Verrucomicrobiota

Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes.

Verrucomicrobiota
Transmission electron micrograph of stage II epixenosomes.
Scientific classification
Domain: Bacteria
Superphylum: PVC superphylum
Phylum: Verrucomicrobiota
Hedlund 2021[1]
Classes
  • Opitutae
  • "Methylacidiphilae"
  • Terrimicrobia
  • Verrucomicrobiae
Synonyms
  • "Verrucomicrobaeota" Oren et al. 2015
  • "Verrucomicrobia" Hedlund et al. 1997
  • "Verrucomicrobia" Hedlund 2010
  • "Verrucomicrobia" Yoon et al. 2010
  • "Verrucomicrobiota" Whitman et al. 2018

Verrucomicrobiota are abundant within the environment, though relatively inactive.[2] This phylum is considered to have two sister phyla: Chlamydiota (formerly Chlamydiae) and Lentisphaerota (formerly Lentisphaerae) within the PVC superphylum.[3] The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs).[4] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobiota and an independent lineage amidst other bacteria.[5] CSIs have also been found that are shared by Verrucomicrobiota and Chlamydiota exclusively of all other bacteria.[6] These CSIs provide evidence that Chlamydiota is the closest relative to Verrucomicrobiota, and that they are more closely related to one another than to the Planctomycetales.

Verrucomicrobiota might belong in the clade Planctobacteria in the larger clade Gracilicutes.[7]

In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologies with Pseudomonadota.[8][9]

Phylogeny
16S rRNA based LTP_01_2022[10][11][12] 120 marker proteins based GTDB 07-RS207[13][14][15]
 
 

Lentisphaeria

 
 
 

Kiritimatiellae

 
Verrucomicrobiota
Opitutae
Opitutales

Opitutaceae

 
Puniceicoccales
 

Alterococcus

 
 

Puniceicoccaceae

 
 
 
"Verrucomicrobia"
 

Limisphaera {"Pedosphaerales"}

 
 
Terrimicrobiles

Terrimicrobiaceae

 
Verrucomicrobiales
 

Verrucomicrobiaceae

 
 
 

Akkermansiaceae

 
 

Rubritaleaceae

 
 
 
 
 
 
 
 
Verrucomicrobiota
 

Lentisphaeria

 
 
 

Kiritimatiellae

 
"Verrucomicrobiia"
Opitutales
 
 

CAG-312

 
 

UBA953

 
 
 
 

KCTC-12870

 
 
 
 

DSM-45221

 
 

Puniceicoccaceae

 
 
 
 

UBA2987

 
 

Opitutaceae

 
 
 
 
 
 
 

NGM72-4 {"Pedosphaerales"}

 
 
 

"Methylacidiphilaceae" {"Methylacidiphilales"}

 
 
"Chthoniobacterales"
 
 

"Chthoniobacteraceae"

 
 

UBA10450

 
 
 
 

Terrimicrobiaceae

 
 

"Xiphinematobacteraceae"

 
 
 
Verrucomicrobiales
 

Verrucomicrobiaceae

 
 

Akkermansiaceae

 
 
 
 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[16] and National Center for Biotechnology Information (NCBI)[17]

