Verrucomicrobia

Verrucomicrobia
Scientific classification
Domain:	Bacteria
Phylum:	Verrucomicrobia Hedlund 2012
Classes, orders, families & genera
Candidatus Epixenosoma ♠ Bauer et al. 2005 Lentimonas ♠ Choo & Cho 2006 Methyloacida ♠ Islam et al. 2008 Methylacidimicrobium ♠ van Teeseling et al. 2014 Methylacidiphilales ♠ Op den Camp 2009 Methylacidiphilaceae ♠ Op den Camp 2009 Methylacidiphilum ♠ Hou et al. 2008 emend. Op den Camp et al. 2009 Spartobacteria Sangwan et al. 2004 Chthoniobacterales Chthoniobacteraceae Chthoniobacter ♠ Sangwan et al. 2004 Candidatus Xiphinematobacter ♠ Vandekerckhove et al. 2000 Opitutae Choo et al. 2007 Opitutales Choo et al. 2007 Opitutaceae Choo et al. 2007 Opitutus Chin et al. 2001 Alterococcus Shieh and Jean 1999 Puniceicoccales Choo et al. 2007 Puniceicoccaceae Choo et al. 2007 Pelagicoccus Yoon et al. 2007 Puniceicoccus Choo et al. 2007 Coraliomargarita Yoon et al. 2007 Cerasicoccus Yoon et al. 2007 Verrucomicrobiae Hedlund et al. 1998 emend. Yoon et al. 2008 Verrucomicrobiales Ward-Rainey et al. 1996 emend. Yoon et al. 2008 Pedosphaeraceae ♠ Pedosphaera ♠ Ozyurt 2008 Akkermansiaceae Akkermansia Derrien et al. 2004 Rubritaleaceae Rubritalea Scheuermayer et al. 2006 Verrucomicrobiaceae Ward-Rainey et al. 1996 emend. Takeda et al. 2008 Fucophilus ♠ Sakai et al. 2001b Haloferula Yoon et al. 2008 emend. Bibi et al. 2011 Persicirhabdus Yoon et al. 2008 Luteolibacter Yoon et al. 2008 Roseibacillus Yoon et al. 2008 Prosthecobacter (ex Staley et al. 1976) Staley et al. 1980 emend. Takeda et al. 2008 Verrucomicrobium Schlesner 1988

Verrucomicrobia is a 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

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 121 by The All-Species Living Tree Project.^[6]

?Candidatus Epixenosoma ejectans ♠ Bauer et al. 2005 ?Lentimonas marisflavi ♠ Choo & Cho 2006 ?Methyloacida ♠ Islam et al. 2008 ?Methylacidimicrobium ♠ M. cyclopophantes ♠ van Teeseling et al. 2014 M. fagopyrum ♠ van Teeseling et al. 2014 M. tartarophylax ♠ van Teeseling et al. 2014 ?Methylacidiphilum ♠ M. fumariolicum ♠ (Pol et al. 2007) Op den Camp et al. 2009 M. infernorum ♠ (Dunfield et al. 2007) Hou et al. 2008 M. kamchatkense ♠ Islam 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. frondis ♠ Yoon et al. 2010 C. maritimus ♠ Yoon 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 colitermitum ♠ Wertz et al. 2012 Opitutus terrae Chin et al. 2001 Alterococcus agarolyticus Shieh and Jean 1999 Chthoniobacteraceae Chthoniobacter flavus ♠ Sangwan et al. 2004 Ca. Xiphinematobacter ♠ Ca. X. americani ♠ Vandekerckhove et al. 2000 Ca. X. brevicolli ♠ Vandekerckhove et al. 2000 Ca. X. rivesi ♠ Vandekerckhove et al. 2000 Verrucomicrobiales ?Fucophilus fucoidanolyticus ♠ Sakai et al. 2001b ?Pedosphaera parvula ♠ Ozyurt 2008 Verrucomicrobiaceae Terrimicrobium sacchariphilum Qiu et al. 2014 Verrucomicrobium spinosum Schlesner 1988 Roseimicrobium gellanilyticum Otsuka et al. 2013 Prosthecobacter P. fluviatilis Takeda et al. 2008 P. vanneervenii Hedlund et al. 1998 Brevifollis gellanilyticus Otsuka et al. 2013 P. algae Lee et al. 2014 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. pohnpeiensis Yoon et al. 2008 (type sp.) L. algae Yoon et al. 2008 L. luojiensis Jiang et al. 2012 L. yonseiensis Park et al. 2013 Haloferula 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. chungangensis Kang et al. 2013 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

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" (PDF). Bergey's Manual Trust: 15
5. See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Verrucomicrobia". Retrieved 2015-08-20.
6. See the All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 121 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2015-08-20.