Verrucomicrobia

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, 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. 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.

Verrucomicrobia
Scientific classification
Domain:
Bacteria
Superphylum:
PVC group
Phylum:
Verrucomicrobia

Hedlund 2012
Classes
  • "Candidatus Epixenosoma" ♠
  • "Lentimonas" ♠
  • "Methyloacida" ♠
  • "Methylacidimicrobium" ♠
  • "Methylacidiphilales" ♠
  • "Spartobacteria"
  • Opitutae
  • Verrucomicrobiae
Synonyms
  • Verrucomicrobaeota Oren et al. 2015

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 within the PVC group.[1] The Verrucomicrobia phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs).[2] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobia and an independent lineage amidst other bacteria.[3] CSIs have also been found that are shared by Verrucomicrobia and Chlamydiae exclusively of all other bacteria.[4] These CSIs provide evidence that Chlamydiae is the closest relative to Verrucomicrobia, and that they are more closely related to one another than to the Planctomycetales.

Cavalier-Smith has postulated that the Verrucomicrobia belong in the clade Planctobacteria in the larger clade Gracilicutes. 16S rRNA data corroborate that view.[5] 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.[6][7]

Phylogeny
See also: Bacterial taxonomy

The phylogeny based on the work of the All-Species Living Tree Project.[8]

 
Opitutae
Puniceicoccaceae
 

Coraliomargarita akajimensis

 
 
 

Puniceicoccus vermicola

 
 

Cerasicoccus arenae

 
 
 
 
Opitutaceae
 

Opitutus terrae

 
 

Alterococcus agarolyticus

 
 
Pelagicoccus
 

P. croceus

 
 
 

P. mobilis (type sp.)

 
 
 

P. albus

 
 

P. litoralis

 
 
 
 
 
 
Verrucomicrobiales
 

Limisphaera ngatamarikiensis

 
 
Verrucomicrobiaceae
 

Terrimicrobium sacchariphilum

 
 
 

Verrucomicrobium spinosum

 
 
 

Roseimicrobium gellanilyticum

 
Prosthecobacter
 
 

P. fluviatilis

 
 

P. vanneervenii

 
 
 
 

Brevifollis gellanilyticus

 
 
 
 

P. algae

 
 

P. dejongeii

 
 
 
 

P. debontii

 
 

P. fusiformis (type sp.)

 
 
 
 
 
 
 
 
 
 

Akkermansia muciniphila

 
 
 
Luteolibacter
 

L. cuticulihirudinis

 
 
 

L. pohnpeiensis (type sp.)

 
 
 

L. algae

 
 
 

L. luojiensis

 
 

L. yonseiensis

 
 
 
 
 
Haloferula
 
 

H. luteola

 
 

H. sargassicola

 
 
 
 

H. helveola

 
 
 

H. phyci

 
 
 

H. harenae

 
 
 

H. chungangensis

 
 

H. rosea (type sp.)

 
 
 
 
 
 
 
 
Roseibacillus
 

R. persicicus

 
 
 

R. ishigakijimensis (type sp.)

 
 

R. ponti

 
 
 
 
 

Persicirhabdus sediminis

 
Rubritalea
 
 

R. sabuli

 
 
 

R. halochordaticola

 
 

R. squalenifaciens

 
 
 
 
 

R. marina (type sp.)

 
 
 

R. spongiae

 
 

R. tangerina

 
 
 
 
 
 
 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[9] and the National Center for Biotechnology Information (NCBI).[10]