  • Genus ?"Ca. Epixenosoma" Bauer et al. 2005
  • Genus ?"Methyloacida" Islam et al. 2008
  • Genus ?"Nucleococcus" Sato et al. 2014
  • Class Opitutae Choo et al. 2007
    • Order Opitutales Choo et al. 2007
      • Family CAG-312
        • Genus "Ca. Merdousia" Gilroy et al. 2021
      • Family UBA953
        • Genus "Ca. Spyradosoma" Gilroy et al. 2021
      • Family KCTC-12870
        • Genus Ruficoccus Lin et al. 2017
        • Genus Cerasicoccus Yoon et al. 2007
      • Family DSM-45221
      • Family Puniceicoccaceae Choo et al. 2007
        • Genus "Ca. Fucivorax" Orellana et al. 2022
        • Genus "Ca. Marcellius" Nixon et al. 2019
        • Genus Oceanipulchritudo Feng et al. 2020
        • Genus "Ca. Pinguicoccus" Serra et al. 2020
        • Genus Puniceicoccus Choo et al. 2007
      • Family UBA2987
        • Genus "Ca. Moanibacter" corrig. Vosseberg, Martijn & Ettema 2018
      • Family Opitutaceae Choo et al. 2007
  • Class "Methylacidiphilae"
    • Order "Methylacidiphilales" Op den Camp 2009
      • Family "Methylacidiphilaceae" Op den Camp 2009
        • Genus "Methylacidimicrobium" van Teeseling et al. 2014
        • Genus "Methylacidiphilum" Hou et al. 2008
        • Genus "Ca. Methylacidithermus" Picone et al. 2021
      • Family NGM72-4
        • Genus Limisphaera Anders et al. 2015
      • Family "Pedosphaeraceae"
        • Genus "Pedosphaera" Ozyurt 2008
  • Class Terrimicrobia García-López et al. 2020
    • Order Terrimicrobiales García-López et al. 2020
      • Family "Chthoniobacteraceae" Sangwan et al. 2004
        • Genus "Chthoniobacter" Sangwan et al. 2004
      • Family Terrimicrobiaceae García-López et al. 2020
      • Family UBA10450
        • Genus "Ca. Udaeobacter" Brewer et al. 2016
      • Family "Xiphinematobacteraceae"
        • Genus "Ca. Xiphinematobacter" Vandekerckhove et al. 2000
  • Class Verrucomicrobiae Hedlund et al. 1998
    • Order Verrucomicrobiales Ward-Rainey et al. 1996
      • Family Akkermansiaceae Hedlund & Derrien 2012
        • Genus Akkermansia Derrien et al. 2004
        • Genus Haloferula Yoon et al. 2008
        • Genus Luteolibacter Yoon et al. 2008
        • Genus Persicirhabdus Yoon et al. 2008
        • Genus Rubritalea Scheuermayer et al. 2006
        • Genus Roseibacillus Yoon et al. 2008
      • Family Verrucomicrobiaceae Ward-Rainey et al. 1996
        • Genus "Fucophilus" Sakai et al. 2001b
        • Genus Brevifollis Otsuka et al. 2013
        • Genus Oceaniferula Jin et al. 2022
        • Genus Phragmitibacter Szuróczki et al. 2021
        • Genus Prosthecobacter Staley et al. 1976 ex Staley et al. 1980
        • Genus Roseimicrobium Otsuka et al. 2013
        • Genus "Sulfuriroseicoccus" Feng et al. 2022
        • Genus Terrimicrobium Qiu et al. 2014
        • Genus Verrucomicrobium Schlesner 1988

See also

References
  1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin; Jansson, Janet K. (2016-06-28). Langille, Morgan (ed.). "Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes". mSystems. 1 (3): mSystems.00045–16, e00045–16. doi:10.1128/mSystems.00045-16. ISSN 2379-5077. PMC 5069762. PMID 27822530.
  3. Cho J, Vergin K, Morris R, Giovannoni S (2004). "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae". Environ Microbiol. 6 (6): 611–21. doi:10.1111/j.1462-2920.2004.00614.x. PMID 15142250.
  4. Gupta RS, Bhandari V, Naushad HS (2012). "Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships". Front Microbiol. 3: 327. doi:10.3389/fmicb.2012.00327. PMC 3444138. PMID 23060863.
  5. Gupta RS (2016). "Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification". FEMS Microbiol Rev. 40 (4): 520–53. doi:10.1093/femsre/fuw011. PMID 27279642.
  6. Griffiths E, Gupta RS (2007). "Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae". Microbiology. 153 (Pt 8): 2648–54. doi:10.1099/mic.0.2007/009118-0. PMID 17660429. S2CID 2094762.
  7. Wagner, M; Horn, M (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–9. doi:10.1016/j.copbio.2006.05.005. PMID 16704931.
  8. Hou, S; Makarova, KS; Saw, JH; Senin, P; Ly, BV; Zhou, Z; Ren, Y; Wang, J; Galperin, MY; Omelchenko, Marina V; Wolf, Yuri I; Yutin, Natalya; Koonin, Eugene V; Stott, Matthew B; Mountain, Bruce W; Crowe, Michelle A; Smirnova, Angela V; Dunfield, Peter F; Feng, Lu; Wang, Lei; Alam, Maqsudul (2008). "Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia". Biology Direct. 3: 26. doi:10.1186/1745-6150-3-26. PMC 2474590. PMID 18593465.
  9. Ludwig, W., Euzéby, J., & Whitman W.B. (2008). "Bergey's Taxonomic Outlines: Volume 4 - Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes" (PDF). Bergey's Manual Trust: 15. Archived from the original (PDF) on 2016-11-08. Retrieved 2011-06-22.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. "The LTP". Retrieved 23 February 2022.
  11. "LTP_all tree in newick format". Retrieved 23 February 2022.
  12. "LTP_01_2022 Release Notes" (PDF). Retrieved 23 February 2022.
  13. "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  14. "bac120_r207.sp_labels". Genome Taxonomy Database. Retrieved 20 June 2022.
  15. "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  16. J.P. Euzéby. "Verrucomicrobiota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
  17. Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.