|Transmission electron micrograph of Wolbachia within an insect cell.|
Credit:Public Library of Science / Scott O'Neill
Garrity et al. 2006
Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy).Its members are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.
In biological classification, class is a taxonomic rank, as well as a taxonomic unit, a taxon, in that rank. Other well-known ranks in descending order of size are life, domain, kingdom, phylum, order, family, genus, and species, with class fitting between phylum and order. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the prefix sub-: subclass. For example, dogs are in the class Mammalia.
Bacteria 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, 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. The study of bacteria is known as bacteriology, a branch of microbiology.
In biology, a phylum is a level of classification or taxonomic rank below Kingdom and above Class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 35 phyla, the plant kingdom Plantae contains about 14, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta.
The Alphaproteobacteria is a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds (e.g., Methylobacteriumspp.), symbionts of plants (e.g., Rhizobium spp.), endosymbionts of arthropods ( Wolbachia ) and intracellular pathogens (e.g. Rickettsia ). Moreover, the class includes (as an extinct member) the protomitochondrion, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells (See endosymbiotic theory).A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique , are alphaproteobacteria that are a widely distributed and may constitute over 10% of the open ocean microbial community.
Phototrophs are the organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes. All phototrophs either use electron transport chains or direct proton pumping to establish an electro-chemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either autotrophs or heterotrophs. As their electron and hydrogen donors are inorganic compounds [Na
3 (PSB) and H
2S (GSB)] they can be also called as lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms: Rhodobacter capsulatus, Chromatium, Chlorobium etc.
Rhizobium is a genus of Gram-negative soil bacteria that fix nitrogen. Rhizobium species form an endosymbiotic nitrogen-fixing association with roots of legumes and Parasponia.
An endosymbiont or endobiont is any organism that lives within the body or cells of another organism in a mutualistic relationship with the host body or cell, often but not always to mutual benefit. The term endosymbiosis is from the Greek: ἔνδον endon "within", σύν syn "together" and βίωσις biosis "living"). Examples are nitrogen-fixing bacteria, which live in root nodules on legume roots, single-cell algae inside reef-building corals, and bacterial endosymbionts that provide essential nutrients to about 10–15% of insects.
There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales , but overall there is some consensus. The discord stems from the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-richness[ jargon ] between members of several orders. Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes.[ jargon ] It has been argued[ by whom? ] that it could be a case of convergent evolution that would result in an artefactual clustering. However, several studies disagree.
In biological classification, the order is
The Pelagibacterales is an order in the Alphaproteobacteria composed of free-living bacteria that make up roughly one in three cells at the ocean's surface. Overall, members of the Pelagibacterales are estimated to make up between a quarter and a half of all prokaryotic cells in the ocean.
Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.
Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales , even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.
Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight, or 3/5 of ribosome mass. Ribosomes contain two major rRNAs and 50 or more proteins. The ribosomal RNAs form two subunits, the large subunit (LSU) and small subunit (SSU). The LSU rRNA acts as a ribozyme, catalyzing peptide bond formation. The SSU and LSU rRNA sequences are widely used for working out evolutionary relationships among organisms, since they are of ancient origin and are found in all known forms of life.
The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria that are endosymbionts of eukaryotic cells. Some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans, and Ehrlichia, which causes diseases in livestock. Another genus of well-known Rickettsiales are the Wolbachia, which infect approximately two-thirds of all arthropods and nearly all filarial nematodes. Genetic studies support the endosymbiotic theory according to which mitochondria and related organelles developed from members of this group.
The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae.The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales. The Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales.
In phylogenetics, basal is the direction of the base of a rooted phylogenetic tree or cladogram. The term may be more strictly applied only to nodes adjacent to the root, or more loosely applied to nodes regarded as being close to the root. Each node in the tree corresponds to a clade; i.e., clade C may be described as basal within a larger clade D if its root is directly linked to the root of D. The terms deep-branching or early-branching are similar in meaning.
Magnetotactic bacteria are a polyphyletic group of bacteria that orient themselves along the magnetic field lines of Earth's magnetic field. Discovered in 1963 by Salvatore Bellini and rediscovered in 1975 by Richard Blakmore, this alignment is believed to aid these organisms in reaching regions of optimal oxygen concentration. To perform this task, these bacteria have organelles called magnetosomes that contain magnetic crystals. The biological phenomenon of microorganisms tending to move in response to the environment's magnetic characteristics is known as magnetotaxis. In contrast to the magnetoreception of animals, the bacteria contain fixed magnets that force the bacteria into alignment—even dead cells are dragged into alignment, just like a compass needle.
