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Gemmatimonadota

From Wikipedia, the free encyclopedia
Phylum of bacteria

Gemmatimonadota
Scientific classificationEdit this classification
Domain:Bacteria
Kingdom:Pseudomonadati
Phylum:Gemmatimonadota
Zhang et al. 2021
Classes
Synonyms
  • "Gemmatimonadaeota"Oren et al. 2015
  • "Gemmatimonadota"Whitman et al. 2018
  • "Gemmatimonadetes"Zhang et al. 2003

TheGemmatimonadota are aphylum ofbacteria established in 2003. Thephylum contains two classesGemmatimonadetes andLongimicrobia.

Species

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The type speciesGemmatimonas 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 wasGemmatirosa kalamazoonensis gen. nov., sp. nov. strain KBS708, which was isolated from organically managed agricultural soil in Michigan USA.[3]

The third cultured speciesGemmatimonas 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 viahorizontal 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

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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

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16S rRNA basedLTP_10_2024[10][11][12]120 marker proteins basedGTDB 09-RS220[13][14][15]
Longimicrobia
Longimicrobiales

Longimicrobium

Longimicrobiaceae
"Gemmatimonadia"
Gemmatimonadales
Gemmatimonadaceae

"Glassbacteria" (RIF5)

"Gemmatimonadia"
Gemmatimonadales
Gemmatimonadaceae
Longimicrobiales

Longimicrobium

Longimicrobiaceae
"Palauibacterales"
KS3‑K002
"Palauibacteraceae"

Taxonomy

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The currently accepted taxonomy is based on theList of Prokaryotic names with Standing in Nomenclature (LSPN)[16] andNational Center for Biotechnology Information.[17]

See also

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References

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  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 ofGemmatimonas 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 bacteriumGemmatimonas phototrophica sp. nov., and emended descriptions of the genusGemmatimonas andGemmatimonas 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.hdl:10668/9832.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 ofGemmatimonadetes in Soil".Appl. Environ. Microbiol.77 (17):6295–300.Bibcode:2011ApEnM..77.6295D.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. ^"The LTP". Retrieved10 December 2024.
  11. ^"LTP_all tree in newick format". Retrieved10 December 2024.
  12. ^"LTP_10_2024 Release Notes"(PDF). Retrieved10 December 2024.
  13. ^"GTDB release 09-RS220".Genome Taxonomy Database. Retrieved10 May 2024.
  14. ^"bac120_r220.sp_labels".Genome Taxonomy Database. Retrieved10 May 2024.
  15. ^"Taxon History".Genome Taxonomy Database. Retrieved10 May 2024.
  16. ^J.P. Euzéby."Gemmatimonadetes".List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved2016-03-20.
  17. ^Sayers; et al."Gemmatimonadetes".National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved2016-03-20.

External links

[edit]
Prokaryotes:Bacteria classification
Candidate Phyla
Radiation
"Synergistetes"
"Thermocalda"
"Cyanoprokaryota"
"Firmicutes"
  • Bacillota
  • Bacillota A
    • "Clostridiia"
    • "Thermoanaerobacteria"
    • Thermosediminibacteria
  • Bacillota D
  • Bacillota E
    • Sulfobacillia
    • Symbiobacteriia
    • Thermaerobacteria
  • Bacillota G
    • "Hydrogenisporia"
    • Limnochordia
  • "Desulfotomaculota"
    • "Carboxydocellia"
    • "Carboxydothermia"
    • "Dehalobacteriia"
    • Desulfitobacteriia
    • Desulfotomaculia
    • "Moorellia"
    • Peptococcia
    • Syntrophomonadia
    • Thermincolia
  • "Halanaerobiaeota"
  • "Selenobacteria"
"Sphingobacteria"
"Planctobacteria"
"Proteobacteria"
Incertae sedis
Incertae sedis
GTDB 09-RS220;LTP_10_2024
Extantlife phyla/divisions by domain
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Archaea
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Protist
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Incertae sedis
Gemmatimonadetes
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