. The species of Lactobacillus are considered as Probiotic bacteria.
Some Firmicutes can form an endospore, a resistant differentiated cell produced under special, usually stressful, conditions. Endospore-forming bacteria such as Bacillus and Clostridium species can be classified by their aerotolerance. Many anaerobic organisms fall under the Clostridium banner. These organisms have very diverse ways of getting energy without using oxygen, but almost all are fermenters. Some Clostridium species are used by industry to produce solvents, an end product of their fermentation activity. Others produce toxins. One famous application of a Clostridium toxin is the use of Clostridium botulinum toxin, also known as BoTox, to paralyze muscles of the face to reduce skin wrinkles. Epulopiscium is closely related to Clostridium species.
Bacilli prefer to live in oxygen-rich environments but some are capable of survival without it. Members of this group are commonly found in soil. Some are responsible for the disease anthrax while others produce antibiotics or insecticides. Bacillus subtilis is one of the primary model organisms used by researchers to understand topics ranging from cell differentiation to iron storage and DNA replication.
The organisms described above represent only a tiny part of the diversity found within the group of Firmicutes. Their huge impact on fields as diverse as agriculture, medicine, food production and ecology make them a vital subject of inquiry.
The genus Bacillus and Paenibacillus: Species of Bacillus and Paenibacillus grow well on defined media containing any of a number of carbon sources. Many bacilli produce extracellular hydrolytic enzymes that break down complex polymers such as polysaccharides, nucleic acids, and lipids, permitting the organisms to use these products as carbon sources and electron donors. Many bacilli produce antibiotics, including bacitracin, polymyxin, tyrocidine, gramicidin, and circulin. In most cases the antibiotics are released when the culture enters the stationary phase of growth and is committed to sporulation.
The genus Clostridium: The clostridia lack a respiratory chain; unlike Bacillus species, they obtain ATP only by substrate-level phosphorylation. Many anaerobic energy-yielding mechanisms are known in the clostridia. A number of clostridia are saccharolytic and ferment sugars, producing butyric acid as a major end product. Some of these also produce acetone and butanol, such as Clostridium pasteurianum, which is also a vigorous nitrogen-fixing bacterium. One group of clostridia ferments cellulose with the formation of acids and alcohols, and these are likely the major organisms decomposing cellulose anaerobically in soil.
The genus Lactobacillus: Lactobacilli are typically rod-shaped, varying from long and slenderto short, bent rods. Lactobacilli are common in dairy products, and some strains are used in the preparation of fermented milk products. For instance,Lactobacillus acidophilus is used in the production of acidophilus milk; Lactobacillus delbrueckii is used in the preparation of yogurt; and other species are used in the production of sauerkraut, silage, and pickles. The lactobacilli are usually more resistant to acidic conditions than are the other lactic acid bacteria and are able to grow well at pH values as low as 4. Because of this, they can be selectively enriched from dairy products and fermenting plant material by use of acidic carbohydrate-containing media. The acid resistance of the lactobacilli enables them to continue growing during natural lactic fermentations, even when the pH value has dropped too low for other lactic acid bacteria to grow. The lactobacilli are therefore typically responsible for the final stages of most lactic acid fermentations.
It is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis (meaning "soft" or "pliable"), and cutis (meaning "skin"). Individuals are very small, typically only 0.2–0.3 μm (200-300 nm) in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma.
Mollicutes are parasites of various animals and plants, living on or in the host's cells. Many cause diseases in humans, attaching to cells in the respiratory or urogenital tracts, particularly species of Mycoplasma and Ureaplasma. Phytoplasma and Spiroplasma are plant pathogens associated with insect vectors.
Whereas formerly the trivial name "mycoplasma" has commonly denoted any member of the class Mollicutes, it now refers exclusively to a member of the genus Mycoplasma.
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities.
Most of the Actinobacteria (the streptomycetes in particular) are saprophytic, soil-dwelling organisms that spend the majority of their life cycles as semi dormant spores, especially under nutrient limited conditions. However, the phylum has adapted to a wide range of ecological environments: actinomycetes are also present in soils, fresh and salt water, and the air. They are more abundant in soils than other media, especially in alkaline soils and soils rich in organic matter, where they constitute an important part of the microbial population. Actinobacteria can be found both on the soil surface and at depths of more than 2 m below ground.
