names for candidate phyla

Proposed names for candidate phyla and associated superphyla

Based on Supplementary Table 5 from Rinke et al. 2013

For each candidatus type species the sampling site (see also Fig. 1), Microbial Dark Matter project ID, name, assembly size (Mbp), estimated genome completeness (%), and IMG taxon ID are provided in parenthesis. See supplementary Table 2 for detailed genome statistics.

Super-

phylum

Candidate phylum

Proposed name and etymology

Candidatus type species
(existing Candidatus species are referenced)

#SAGs

(#total)

PVC

OP3

“Omnitrophica”

Om.ni.tro’phi.ca. A higher taxonomic unit comprising the genus Omnitrophus

Candidatus Omnitrophus fodinae

(HSM, MDM ID 263, SCGC AAA011-A17, 2.0 Mbp, 79.9%, 2264867162)

Om.ni.tro’phus. L. adj. omnis, all; N.L. n. trophus (from Gr. trepho, to eat), eating; N.L. masc. n. Omnitrophus, eating all

fo.di’nae. L. gen. n. fodinae, of (from) a mine, coal mine

4 (4)

FCB

SAR406 (Marine Group A)

“Marinimicrobia”

Ma.ri.ni.mi.cro’.bi.a. A higher taxonomic unit comprising the genus Marinisoma

Candidatus Marinisoma atlanticum*

(GOM, combined assembly Marinimicrobia -2, 1.1 Mbp, 100%,  2518285581)

Ma.ri.ni.so.ma. L. adj. marinus, marine; Gr. neutr. n. soma, the body of an organism; N.L. neutr. n. Marinisoma, a marine organism. at.lan’ti.cum. N.L. adj. atlanticum referring to the Atlantic ocean from where the sample was taken

17 (17)

WS3

“Latescibacteria”

La.tes.ci.bac.te’ri.a. A higher taxonomic unit comprising the genus Latescibacter

Candidatus Latescibacter anaerobius

(SAK, MDM ID 42, SCGC AAA252-E07, 2.3Mbp, 72.7%, 2264867254)

La.tes.ci.bac’ter. L. v. latesco, to hide; -i- connecting vowel; N. L. n. bacter, a small rod; N.L. masc. n. Latescibacter a hiding small rod.

an.a.er.o’bi.us. Gr. pref. an- negating; Gr. n. aer, air; Gr. n. bios life; N.L. adj. anaerobius living without air (i. e. oxygen)

4 (4)

WWE1

“Cloacimonetes”

Clo.a.ci.mo.ne’tes. A higher taxonomic unit comprising the genus Cloacimonas.

Candidatus Cloacimonas acidaminovorans1

Clo.a.ci.mo’nas. L. n. cloaca, sewer; -i- connecting vowel; N.L. n. monas a unit, N.L. fem. n. Cloacimonas a unit from a sewer

a.cid.a.mi.no.vo'rans. L. n. acidum an acid; N.L. n. aminum an amine; L. part. adj. vorans eating. N.L. adj. acidaminovorans, amino acid eating. 

37 (38)

 

 

OP8

“Aminicenantes”

A.mi.ni.ce.nan’tes. A higher taxonomic unit comprising the genus Aminicenans.

Candidatus Aminicenans sakinawicola

(SAK, combined assembly Aminicenantes -1, 3.0 Mbp, 100%, 2518285573)

A.mi.ni.ce’nans. N.L. n. aminum, amine; L. v. cenare, to eat; N.L. masc. n. Aminicenans a (bacterium) degrading amino acids

-sa.ki.na.wi’co.la. N. L. n. sakinaw referring to the sampling site, Lake Sakinaw; -i- connecting vowel; L. suffix –cola, a dweller; N.L. n. sakinawicola dwelling in Lake Sakinaw

36 (36)

Patesci-bacteria‡

-patesco (lat.), bare

OP11

“Microgenomates”

A higher taxonomic unit comprising the genus Microgenomatus

Candidatus Microgenomatus auricola

(HSM, MDM ID 182,  SCGC AAA011-E14, 0.5 Mbp, 65.5%, 2264867148)

Mi.cro.ge.no.ma’tus. Gr. Adj. mikros, small; N.L. n. genomum, genome; N.L. n. Microgenomatus; an organism with a small genome size (~1 Mbp)

au.ri’co.la. L. n. aurum, gold; L. suff. –cola, a dweller; N.L. n. auricola, a dweller on gold

