Verrucomicrobia

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Verrucomicrobia
Scientific classification
Domain: Bacteria
Phylum: Verrucomicrobia
Hedlund 2012
Classes
Synonyms
  • Verrucomicrobaeota Oren et al. 2015

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 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[edit]

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[edit]

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]

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[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. PMID 15142250. doi:10.1111/j.1462-2920.2004.00614.x. 
  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. PMC 3444138Freely accessible. PMID 23060863. doi:10.3389/fmicb.2012.00327. 
  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. PMID 27279642. doi:10.1093/femsre/fuw011. 
  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. PMID 17660429. doi:10.1099/mic.0.2007/009118-0. 
  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. PMID 16704931. doi:10.1016/j.copbio.2006.05.005. 
  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. PMC 2474590Freely accessible. PMID 18593465. doi:10.1186/1745-6150-3-26. 
  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 
  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.