The population density of Actinobacteria depends on their habitat and the prevailing climate conditions. They are typically present at densities on the order of 10^6 to 10^9 cells per gram of soil; soil populations are dominated by the genus Streptomyces, which accounts for over 95% of the Actinomycetales strains isolated from soil. Other factors, such as temperature, pH, and soil moisture, also influence the growth of Actinobacteria. Like other soil bacteria, Actinobacteria are mostly mesophilic, with optimal growth at temperatures between 25 and 30°C. However, thermophilic Actinobacteria can grow at temperatures ranging from 50 to 60°C. Vegetative growth of Actinobacteria in the soil is favored by low humidity, especially when the spores are submerged in water. In dry soils where the moisture tension is greater, growth is very limited and may be halted. Most Actinobacteria grow in soils with a neutral pH. They grow best at a pH between 6 and 9, with maximum growth around neutrality. However, a few strains of Streptomyces have been isolated from acidic soils (pH3.5).
The genus Mycobacterium. This group shares an unusual waxy cell envelope that contains mycolic acids, meaning these bacteria are unusual in being acid fast and alcohol fast. The mycobacterial cell wall contains various polysaccharide polymers, including arabinogalactan, lipomannan, lipoarabinomannan, and phosphatidylinositol mannosides. Mycobacteria are generally free-living saprophytes and they are the causative agents of a broad spectrum of human diseases. Mycobacterial diseases are very often associated with immunocompromised patients, especially those with AIDS. In addition, M. bovis and M. tuberculosis, isolated initially from infected animals, are most likely obligate parasites of humans. Both species can survive within macrophages and cause pulmonary disease, although organs other than lungs may be affected. M. leprae, which causes leprosy, lives in Schwann cells and macrophages; infection with this species results in a chronic granulomatous disease of the skin and peripheral nerves. Interestingly, the pathogenic M. ulcerans, which is the third most common causative agent of mycobacterial disease, has also been isolated as a soil inhabitant in symbiosis with roots of certain plants living in tropical rain forests and similar environments.
The genus Nocardia. The genus Nocardia is a ubiquitous group of environmental bacteria that is most widely known as the causative agent of opportunistic infection in immunocompromised hosts. Nocardia species are ubiquitous soilborne aerobic actinomycetes, with more than 80 different species identified, of which at least 33 are pathogenic. The pathogen can spread to the brain, kidneys, joints, bones, soft tissues, and eyes, causing disseminated nocardiosis in humans and animals. Moreover, Nocardia species produce industrially important bioactive molecules, such as antibiotics and enzymes.
The genus Corynebacterium: Among the known pathogenic members of Corynebacterium are C. diphtheria, which is a notorious strictly human-adapted species and the causative agent of the acute, communicable disease diphtheria, which is characterized by local growth of the bacterium in the pharynx along with the formation of an inflammatory pseudomembrane. The virulence factor in diphtheria is an exotoxin that targets host protein synthesis. Another important Corynebacterium pathogen is C. ulcerans, which is increasingly acknowledged as an emerging pathogen in various countries; infections with this species can mimic diphtheria.
The genus Bifidobacterium. Bifidobacterium has different shapes, including curved, short and bifurcated Y shapes. The cells have no capsule and they are non-sporeforming, nonmotile and nonfilamentous bacteria. The genus encompasses bacteria with health-promoting or probiotic properties, such as antimicrobial activity against pathogens that is mediated through the process of competitive exclusion and also bile salt hydrolase activity, immune modulation, and the ability to adhere to mucus or the intestinal epithelium. This bacterium is considered as one of the Probiotic bacteria.
The genus Streptomyces. Among the various mycelial genera of Actinobacteria, Streptomyces has received particular attention for several reasons: (1) Streptomyces are abundant and important in the soil, where they play major roles in the cycling of carbon trapped in insoluble organic debris, particularly from plants and fungi (Carbon sequestration). This action is enabled by the production of diverse hydrolytic exoenzymes. (2) the genus exhibits a fairly wide phylogenetic spread. Third, streptomycetes are among Nature’s most competent chemists and produce a stunning multitude and diversity of bioactive secondary metabolites; consequently, they are of great interest in medicine and industry.
