Gemmatimonadetes

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Gemmatimonadetes
Scientific classification
Domain:
Bacteria
(unranked):
FCB group
Phylum:
Gemmatimonadetes

Zhang et al. 2003
Class
  • Gemmatimonadetes
Synonyms
  • Gemmatimonadaeota Oren et al. 2015
  • "Gemmatimonadota" Whitman et al. 2018
  • "Glassbacteria" Anantharaman et al. 2016

The Gemmatimonadetes (alternatively Gemmatimonadota) are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia.

Contents

Species

The type species Gemmatimonas aurantiaca strain T-27T was isolated from activated sludge in a sewage treatment system in 2003. [1] It is a Gram-negative bacterium able to grow by both aerobic and anaerobic respiration. [2]

The second cultured species was Gemmatirosa kalamazoonensis gen. nov., sp. nov. strain KBS708, which was isolated from organically managed agricultural soil in Michigan USA. [3]

The third cultured species Gemmatimonas phototrophica strain AP64T was isolated from a shallow freshwater desert lake Tiān é hú (Swan Lake) in North China. [4] A unique feature of this organism is the presence of bacterial photosynthetic reaction centers. It probably acquired genes for anoxygenic photosynthesis via horizontal gene transfer. G. phototrophica is a facultative photoheterotrophic organism. It requires the supply of organic substrate for growth, but it may obtain additional energy for its metabolism from light. [5]

Longimicrobium terrae strain CB-286315T was isolated from a soil sample from a typical Mediterranean forest ecosystem located in Granada, Spain. Due to this large phylogenetic distance from other cultured Gemmatimonades, it established a novel class named Longimicrobia. [6]

Environmental distribution

Data from culture-independent studies indicate that Gemmatimonadetes are widely distributed in many natural habitats. They make up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates. [7] Gemmatimonadetes have been found in a variety of arid soils, such as grassland, prairie, and pasture soil, as well as eutrophic lake sediments and alpine soils. This wide range of environments where Gemmatimonadetes have been found suggests an adaptation to low soil moisture. [8] A study conducted showed that the distribution of the Gemmatimonadetes in soil tends to be more dependent on the moisture availability than aggregation, reinforcing the belief that the members of this phylum prefer dryer soils. [9] Smaller numbers were also found in various aquatic environments, such as fresh waters and sediments.

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN), [10] National Center for Biotechnology Information, [11] All-Species Living Tree Project [12] and GTDB 05-RS95 (Genome Taxonomy Database). [13] [14]

See also

Related Research Articles

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<i>Deinococcus</i> Genus of bacteria

Deinococcus is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum Deinococcus-Thermus highly resistant to environmental hazards. 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 Gram-negative bacteria. Deinococcus survive when their DNA is exposed to high doses of gamma and UV radiation. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, Deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. They are also characterized by the presence of the carotenoid pigment deinoxanthin that give them their pink color. They are usually isolated according to these two criteria. In August 2020, scientists reported that bacteria from Earth, particularly Deinococcus bacteria, were found to survive for three years in outer space, based on studies conducted on the International Space Station. These findings support the notion of panspermia, the hypothesis that life exists throughout the Universe, distributed in various ways, including space dust, meteoroids, asteroids, comets, planetoids or contaminated spacecraft.

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The phylum Elusimicrobia, previously known as "Termite Group 1", has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils, and toxic wastes. The high abundance of 'Elusimicrobia' representatives is only evidenced for the lineage of symbionts found in termites and ants.

The Negativicutes are a class of bacteria in the phylum Firmicutes, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Firmicutes. Although several neighbouring Clostridia species also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Proteobacteria. Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

Actinocorallia is a genus in the phylum Actinobacteria (Bacteria).

Dactylosporangium is a genus in the phylum Actinobacteria (Bacteria).

Agromyces is a genus in the phylum Actinobacteria (Bacteria).

<i>Gemmatimonas aurantiaca</i> Species of bacterium

Gemmatimonas aurantiaca is a Gram-negative, aerobic, polyphosphate-accumulating micro-organism. It is a Gram-negative, rod-shaped aerobe, with type strain T-27T. It replicates by budding.

Chthonomonas calidirosea is a Gram-negative bacterium and also the first representative of the new class Chthonomonadetes within the phylum Armatimonadetes. The Armatimonadetes were previously known as candidate phylum OP10. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to C. calidirosea's relative, Armatimonas rosea's discovery. It is now known that bacterial communities from geothermal environments, are generally constituted by, at least 5–10% of bacteria belonging to Armatimonadetes.

