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In bacteriology, 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 type of cell wall.
The "Actinobacteria" are a phylum of mostly 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 help to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. While this role is also played by fungi, Actinobacteria are much smaller and likely do not occupy the same ecological niche. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales, reflects that they were long believed to be fungi. Some soil actinobacteria 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 the genus Mycobacterium, are important pathogens.
Deinococcus–Thermus is a phylum of bacteria with a single order, Deinococci, 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.
The phylum "Bacteroidetes" is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.
"Candidatus Pelagibacter", with the single species "Ca. P. communis", 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. "Ca. P. communis" 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 "Ca. P. communis" and relatives is estimated to be about 2 × 1028 microbes.
Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm 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.
In prokaryote nomenclature, Candidatus is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide much information about the analyzed organisms and thus allow to identify and characterize individual species. However, the majority of prokaryotic species remain uncultivable and hence inaccessible for further characterization in in vitro study. The recent discoveries of a multitude of candidate taxa has led to candidate phyla radiation expanding the tree of life through the new insights in bacterial diversity.
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.
Fibrobacteres is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.
The Chloroflexi or Chlorobacteria are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis ; and anaerobic halorespirers, which uses halogenated organics as electron acceptors.
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 contains approximately 31 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 Thaumarchaeota or Thaumarchaea are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Crenarchaeota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Thaumarchaea, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.
The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacteres, Chlorobi, and Bacteroidetes. The members are considered to form a clade due to a number of conserved signature indels.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.
This is a list of terms and symbols used in scientific names for organisms, and in describing the names. For proper parts of the names themselves, see List of Latin and Greek words commonly used in systematic names. Note that many of the abbreviations are used with or without a stop.
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (Porifera). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation, glycolysis, and autotrophic carbon fixation via the Wood – Ljungdahl pathway. Poribacterial heterotrophy is characterised by an enriched set of glycoside hydrolases, uronic acid degradation, as well as several specific sulfatases. This heterotrophic repertoire of poribacteria was suggested to be involved in the degradation of the extracellular sponge host matrix.
The Latescibacteria, OD1, OP11, TM7 RNA motif is a conserved RNA structure that was discovered by bioinformatics. LOOT motif RNAs are found in multiple bacterial phyla that have only recently been discovered, and are currently not well understood: Latescibacteria, OD1/Parcubacteria, OP11 AND TM7. In some cases, no specific organism has been isolated in the relevant phylum, but the existence of the bacterial phylum is known only through analysis of metagenomic sequences. Curiously, the LOOT motif is not known in any phylum that has been studied for a long time.
Zixibacteria is a bacterial phylum with candidate status, meaning it had no cultured representatives. It is a member of the FCB group
References
- ↑ 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. doi:10.1128/JB.180.18.4765-4774.1998. PMC 107498 . PMID 9733676.
- ↑ Frederiksen W (1995). "Judicial commission of the international committee on systematic bacteriology: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic" (PDF). Int. J. Syst. Bacteriol. 45 (1): 195–196. doi: 10.1099/00207713-45-1-195 .