Comparative analyses of the sequenced genomes have also led to discovery of many conserved insertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae).
Whole genome sequencing is ostensibly the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. In practice, genome sequences that are nearly complete are also called whole genome sequences.
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.
Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that may be separated by many years, and may not be related to each other in any way. A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides.
These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups.Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)
Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens ,Methylobacterium organophilum , and Bradyrhizobium japonicum . Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination.
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.
Deinococcus–Thermus is a phylum of bacteria that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria.
Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.
Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are caused by the insertion of a small segment of DNA, from a plasmid, into the plant cell, which is incorporated at a semi-random location into the plant genome.
Agrobacterium is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. Agrobacterium tumefaciens is the most commonly studied species in this genus. Agrobacterium is well known for its ability to transfer DNA between itself and plants, and for this reason it has become an important tool for genetic engineering.
Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name, although it has not yet been described as required by the bacteriological code. It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide – possibly the most numerous bacterium in the world, and were originally known only from their rRNA genes, which were first identified in environmental samples from the Sargasso Sea in 1990 by Stephen Giovannoni's laboratory in the Department of Microbiology at Oregon State University and later found in oceans worldwide. P. ubique and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of P. ubique and relatives is estimated to be about 2 × 1028 microbes.
The Rhizobiaceae is a family of proteobacteria comprising multiple subgroups that enhance and hinder plant development. Some bacteria found in the family are used for plant nutrition and collectively make up the rhizobia. Other bacteria such as Agrobacterium tumefaciens and A. rhizogenes severely alter the development of plants in their ability to induce crown galls or hairy roots found on the stem. The family has been of an interest to scientists for centuries in their ability to associate with plants and modify plant development. The Rhizobiaceae are, like all Proteobacteria, Gram-negative. They are aerobic, and the cells are usually rod-shaped. Many species of the Rhizobiaceae are diazotrophs which are able to fix nitrogen and are symbiotic with plant roots.
Caulobacteraceae is a family of proteobacteria, given its own order (Caulobacterales) within the alpha subgroup. Like all Proteobacteria, the Caulobacteraceae are gram-negative. Caulobacteraceae includes the genera Asticcacaulis, Brevundimonas, Phenylobacterium and Caulobacter.
The Rhizobiales are an order of Gram-negative Alphaproteobacteria.
The Holosporaceae are a family of bacteria, formerly included in the order Rickettsiales, but now raised to their own order, the Holosporales. The member Holospora is an intracellular parasite found in the unicellular protozoa Paramecium.
The proto-mitochondrion is the hypothetical ancestral bacterial endosymbiont from which all mitochondria in eukaryotes are thought to descend.
Midichloria is a genus of Gram-negative, non spore-forming bacteria, with bacillus shape around 0.45 µm in diameter and 1.2 µm in length. First described in 2004 with the temporary name IricES1, Midichloria species are symbionts of the hard tick Ixodes ricinus. They live in the cells of the ovary of the females of this tick species. These bacteria have been observed in the mitochondria of the host cells, a trait that has never been described in any other symbiont of animals.
The SAM-II riboswitch is a RNA element found predominantly in alpha-proteobacteria that binds S-adenosyl methionine (SAM). Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens, and other methionine and SAM biosynthesis genes in other alpha-proteobacteria. Like the other SAM riboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM-II riboswitches was found in Pelagibacter ubique and related marine bacteria and called SAM-V. Also, like many structured RNAs, SAM-II riboswitches can tolerate long loops between their stems.
There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.
Allorhizobium vitis is a plant pathogen that infects grapevines. The species is best known for causing a tumor known as crown gall disease. One of the virulent strains, A. vitis S4, is responsible both for crown gall on grapevines and for inducing a hypersensitive response in other plant species. Grapevines that have been affected by crown gall disease produce fewer grapes than unaffected plants. Though not all strains of A. vitis are tumorigenic, most strains can damage plant hosts.
Magnetococcus marinus is a species of Alphaproteobacteria that has the peculiar ability to form a structure called a magnetosome, a membrane encased single-magnetic-domain mineral crystals formed by biomineralisation, which allows the cells to orientate along the Earth’s geomagnetic field.
Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell's genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.