Acidobacteriota is a

phylum In biology, a phylum (; plural: phyla) 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 ...

Gram-negative 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 wa ...

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.

Description

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,

hot spring A hot spring, hydrothermal spring, or geothermal spring is a spring produced by the emergence of geothermally heated groundwater onto the surface of the Earth. The groundwater is heated either by shallow bodies of magma (molten rock) or by circ ...

s, oceans, caves, and metal-contaminated soils. The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community. Environmental factors such as pH and nutrients have been seen to drive Acidobacteriota dynamics. Many Acidobacteriota are

acidophilic Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 5.0 or below). These organisms can be found in different branches of the tree of life, including Archaea, Bacteria,Becker, A.Types of Bacter ...

, including the first described member of the phylum, ''

Acidobacterium capsulatum ''Acidobacterium capsulatum'' is a bacterium. It is an acidophilic chemoorganotrophic bacterium containing menaquinone. It is gram-negative, facultative anaerobic, mesophilic, non-spore-forming, capsulated, saccharolytic and rod-shaped. It is a ...

''. Other notable species are ''

Holophaga foetida ''Holophaga foetida'' is a bacterium, the type species of its genus. It is a homoacetogenic bacterium degrading methoxylated aromatic compounds. It is gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet s ...

'', ''

Geothrix fermentans ''Geothrix fermentans'' is a rod-shaped, anaerobic bacterium. It is about 0.1 µm in diameter and ranges from 2-3 µm in length. Cell arrangement occurs singly and in chains. ''Geothrix fermentans'' can normally be found in aquatic sed ...

'', ''

Acanthopleuribacter pedis ''Acanthopleuribacter pedis'' is a Gram-negative, rod-shaped bacterium found in marine environments. ''Acanthopleuribacter pedis'' is one of only two species of acidobacteria to have been isolated from animals. Colonies on marine agar are circu ...

'' and '' Bryobacter aggregatus''. Since they have only recently been discovered and the large majority have not been cultured, the

ecology Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overl ...

and

metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...

of these bacteria is not well understood. However, these bacteria may be an important contributor to

ecosystem An ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the syst ...

s, since they are particularly abundant within

soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former ...

s. Members of subdivisions 1, 4, and 6 are found to be particularly abundant in soils. As well as their natural soil habitat, unclassified subdivision 2 Acidobacteriota have also been identified as a contaminant of DNA extraction kit reagents, which may lead to their erroneous appearance in microbiota or metagenomic datasets. Members of subdivision 1 have been found to dominate in low pH conditions. Additionally, Acidobacteriota from acid mine drainage have been found to be more adapted to acidic pH conditions (pH 2-3) compared to Acidobacteriota from soils, potentially due to cell specialization and enzyme stability. The

G+C content G, or g, is the seventh letter in the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is ''gee'' (pronounced ), plural ''gees''. History Th ...

of Acidobacteria genomes are consistent within their subdivisions - above 60% for group V fragments and roughly 10% lower for group III fragments. The majority of Acidobacteriota are considered aerobes. There are some Acidobacteriota that are considered anaerobes within subdivision 8 and subdivision 23. It has been found that some strains of Acidobacteriota originating from soils have the genomic potential to respire oxygen at atmospheric and sub-atmospheric concentrations. Members of the ''Acidobacteriota'' phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments. However, the variation in this phylum may indicate that they may not have the same ecological strategy.

History

The first species, ''

'', of this phylum was discovered in 1991. However, Acidobacteriota were not recognized as a distinct clade until 1997, and were not recognized as a phylum until 2012. First genome was sequenced in 2006.

Metabolism

Carbon

Some members of subdivision 1 are able to use D-glucose, D-xylose, and

lactose Lactose is a disaccharide sugar synthesized by galactose and glucose subunits and has the molecular formula C12H22O11. Lactose makes up around 2–8% of milk (by mass). The name comes from ' (gen. '), the Latin word for milk, plus the suffix ' ...

as carbon sources, but are unable to use

fucose Fucose is a hexose deoxy sugar with the chemical formula C6H12O5. It is found on ''N''-linked glycans on the mammalian, insect and plant cell surface. Fucose is the fundamental sub-unit of the seaweed polysaccharide fucoidan. The α(1→3) li ...

sorbose Sorbose is a ketose belonging to the group of sugars known as monosaccharides. It has a sweetness that is equivalent to sucrose (table sugar). The commercial production of vitamin C (ascorbic acid Vitamin C (also known as ascorbic acid ...

. Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars. Members of subdivision 4 have been found to use

chitin Chitin ( C8 H13 O5 N)n ( ) is a long-chain polymer of ''N''-acetylglucosamine, an amide derivative of glucose. Chitin is probably the second most abundant polysaccharide in nature (behind only cellulose); an estimated 1 billion tons of chit ...

as a carbon source.

Nitrogen

There has been no clear evidence that Acidobacteriota are involved in nitrogen-cycle processes such as

nitrification ''Nitrification'' is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of ...

denitrification Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denit ...

, or

nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...

. However, '' Geothrix fermantans'' was shown to be able to reduce nitrate and contained the norB gene. The NorB gene was also identified in '' Koribacter verstailis'' and '' Solibacter usitatus''. In addition, the presence of the nirA gene has been observed in members of subdivision 1. Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes. Acidobacteriota can use both inorganic and organic nitrogen as their nitrogen sources.

Phylogeny

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the nomenclature, naming and Taxonomy (biology), taxonomy of prokaryotes, following the taxonomy requirements and rulings of the In ...

and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. Th ...

References

External links

''Acidobacteria bacterium Ellin345'' Genome Page

Acidobacterium Genome Projects
(fro
Genomes OnLine Database

Scientific American article

acidoseq, A Python package for studying Acidobacteria
{{Taxonbar, from=Q41579 Acidophiles