Verrucomicrobia

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Verrucomicrobia
TEM - Epixenosomes.jpg
Transmission electron micrograph of stage II epixenosomes.
Scientific classification Red Pencil Icon.png
Domain: Bacteria
Phylum: Verrucomicrobia
Hedlund 2012
Classes
Synonyms
  • Verrucomicrobaeota Oren et al. 2015

Verrucomicrobia is a phylum of Gram-negative bacteria that contains only a few described species. 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.[ citation needed ]

Contents

Verrucomicrobia are abundant within the environment, though relatively inactive. [1] This phylum is considered to have two sister phyla: Chlamydiae and Lentisphaerae within the PVC superphylum. [2] The Verrucomicrobia phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). [3] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobia and an independent lineage amidst other bacteria. [4] CSIs have also been found that are shared by Verrucomicrobia and Chlamydiae exclusively of all other bacteria. [5] 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 .

Verrucomicrobia might belong in the clade Planctobacteria in the larger clade Gracilicutes. [6]

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. [7] [8]

Phylogeny

The phylogeny based on the work of the All-Species Living Tree Project. [9]

 
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) [10] and the National Center for Biotechnology Information (NCBI). [11]

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:

Related Research Articles

Chlamydiota Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

PVC superphylum Superphylum of bacteria

The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetes, Verrucomicrobia, and Chlamydiae. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.

Lentisphaerota is a phylum of bacteria closely related to Chlamydiae and Verrucomicrobia.

Dokdonia is a genus of bacteria from the family of Flavobacteriaceae. Dokdonia is named after Dokdo a Korean name for the Liancourt Rock which sovereignty disputed between Japan and Korea.

Sneathia is a Gram-negative, rod-shaped, non-spore-forming and non-motile genus of bacteria from the family of Leptotrichiaceae. Species have been identified as pathogens associated with bacterial vaginosis.

Humibacter is a Gram-positive, mesophilic, strictly aerobic, chemoorganotrophic and motile genus of bacteria from the family of Microbacteriaceae. Humibacter occur in sewage sludge.

Singulisphaera is a moderately acidophilic and mesophilic genus of bacteria from the family of Planctomycetaceae.

Mariniflexile is a genus in the phylum Bacteroidota (Bacteria). The various species have been recovered from sea water, sea urchins, springs, brackish water, and an oyster.

Gaetbulibacter is a Gram-negative genus of bacteria from the family of Flavobacteriaceae.

Kordia is a Gram-negative, strictly aerobic and non-motile genus of bacteria from the family of Flavobacteriaceae.

Lutibacter is an aerobic or facultatively anaerobic genus of bacteria from the family of Flavobacteriaceae.

Mesonia is a strictly aerobic and chemoorganotrophic genus of bacteria from the family of Flavobacteriaceae.

Riemerella is a Gram-negative, non-spore-forming and non-motile genus of bacteria from the family of Weeksellaceae.Riemerella is named after O.V. Riemer.

Riemerella columbina is a Gram-negative bacterium from the genus of Riemerella which can cause respiratory disease in pigeons.

Robiginitalea is a genus of bacteria from the family of Flavobacteriaceae.

Robiginitalea biformata is a Gram-negative, chemoheterotrophic and non-motile bacterium from the genus of Robiginitalea which has been isolated from the Sargasso Sea.

Sediminicola is a Gram-negative and aerobic genus of bacteria from the family of Flavobacteriaceae.

Winogradskyella is a genus of bacteria from the family of Flavobacteriaceae. Winogradskyella is named after the Russian microbiologist Sergei Winogradsky.

Cerasicoccus is a Gram-negative, non-motile, obligately aerobic and chemoheterotrophic bacterial genus from the family Puniceicoccaceae.

The Opitutaceae are a Gram-negative and chemoheterotrophic order of the domain Bacteria. Opitutaceae bacteria were isolated from soil and coastal marine springs.

References

  1. ↑ White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin; Jansson, Janet K. (2016-06-28). Langille, Morgan (ed.). "Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes". mSystems. 1 (3): mSystems.00045–16, e00045–16. doi:10.1128/mSystems.00045-16. ISSN   2379-5077. PMC   5069762 . PMID   27822530.
  2. ↑ 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.
  3. ↑ 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.
  4. ↑ 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.
  5. ↑ 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. S2CID   2094762.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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. Archived from the original (PDF) on 2016-11-08. Retrieved 2011-06-22.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ↑ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2016-03-20.
  10. ↑ J.P. Euzéby. "Verrucomicrobia". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  11. ↑ Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
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