Gemmatimonadota
| Gemmatimonadota | |
|---|---|
| Scientific classification | |
| Domain: | Bacteria |
| Clade: | FCB group |
| Phylum: | Gemmatimonadota Zhang et al. 2021 |
| Classes | |
| Synonyms | |
| |
The Gemmatimonadota are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia.
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 Gemmatimonadota 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] Gemmatimonadota 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 Gemmatimonadota have been found suggests an adaptation to low soil moisture.[8] A study conducted showed that the distribution of the Gemmatimonadota 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, and in meadows and cropland located in boreal ecosystems [1].
Phylogeny
| 16S rRNA based LTP_12_2021[10][11][12] | 120 single copy marker proteins based GTDB 08-RS214[13][14][15] | |||||||||||||||||||||||||||||||||
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Taxonomy
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[16] and National Center for Biotechnology Information.[17]
- Phylum Gemmatimonadota Zhang et al. 2003
- Class Gemmatimonadetes Zhang et al. 2003 ["Gemmatimonadia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020]
- Order ?"Palaucibacterales" Aldeguer-Riquelme, Antón & Santos 2022 [PAUC43f]
- Order Gemmatimonadales Zhang et al. 2003
- Family Gemmatimonadaceae Zhang et al. 2003
- Genus Roseisolibacter Pascual et al. 2018
- Species R. agri Pascual et al. 2018
- Genus "Gemmatirosa" DeBruyn et al. 2013
- Species G. kalamazoonesis DeBruyn et al. 2013
- Genus Gemmatimonas Zhang et al. 2003 em. Zeng et al. 2015
- Species G. aurantiaca Zhang et al. 2003 em. Zeng et al. 2015
- Species "G. groenlandica" Zeng et al. 2020
- Species G. phototrophica Zeng et al. 2015
- Genus Roseisolibacter Pascual et al. 2018
- Family Gemmatimonadaceae Zhang et al. 2003
- Class Longimicrobia Pascual et al. 2016
- Order Longimicrobiales Pascual et al. 2016
- Family Longimicrobiaceae Pascual et al. 2016
- Genus Longimicrobium Pascual et al. 2016
- Species L. terrae Pascual et al. 2016
- Genus Longimicrobium Pascual et al. 2016
- Family Longimicrobiaceae Pascual et al. 2016
- Order Longimicrobiales Pascual et al. 2016
- Class Gemmatimonadetes Zhang et al. 2003 ["Gemmatimonadia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020]
See also
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Fawaz, Mariam (2013). "Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils". Master's Thesis, University of Tennessee: vi.
- ^ 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. Bibcode:2011ApEnM..77.6295D. doi:10.1128/AEM.05005-11. PMC 3165389. PMID 21764958.
- ^ Fawaz, Mariam (2013). "Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils". Master's Thesis, University of Tennessee: vi.
- ^ "The LTP". Retrieved 23 February 2021.
- ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
- ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
- ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ J.P. Euzéby. "Gemmatimonadetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
- ^ Sayers; et al. "Gemmatimonadetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
External links
- Brief taxonomy
- Fawaz, M. N. (2013). Revealing the Ecological Role of Gemmatimonadetes Through Cultivation and Molecular Analysis of Agricultural Soils. 44–60. Brief review of the phylum.
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