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The Info List - Verrucomicrobia



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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 . The Verrucomicrobia phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobia and an independent lineage amidst other bacteria. CSIs have also been found that are shared by Verrucomicrobia and Chlamydiae exclusively of all other bacteria. 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. 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 .

PHYLOGENY

See also: Bacterial taxonomy
Bacterial taxonomy

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

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) and the National Center for Biotechnology Information (NCBI).

* Phylum VERRUCOMICROBIA Hedlund 2012

* Genus ?"Candidatus Epixenosoma " ♠ Bauer et al. 2005

* Species "Candidatus Epixenosoma ejectans " ♠ 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

* Species Opitutus terrae 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

* 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 ">

* ^ 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 . * ^ Gupta RS, Bhandari V, Naushad HS (2012). "Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria
Bacteria
Provide Insights into Their Evolutionary Relationships" . Front Microbiol. 3: 327. doi :10.3389/fmicb.2012.00327 . PMC 3444138  . PMID 23060863 . * ^ 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 . * ^ 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 . * ^ 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 . * ^ 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 . * ^ Ludwig, W., Euzéby, J., ">(PDF). Bergey's Manual Trust: 15 CS1 maint: Multiple names: authors list (link ) * ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2016-03-20. * ^ J.P. Euzéby. "Verrucomicrobia". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20. * ^ Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.

* v * t * e

Prokaryotes : Bacteria
Bacteria
classification (phyla and orders )

*

Domain Archaea Bacteria
Bacteria
Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta Animal Fungi )

G- / OM

Terra-/ Glidobacteria (BV1 )

EOBACTERIA

* Deinococcus–Thermus

* Deinococcales * Thermales

* Chloroflexi

* Anaerolineales * Caldilineales * Chloroflexales * Herpetosiphonales * Dehalococcoidales * Ktedonobacterales * Thermogemmatisporales * Thermomicrobiales * Sphaerobacterales

OTHER GLIDOBACTERIA

* Thermodesulfobacteria

* thermophiles

* Aquificae * Thermotogae

* Cyanobacteria
Cyanobacteria

Proteobacteria (BV2 )

ALPHA

* Caulobacterales * Kiloniellales * Kordiimonadales * Magnetococcales * Parvularculales * Rhizobiales
Rhizobiales
* Rhodobacterales * Rhodospirillales * Rickettsiales * Sneathiellales * Sphingomonadales

BETA

* Burkholderiales * Hydrogenophilales * Methylophilales * Neisseriales * Nitrosomonadales * Procabacteriales * Rhodocyclales

GAMMA

* Acidithiobacillales * Aeromonadales * Alteromonadales * Cardiobacteriales * Chromatiales * Enterobacteriales * Legionellales
Legionellales
* Methylococcales
Methylococcales
* Oceanospirillales * Orbales * Pasteurellales * Pseudomonadales
Pseudomonadales
* Salinisphaerales * Thiotrichales * Vibrionales * Xanthomonadales

DELTA

* Bdellovibrionales * Desulfarculales * Desulfobacterales * Desulfovibrionales * Desulfurellales * Desulfuromonadales * Myxococcales * Syntrophobacterales * Syntrophorhabdales

EPSILON

* Campylobacterales * Nautiliales

ZETA

* Mariprofundales

BV4

SPIROCHAETES

* Spirochaetes

Sphingobacteria ( FCB group )

* Fibrobacteres

* Chlorobi

* Chlorobiales * Ignavibacteriales

* Bacteroidetes

* Bacteroidales
Bacteroidales
* Cytophagales * Flavobacteriales * Sphingobacteriales

Planctobacteria / ( PVC group )

* Chlamydiae

* Lentisphaerae

* Lentisphaerales * Oligosphaerales * Victivallales

* Planctomycetes

* Phycisphaerales * Planctomycetales

* Verrucomicrobia

* Puniceicoccales * Opitutales * Chthoniobacterales * Verrucomicrobiales

* " Poribacteria "

OTHER GN

* Acidobacteria

* Acidobacteriales * Acanthopleuribacterales * Holophagales * Solibacterales

* Armatimonadetes

* Armatimonadales * Chthonomonadales * Fimbriimonadales

* Caldiserica * Chrysiogenetes * Deferribacteres * Dictyoglomi * Elusimicrobia * Fusobacteria * Gemmatimonadetes * Nitrospirae * Synergistetes

G+ / no OM

Firmicutes (BV3 )

BACILLI

* Bacillales * Lactobacillales

CLOSTRIDIA

* Clostridiales * Halanaerobiales * Thermoanaerobacteriales *