  • Phylum Verrucomicrobia Hedlund 2012 [Verrucomicrobaeota Oren et al. 2015]
    • Genus ?"Candidatus Epixenosoma" ♠ Bauer et al. 2005
    • Genus ?Lentimonas ♠ Choo & Cho 2006
      • Species "Lentimonas marisflavi" ♠ Choo & Cho 2006
    • Genus? "Methyloacida" ♠ Islam et al. 2008
    • Genus ?"Methylacidimicrobium" ♠ van Teeseling et al. 2014
      • Species "M. cyclopophantes" ♠ van Teeseling et al. 2014
      • Species "M. fagopyrum" ♠ van Teeseling et al. 2014
      • Species "M. tartarophylax" ♠ van Teeseling et al. 2014
    • Order ?"Methylacidiphilales" ♠ Op den Camp 2009
      • Family "Methylacidiphilaceae" ♠ Op den Camp 2009
        • Genus "Methylacidiphilum" ♠ Hou et al. 2008 emend. Op den Camp et al. 2009
          • Species "M. fumariolicum" ♠ (Pol et al. 2007) Op den Camp et al. 2009
          • Species "M. infernorum" ♠ (Dunfield et al. 2007) Hou et al. 2008
          • Species "M. kamchatkense" ♠ Islam et al. 2008
    • Class ?"Spartobacteria" Sangwan et al. 2004
      • Genus "Candidatus Xiphinematobacter" ♠ Vandekerckhove et al. 2000
        • Species "Ca. X. americani" ♠ Vandekerckhove et al. 2000
        • Species "Ca. X. brevicolli" ♠ Vandekerckhove et al. 2000
        • Species "Ca. X. rivesi" ♠ Vandekerckhove et al. 2000
      • Order "Chthoniobacterales" Sangwan et al. 2004
        • Family "Chthoniobacteraceae" Sangwan et al. 2004
          • Genus "Chthoniobacter" ♠ Sangwan et al. 2004
            • Species "Chthoniobacter flavus" ♠ Sangwan et al. 2004
    • Class Opitutae Choo et al. 2007
      • Order Opitutales Choo et al. 2007
        • Family Opitutaceae Choo et al. 2007
          • Genus ?"Diplosphaera" ♠ Wertz et al. 2012 non Bialosuknia 1909
            • Species "Diplosphaera colitermitum" ♠ Wertz et al. 2012
          • Genus Alterococcus Shieh and Jean 1999
            • Species Alterococcus agarolyticus Shieh and Jean 1999
          • Genus Opitutus Chin et al. 2001
          • Genus Cephaloticoccus Lin et al. 2016
            • Species C. capnophilus Lin et al. 2016
            • Species C. primus Lin et al. 2016
      • Order Puniceicoccales Choo et al. 2007
        • Family Puniceicoccaceae Choo et al. 2007
          • Genus Cerasicoccus Yoon et al. 2007
            • Species C. arenae Yoon et al. 2007 (type sp.)
            • Species "C. frondis" ♠ Yoon et al. 2010
            • Species "C. maritimus" ♠ Yoon et al. 2010
          • Genus Coraliomargarita Yoon et al. 2007
            • Species Coraliomargarita akajimensis Yoon et al. 2007
          • Genus Pelagicoccus Yoon et al. 2007
            • Species P. albus Yoon et al. 2007
            • Species P. croceus Yoon et al. 2007
            • Species P. litoralis Yoon et al. 2007
            • Species P. mobilis Yoon et al. 2007 (type sp.)
          • Genus Puniceicoccus Choo et al. 2007
            • Species Puniceicoccus vermicola Choo et al. 2007
    • Class Verrucomicrobiae Hedlund et al. 1998 emend. Yoon et al. 2008
      • Order Verrucomicrobiales Ward-Rainey et al. 1996 emend. Yoon et al. 2008
        • Family Verrucomicrobia subdivision 3 [Pedosphaeraceae]
          • Genus ?"Pedosphaera" ♠ Ozyurt 2008
            • Species "Pedosphaera parvula" ♠ Ozyurt 2008
          • Genus Limisphaera ngatamarikiensis Anders et al. 2015
            • Species Limisphaera ngatamarikiensis Anders et al. 2015
        • Family Akkermansiaceae Hedlund & Derrien 2012
        • Family Rubritaleaceae Hedlund 2012
          • Genus Rubritalea Scheuermayer et al. 2006
            • Species R. halochordaticola Yoon et al. 2011
            • Species R. marina Scheuermayer et al. 2006 (type sp.)
            • Species R. sabuli Yoon et al. 2008
            • Species R. spongiae Yoon et al. 2007
            • Species R. squalenifaciens Kasai et al. 2007
            • Species R. tangerina Yoon et al. 2007
        • Family Verrucomicrobiaceae Ward-Rainey et al. 1996 emend. Takeda et al. 2008
          • Genus ?Fucophilus ♠ Sakai et al. 2001b
            • Species Fucophilus fucoidanolyticus ♠ Sakai et al. 2001b
          • Genus Brevifollis Otsuka et al. 2013
            • Species Brevifollis gellanilyticus Otsuka et al. 2013
          • Genus Haloferula Yoon et al. 2008 emend. Bibi et al. 2011
            • Species H. chungangensis Kang et al. 2013
            • Species H. harenae Yoon et al. 2008
            • Species H. helveola Yoon et al. 2008
            • Species H. luteola Bibi et al. 2011
            • Species H. phyci Yoon et al. 2008
            • Species H. rosea Yoon et al. 2008 (type sp.)
            • Species H. sargassicola Yoon et al. 2008
          • Genus Persicirhabdus Yoon et al. 2008
            • Species Persicirhabdus sediminis Yoon et al. 2008
          • Genus Luteolibacter Yoon et al. 2008
            • Species L. algae Yoon et al. 2008
            • Species L. cuticulihirudinis Glaeser et al. 2012
            • Species L. luojiensis Jiang et al. 2012
            • Species L. pohnpeiensis Yoon et al. 2008 (type sp.)
            • Species L. yonseiensis Park et al. 2013
          • Genus Roseibacillus Yoon et al. 2008
            • Species R. persicicus Yoon et al. 2008
            • Species R. ishigakijimensis Yoon et al. 2008 (type sp.)
            • Species R. ponti Yoon et al. 2008
          • Genus Roseimicrobium Otsuka et al. 2013
            • Species Roseimicrobium gellanilyticum Otsuka et al. 2013
          • Genus Prosthecobacter (ex Staley et al. 1976) Staley et al. 1980 emend. Takeda et al. 2008
            • Species P. algae Lee et al. 2014
            • Species P. dejongeii Hedlund et al. 1998
            • Species P. debontii Hedlund et al. 1998
            • Species P. fluviatilis Takeda et al. 2008
            • Species P. fusiformis (ex Staley et al. 1976) Staley et al. 1980 (type sp.)
            • Species P. vanneervenii Hedlund et al. 1998
          • Genus Terrimicrobium Qiu et al. 2014
            • Species Terrimicrobium sacchariphilum Qiu et al. 2014
          • Genus Verrucomicrobium Schlesner 1988

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:

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. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.CS1 maint: multiple names: authors list (link)
  8. "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.
  9. J.P. Euzéby. "Verrucomicrobia". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  10. Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
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