The genus Frankia. Frankia is the only nitrogen-fixing actinobacterium and can be distinguished by its ability to enter into symbiotic associations with diverse woody angiosperms known collectively as actinorhizal plants. The most notable plant genera in this group are Alnus, Casuarina, and Elaeaginus, and their symbiosis with Frankia enables them to grow well in nitrogen-poor soils.
Cyanobacteria comprise a large, morphologically and ecologically heterogeneous group of oxygenic, phototrophic Bacteria. Cyanobacteria represent one of the major phyla of Bacteria and show a distant relationship to gram-positive bacteria. These organisms were the first oxygen-evolving phototrophic organisms on Earth, and over billions of years converted the originally anoxic atmosphere of Earth to the highly oxic atmosphere we see today.
The morphological diversity of the cyanobacteria is impressive. Both unicellular and filamentous forms are known, and there is considerable variation within these morphological types. Cyanobacteria can be divided into five morphological groups: (1) unicellular, dividing by binary fission; (2) unicellular, dividing by multiple fission (colonial); (3) filamentous, containing differentiated cells called heterocysts that function in nitrogen fixation; (4) filamentous non-heterocystous forms; and (5) branching filamentous species
Cyanobacterial cells range in size from 0.5–1 µm in diameter to cells as large as 40 µm in diameter. Phylogenetically, cyanobacteria group along morphological lines in most cases. Filamentous, heterocystous, and nonheterocystous species form distinct groups, as do the branching forms. However, unicellular cyanobacteria are highly diverse, with different representatives showing phylogenetic relationships to different morphological groups. The cell wall of cyanobacteria is similar to that of gram negative bacteria, and peptidoglycan is present in the walls. Many cyanobacteria produce extensive mucilaginous envelopes. The photosynthetic membrane system is often complex and multilayered, although the thylakoid membranes are regularly arranged in concentric circles around the periphery of the cytoplasm in some of the structurally simpler cyanobacteria. Cyanobacteria produce chlorophyll a, and all of them also have characteristic biliprotein pigments, phycobilins, which function as accessory pigments in photosynthesis. One class of phycobilins, phycocyanins, are blue and together with the green chlorophyll a, are responsible for the blue-green color of most cyanobacteria (in past these group of bacteria were called as Blue Green Algae). However, some cyanobacteria produce phycoerythrin, a red phycobilin, and species producing phycoerythrin are red or brown.
The rickettsias are small, gram-negative, coccoid or rod-shaped Alpha- or Gammaproteobacteria in the size range of 0.3–0.7 x 1–2 µm. They are, obligate intracellular parasites and have not yet been cultivated in the absence of host cells. Rickettsias are the causative agents of several human diseases, including typhus, Rocky Mountain spotted fever, and Q fever. The penetration of a host cell by a rickettsial cell is an active process, requiring both host and parasite to be alive and metabolically active. Once inside the host cell, the bacteria multiply primarily in the cytoplasm and continue replicating until the host cell is loaded with parasites. The host cell then bursts and liberates the bacterial cells. Rickettsias do not survive long outside their hosts, and they must be transmitted from animal to animal by arthropod vectors.
The chlamydia, a group of very small gram negative bacteria that cause some serious human and animal diseases. Organisms of the genera Chlamydia and Chlamydophila are obligate intracellular parasites with poor metabolic capacities; they constitute the phylum Chlamydia. Several species are recognized: Chlamydophila psittaci, the causative agent of the disease psittacosis; Chlamydia trachomatis, the causative agent of trachoma and a variety of other human diseases; and Chlamydophila pneumoniae, the cause of some respiratory syndromes. Chlamydia having two cellular types are seen in the life cycle: (1) a small, dense cell, called an elementary body, which is relatively resistant to drying and is the means of dispersal, and (2) a larger, less dense cell, called a reticulate body, which divides by binary fission and is the vegetative form.