Verrucomicrobiota

Last updated

Verrucomicrobiota
TEM - Epixenosomes.jpg
Transmission electron micrograph of stage II epixenosomes.
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Superphylum: PVC superphylum
Phylum: Verrucomicrobiota
Hedlund 2021 [1]
Classes
Synonyms
  • "Verrucomicrobaeota" Oren et al. 2015
  • "Verrucomicrobia" Hedlund et al. 1997
  • "Verrucomicrobia" Hedlund 2010
  • "Verrucomicrobia" Yoon et al. 2010
  • "Verrucomicrobiota" Whitman et al. 2018

Verrucomicrobiota 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 from genus Xiphinema, residing in their gametes. [2] [3]

Contents


Verrucomicrobiota are abundant within the environment, though relatively inactive. [4] This phylum is considered to have two sister phyla: Chlamydiota (formerly Chlamydiae) and Lentisphaerota (formerly Lentisphaerae) within the PVC superphylum. [5] The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). [6] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobiota and an independent lineage amidst other bacteria. [7] CSIs have also been found that are shared by Verrucomicrobiota and Chlamydiota exclusively of all other bacteria. [8] These CSIs provide evidence that Chlamydiota is the closest relative to Verrucomicrobiota, and that they are more closely related to one another than to the Planctomycetales .

Verrucomicrobiota might belong in the clade Planctobacteria in the larger clade Gracilicutes. [9]

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 Pseudomonadota. [10] [11]

Phylogeny

16S rRNA based LTP_01_2022 [12] [13] [14] 120 single copy marker proteins based GTDB 08-RS214 [15] [16] [17]
Lentisphaerota

Lentisphaeria

Kiritimatiellota

Kiritimatiellae

Verrucomicrobiota
Opitutae
Opitutales

Opitutaceae

Puniceicoccales

Alterococcus

Puniceicoccaceae

"Verrucomicrobia"

"Pedosphaerales"

Terrimicrobiales

Terrimicrobiaceae

Verrucomicrobiales

Verrucomicrobiaceae

Akkermansiaceae

Rubritaleaceae

Verrucomicrobiota
Lentisphaeria
Lentisphaerales

Lentisphaeraceae

Oligosphaerales

Oligosphaeraceae

Victivallales

Victivallaceae

Kiritimatiellia
"Spyradenecales"

"Spyradenecaceae"

Kiritimatiellales

Kiritimatiellaceae

Tichowtungiaceae

Pontiellaceae

"Verrucomicrobiia"
Opitutales

Opitutaceae

"Moanibacteraceae"

Verruco-01

"Merdousiaceae"

"Spyradosomataceae"

"Cerasicoccaceae"

"Coraliomargaritaceae"

Puniceicoccaceae

"Limisphaerales"

"Limisphaeraceae"

"Pedosphaeraceae"

"Methylacidiphilales"

"Methylacidiphilaceae"

Terrimicrobiales

"Chthoniobacteraceae"

"Udaeobacteraceae"

Terrimicrobiaceae

"Xiphinematobacteraceae"

Verrucomicrobiales

Akkermansiaceae

SLCJ01

Verrucomicrobiaceae

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [18] and National Center for Biotechnology Information (NCBI) [19]

See also

Related Research Articles

<span class="mw-page-title-main">Spirochaete</span> Phylum of bacteria

A spirochaete or spirochete is a member of the phylum Spirochaetota, which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.

The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

<span class="mw-page-title-main">Chlamydiota</span> 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.

<span class="mw-page-title-main">PVC superphylum</span> Superphylum of bacteria

The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. 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.

<span class="mw-page-title-main">Acidobacteriaceae</span> Family of bacteria

The Acidobacteriaceae are a family of Acidobacteriota.

The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis ; and anaerobic halorespirers, which uses halogenated organics as electron acceptors.

Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.

Lentisphaerota is a phylum of bacteria closely related to Chlamydiota and Verrucomicrobiota.

<span class="mw-page-title-main">Sphingobacteria (phylum)</span> Phylum of bacteria

The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacterota, Chlorobiota, and Bacteroidota. The members are considered to form a clade due to a number of conserved signature indels.

The phylum Elusimicrobiota, previously known as "Termite Group 1", has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils, and toxic wastes. The high abundance of Elusimicrobiota representatives is only seen for the lineage of symbionts found in termites and ants.

Armatimonadota is a phylum of gram-negative bacteria.

Methylacidiphilum infernorum is an extremely acidophilic methanotrophic aerobic bacteria first isolated and described in 2007 growing on soil and sediment on Hell's Gate, New Zealand. Similar organisms have also been isolated from geothermal sites on Italy and Russia.

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.

Chitinophagaceae is an aerobic or facultatively anaerobic and rod-shaped family of bacteria in the phylum Bacteroidota.

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

Fucophilus is a fucoidan-utilizing genus of bacteria from the phylum Verrucomicrobiota with one known species. Fucophilus fucoidanolyticus has been isolated from the gut contend of a sea cucumber.

The Opitutales is an order in the phylum Verrucomicrobiota.

<span class="mw-page-title-main">Acidobacteriia</span> Class of bacteria

The "Acidobacteriia" is a class of Acidobacteriota.

References

  1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987. S2CID   239887308.
  2. Coomans A, Vandekerckhove TT, Claeys M (1 January 2000). "Transovarial transmission of symbionts in Xiphinema brevicollum (Nematoda: Longidoridae)". Nematology. Brill. 2 (4): 443–449. doi:10.1163/156854100509303. eISSN   1568-5411. ISSN   1388-5545.
  3. Vandekerckhove TT, Willems A, Gillis M, Coomans A (2000). "Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae)". International Journal of Systematic and Evolutionary Microbiology. Microbiology Society. 50 (6): 2197–2205. doi:10.1099/00207713-50-6-2197. ISSN   1466-5034. PMID   11155997.
  4. 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): e00045–16. doi:10.1128/mSystems.00045-16. ISSN   2379-5077. PMC   5069762 . PMID   27822530.
  5. 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. Bibcode:2004EnvMi...6..611C. doi:10.1111/j.1462-2920.2004.00614.x. PMID   15142250.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. Ludwig W, Euzéby J, Whitman WB (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.
  12. "The LTP" . Retrieved 23 February 2022.
  13. "LTP_all tree in newick format". Archived from the original on 4 September 2022. Retrieved 23 February 2022.
  14. "LTP_01_2022 Release Notes" (PDF). Retrieved 23 February 2022.
  15. "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  16. "bac120_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  17. "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
  18. J.P. Euzéby. "Verrucomicrobiota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
  19. Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.