The Coriobacteriia are a class of Gram-positive bacteria within the Actinobacteria phylum. Species within this group are nonsporulating, strict or facultative anaerobes that are capable of thriving in a diverse set of ecological niches. Gordonibacter species are the only members capable of motility by means of flagella within the class. Several species within the Coriobacteriia class have been implicated with human diseases that range in severity. Atopobium, Olsenella, and Cryptobacterium species have responsible for human oral infections including periodontitis, halitosis, and other endodontic infections. Eggerthella species have been associated with severe blood bacteraemia and ulcerative colitis.

Dyadobacter is a genus of gram negative rod-shaped bacteria belonging to the family Spirosomaceae in the phylum Bacteroidetes. Typical traits of the genus include yellow colony colour, positive flexirubin test and non-motile behaviours. They possess an anaerobic metabolism, can utilise a broad range of carbon sources, and test positive for peroxide catalase activity. The type species is Dyadobacter fermentans, which was isolated from surface sterilised maize leaves,.

Mameliella is a genus in the phylum Proteobacteria (Bacteria). The name Mameliella derives from: New Latin feminine gender dim. noun Mameliella, arbitrary name derived from the acronym MMEL, marine microbial ecology laboratory.

Chitinophagaceae is an aerobic or facultatively anaerobic and rod-shaped family of bacteria in the phylum "Bacteroidetes".

References

  1. ↑ Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K (2003). "Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov". Int J Syst Evol Microbiol. 53 (Pt 4): 1155–63. doi: 10.1099/ijs.0.02520-0 . PMID   12892144.
  2. ↑ Takaichi, S; Maoka, T; Takasaki, K; Hanada, S (2009). "Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2,2′-dirhamnoside". Microbiology. 156 (3): 757–763. doi: 10.1099/mic.0.034249-0 . PMID   19959572.
  3. ↑ DeBruyn J.M.; Fawaz M.N.; Peacock, A.D.; Dunlap J.R.; Nixon L.T.; Cooper K.E.; Radosevich M. (2013). "Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarelycultivated bacterial phylum Gemmatimonadetes". J Gen Appl Microbiol. 59 (4): 305–312. doi: 10.2323/jgam.59.305 . PMID   24005180.
  4. ↑ Zeng Y.; Selyanin V.; Lukeš M.; Dean J.; Kaftan D.; Feng F.; Koblížek M. (2015). "Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca". Int J Syst Evol Microbiol. 65 (8): 2410–2419. doi: 10.1099/ijs.0.000272 . PMID   25899503.
  5. ↑ Zeng Y.; Feng F.; Medová H.; Dean J.; Koblížek M. (2014). "Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes". Proc Natl Acad Sci USA. 111 (21): 7795–7800. Bibcode:2014PNAS..111.7795Z. doi: 10.1073/pnas.1400295111 . PMC   4040607 . PMID   24821787.
  6. ↑ Pascual J.; García-López M.; Bills G.F.; Genilloud O. (2016). "Longimicrobium terrae gen. nov., sp. nov., a novel oligotrophic bacterium of the underrepresented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers". Int J Syst Evol Microbiol. 66 (5): 1976–1985. doi: 10.1099/ijsem.0.000974 . PMID   26873585.
  7. ↑ Fawaz, Mariam (2013). "Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils". Master's Thesis, University of Tennessee: vi.
  8. ↑ DeBruyn, J; Nixon, L; Fawaz, M; Johnson, M; Radosevich, M (2011). "Global Biogeography and Quantitative Season Dynamics of Gemmatimonadetes in Soil". Appl. Environ. Microbiol. 77 (17): 6295–300. doi:10.1128/AEM.05005-11. PMC   3165389 . PMID   21764958.
  9. ↑ Fawaz, Mariam (2013). "Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils". Master's Thesis, University of Tennessee: vi.
  10. ↑ J.P. Euzéby. "Gemmatimonadetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  11. ↑ Sayers; et al. "Gemmatimonadetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
  12. ↑ All-Species Living Tree Project "16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database . Retrieved 2015-08-20.
  13. ↑ "GTDB release 05-RS95". Genome Taxonomy Database .
  14. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv   10.1101/771964 . doi:10.1038/s41587-020-0501-8. PMID   32341564. S2CID   216560589.


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