10 (22)

OD1

”Parcubacteria”

-parcus (lat.), thrifty

A higher taxonomic unit comprising the genus Paceibacter

Candidatus Paceibacter normanii

(SAK, MDM ID 138, SCGC AAA255-P19, 0.6 Mbp, 70.3%, 2264867004)

Pa.ce.i.bac’ter. Pace referring to Norman Pace. N.L. n. bacter (from Gr. bakterion) a small rod. N.L. masc. n. Paceibacter  Pace’s bacterium

norman’i.i. N.L. gen. N. of Norman, referring to Norman Pace (Norman Richard Pace, Jr. is an American biochemist, Distinguished Professor of Molecular, Cellular and Developmental Biology at the University of Colorado, and principal investigator at the Pace lab)

9 (23)

GN02 (BD1-5)

”Gracilibacteria”

-gracilis (lat.), slim, slender, slight, meager, simple
A higher taxonomic unit comprising the genus Altimarinus

Candidatus Altimarinus pacificus

(EPR, MDM ID 255, JGI 0000068-E11, 0.5 Mbp, 36%, 2264867094)

Al.ti.ma.ri’nus. L. adj. altus, high, deep; L. adj. marinus, marine; N. L. masc. n. Altimarinus a (bacterium) from the Deep Sea

pa.ci’fi.cus. N.L. masc. adj. referring to the Pacific Ocean. 

2 (7)

 

OP9

“Atribacteria”  A.tri.bac.te'ri.a. N.L. n.
A higher taxonomic unit comprising the genus Caldatribacterium

Candidatus Caldatribacterium californiense2

Cald.at.ri.bac.te’ri.um. L. adj. caldus, hot; L. adj. ater, black, dark; N.L. n. bacterium, a small rod; N.L. neutr. n. Caldatribacterium a small rod from hot dark matter

ca.li.for.ni.en’se. N.L. adj. of/from the state California

14 (16)

 

EM19

“Calescamantes”

Ca.lesc.a.man’tes. L. v. calesco, to become warm, grow hot; L. v.

amo, to love, N.L. n. Calescamantes heat lovers
A higher taxonomic unit comprising the genus Calescibacterium

Candidatus Calescibacterium nevadense

(GBS, combined assembly Calescamantes, 2.2 Mbp, 92%, 2518285568)

Cal.es.ci.bac.te’ri.um. L. v.  calesco, to become warm , grow hot; N.L. n. bacterium a small rod. N.L. n. Calescibacterium a bacterium from an extremely hot environment.

ne.va.den’se. N.Ladj.  nevadense of/from the state of Nevada

10 (1)

 

CD12 (BHI80-139)

“Aerophobetes”

A higher taxonomic unit comprising the genus Aerophobus

Candidatus Aerophobus profundus

(SAK, MDM ID 70, SCGC AAA252-L23, 2.3 Mbp, 67.1%, 2264867061)

A.er.o.pho’bus. Gr. n. aer, air; Gr. adj. phobos, fear. N. L. n. Aerophobus, fearing of air (i. e. oxygen).

pro.fun’dus. L. adj. profundus, deep

4 (4)

 

NKB19

“Hydrogenedentes”

A higher taxonomic unit comprising the genus Hydrogenedens

Candidatus Hydrogenedens terephthalicus

(TA, combined assembly Hydrogenedentes-1, 2.9 Mbp, 96.7%, 2518285572)

Hy.dro.ge.ne’dens. N.L.n. hydrogenium, hydrogen; L. V. edo, eat; N.L. n. Hydrogenedens a hydrogen consumer

te.re.phtha’li.cus. N.L. n. (acidum) terephthalicum,  terephthalic acid. N.L. adj. terephthalicus, referring to the environment of isolation, a terephthalate reactor. 

4 (4)

 

OP1

“Acetothermia”
A.ce.to.ther’mi.a. A higher taxonomic unit comprising the genus Acetothermum

Candidatus Acetothermum autotrophicum3

 ‘Acetothermus’ (A.ce.to.ther'mus. L.n. acetum vinegar; Gr. Adj. thermos hot; M.L. masc. n. Acetothermus indicates a vinegar organism living in hot places.) and ‘autotrophicum’ (au.to.tro'phi.cum. Gr. pron.autos self; Gr. adj. trophikos nursing, tending or feeding; N.L. neut. adj. autotrophicum self-nursing or self-feeding).

