Verrucomicrobia

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Verrucomicrobia
Scientific classification
Domain: Bacteria
Phylum: Verrucomicrobia
Classes, orders, families & genera

Verrucomicrobia is a recently[when?] described phylum of bacteria. This phylum contains only a few described species (Verrucomicrobium spinosum, is an example, the phylum is named after this). The species identified have been isolated from fresh water 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. While verrucae is another name for the warts often found on hands and feet, this phylum is so called not because it is a causative agent thereof, but because of its wart-like morphology.

Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures). This phylum is considered to have two sister phyla: Chlamydiae and Lentisphaerae.[1]

Cavalier-Smith has postulated that the Verrucomicrobia belong in the clade Planctobacteria in the larger clade Gracilicutes. 16S rRNA data corroborate that view.[2] 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 Proteobacteria.[3][4]

Phylogeny[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) [5] and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project [6]



?Candidatus Epixenosoma ejectans



?Lentimonas marisflaviChoo & Cho 2006



?MethyloacidaIslam et al. 2008


?Methylacidiphilum

M. fumariolicum(Pol et al. 2007) Op den Camp et al. 2009



M. infernorum(Dunfield et al. 2007) Hou et al. 2008



M. kamchatkenseIslam et al. 2008



Opitutae
Puniceicoccaceae

Puniceicoccus vermicola Choo et al. 2007




Coraliomargarita akajimensis Yoon et al. 2007


Cerasicoccus

C. arenae Yoon et al. 2007 (type sp.)



C. frondisYoon et al. 2010



C. maritimusYoon et al. 2010






Pelagicoccus

P. croceus Yoon et al. 2007




P. mobilis Yoon et al. 2007 (type sp.)




P. albus Yoon et al. 2007



P. litoralis Yoon et al. 2007





Opitutaceae

?Diplosphaera colitermitumWertz et al. 2012



Opitutus terrae Chin et al. 2001



Alterococcus agarolyticus Shieh and Jean 1999






Chthoniobacteraceae

Chthoniobacter flavusSangwan et al. 2004


Candidatus Xiphinematobacter

Candidatus X. americaniVandekerckhove et al. 2000



Candidatus X. brevicolliVandekerckhove et al. 2000



Candidatus X. rivesiVandekerckhove et al. 2000




Verrucomicrobiales

?Fucophilus fucoidanolyticusSakai et al. 2001b



?Pedosphaera parvulaOzyurt 2008


Verrucomicrobiaceae

Verrucomicrobium spinosum Schlesner 1988


Prosthecobacter


P. fluviatilis Takeda et al. 2008



P. vanneervenii Hedlund et al. 1998





P. dejongeii Hedlund et al. 1998




P. debontii Hedlund et al. 1998



P. fusiformis (ex Staley et al. 1976) Staley et al. 1980 (type sp.)








Akkermansia muciniphila Derrien et al. 2004




Luteolibacter

?L. cuticulihirudinis Glaeser et al. 2012



?L. luojiensis Jiang et al. 2012



L. algae Yoon et al. 2008



L. pohnpeiensis Yoon et al. 2008 (type sp.)



Haloferula

?H. chungangensis Kang et al. 2013




H. luteola Bibi et al. 2011



H. sargassicola Yoon et al. 2008





H. helveola Yoon et al. 2008




H. phyci Yoon et al. 2008




H. harenae Yoon et al. 2008



H. rosea Yoon et al. 2008 (type sp.)








Roseibacillus

R. persicicus Yoon et al. 2008




R. ishigakijimensis Yoon et al. 2008 (type sp.)



R. ponti Yoon et al. 2008






Persicirhabdus sediminis Yoon et al. 2008


Rubritalea


R. sabuli Yoon et al. 2008




R. halochordaticola Yoon et al. 2011



R. squalenifaciens Kasai et al. 2007






R. marina Scheuermayer et al. 2006 (type sp.)




R. spongiae Yoon et al. 2007



R. tangerina Yoon et al. 2007












Notes:
♠ Strain found at the National Center for Biotechnology Information (NCBI) but has no standing with the Bacteriological Code (1990 and subsequent Revision) as detailed by List of Prokaryotic names with Standing in Nomenclature (LPSN) as a result of the following reasons:
• No pure culture isolated or available for Prokayotes.
• Not validly published because the effective publication only documents deposit of the type strain in a single recognized culture collection.
• Not approved and published by the International Journal of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM).

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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". Bergey's Manual Trust: 15 
  5. ^ See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Verrucomicrobia". Retrieved 2013-03-20. 
  6. ^ See the All-Species Living Tree Project [1]. Data extracted from the "16S rRNA-based LTP release 111 (full tree)". Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.