1 (2)

 

Oct-Spa1-106

“Fervidibacteria”

Fer.vi.di.bac.te’ri.a. A higher taxonomic unit comprising the genus Fervidibacter

Candidatus Fervidibacter sacchari

(GBS, MDM ID 117,  JGI_0000001-G10, 1.0 Mbp, 45.6%, 2264867076)

Fer.vi.do.bac’ter. L. adj. fervidus, hot, steaming; -i- connecting vowel; N.L. n. bacter, a rod; N.L. n. Fervidibacter a hot rod.

sac.cha’ri. N.L. n. saccharum, sugar; N.L. gen. n. sacchari, of sugar

5 (5)

DPANN

pMC2A 384

“Diapherotrites”

(Dia.phe.ro.tri’tes. Gr. v. diaphero, to differ; Gr. adj. trítos the third; N. L. n. Diapherotrites the 3rd HSM group discovered) A higher taxonomic unit comprising the genus Iainarchaeum

Candidatus Iainarchaeum andersonii

(HSM, MDM ID 206, SCGC_AAA011-E11, 1.1 Mbp, 88.5%, 2264867067)

(Ia.in.ar.chae’um. Iain, first name of Iain Anderson (in memoriam of Iain Anderson, a Ph.D. in biochemistry from the University of Wisconsin-Madison and a key member of IMG team). N.L. n. archaeum a taxonomic unit. N.L. neutr. n. Iainarchaeum, Iain’s archaeum.)
(an.der.so’ni.i.  N.L. gen. n. andersonii, of Anderson

3 (3)

ARMAN group

“Parvarchaeota”

Parv.ar.chae’a. A higher taxonomic unit comprising the genera Parvarchaeum and Micrarchaeum

Candidatus Parvarchaeum acidiphilum (ARMAN-4)4

Parv.ar.chae’um. L. adj. parvus small; N.L. n. archaeum, a taxonomic unit; N.L. n. Parvarchaeum the small archaeum

a.ci.di’phi.lum. L. n. acidum acid, N.L. adj. philus (from Gr. philos) friend, loving; N.L. neutr. adj. acidiphilum acid-loving

0 (3)

DSEG

“Aenigmarchaeota” Ae.nig.mar.chae’a. A higher taxonomic unit comprising the genus Aenigmarchaeum

Candidatus Aenigmarchaeum subterraneum

(HSM, MDM ID 271, AAA011-O16, 0. 42 Mbp, 47.3%, 2264867065)

Ae.nig.mar.chae’um. L. n. aenigma, riddle; N.L. n. archaeum, a taxonomic unit; N.L. neutr. n. Aenigmarchaeum the enigmatic archaeum.

Sub.terr.a’ne.um. L. neutr. adj. subterraneum underground, subterranean

3 (3)

 

“Nanohaloarchaeota”
(Na.no.ha.lo.ar.chae.o'ta. Gr. n. nanos, dwarf; Gr. n. hal, -los, salt; Gr. adj. archaios, old; N.L. suffix -ota ending to design a phylum; N.L. n. Nanohaloarchaeota, small salt-loving Archaeota.  A higher taxonomic unit comprising the genus  Nanosalina

Candidatus Nanosalina sp. J07AB435

Na.no.sa.li’na.. Gr. n. nanos, dwarf; L. n. salina, a salt-work, a place

where salt is made N. L. n. Nanosalina a small archaeum from a place

where salt is made

0 (2)

1 Pelletier, E. et al. ‘Candidatus Cloacamonas Acidaminovorans’: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division. J. Bacteriol. 190, 2572–2579 (2008).

2Dodsworth, J. et al. Single-cell and metagenomic analyses indicate a fermentative, saccharolytic lifestyle for members of the OP9 lineage. Nature Communications. Passed pre-review.

3 Takami, H. et al. A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem. PLoS ONE 7, e30559 (2012).

4 Baker, B. J. et al. Enigmatic, ultrasmall, uncultivated Archaea. PNAS 107, 8806–8811 (2010).

5Narasingarao, P. et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6, 81–93 (2012).

† We update the naming of Candidatus Cloacimonas acidaminovorans to honor the Latin origin which requires -i- as a connecting vowel, according to the naming convention for prokaryotes60.

 

‡ See also Supplementary Fig. 8 for evidence of a possible association of the Patescibacteria with the Terrabacteria.

* updated and corrcted from Marinimicrobium atlanticum on 02/10/2014