Candidatus List. Lists of names of prokaryotic Candidatus phyla

References

1. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes – Prokaryotic Code (2008 Revision). Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article]
   [Google Scholar]
2. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73,in press:
   [Google Scholar]
3. Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Candidatus List No.1. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956–4042
   [Google Scholar]
4. Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71:004671 [View Article] [PubMed]
   [Google Scholar]
5. Oren A, Garrity GM. Candidatus List No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72:005186
   [Google Scholar]
6. Oren A. Candidatus List No. 4: Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72:005545 [View Article]
   [Google Scholar]
7. Oren A, Arahal DR, Rosselló-Móra R, Sutcliffe IC, Moore ERB. Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum. Int J Syst Evol Microbiol 2021; 71:004851 [View Article] [PubMed]
   [Google Scholar]
8. Williams TJ, Allen MA, Panwar P, Cavicchioli R. Into the darkness: the ecologies of novel “microbial dark matter” phyla in an Antarctic lake. Environ Microbiol 2022; 24:2576–2603 [View Article] [PubMed]
   [Google Scholar]
9. Tamarit D, Caceres EF, Krupovic M, Nijland R, Eme L et al. A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses. Nat Microbiol 2022; 7:948–952 [View Article] [PubMed]
   [Google Scholar]
10. Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling. Sci Adv 2022; 8:eabm9651 [View Article]
    [Google Scholar]
11. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499:431–437 [View Article] [PubMed]
    [Google Scholar]
12. Seitz KW, Lazar CS, Hinrichs K-U, Teske AP, Baker BJ. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J 2016; 10:1696–1705 [View Article] [PubMed]
    [Google Scholar]
13. Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P. Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Mol Biol Evol 2016; 33:915–927 [View Article]
    [Google Scholar]
14. Liu Y, Makarova KS, Huang W-C, Wolf YI, Nikolskaya AN et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 2021; 593:553–557 [View Article]
    [Google Scholar]
15. Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW et al. The importance of designating type material for uncultured taxa. Syst Appl Microbiol 2019; 42:15–21 [View Article] [PubMed]
    [Google Scholar]
16. Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY et al. Novel prosthecate bacteria from the candidate phylum Acetothermia. ISME J 2018; 12:2225–2237 [View Article] [PubMed]
    [Google Scholar]
17. Hahn CJ, Laso-Pérez R, Vulcano F, Vaziourakis KM, Stokke R et al. “Candidatus Ethanoperedens”, a thermophilic genus of archaea mediating the anaerobic oxidation of ethane. mBio 2020; 11:e00600–20
    [Google Scholar]
18. Colman DR, Jay ZJ, Inskeep WP, Jennings R deM, Maas KR et al. Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Front Microbiol 2016; 7:304 [View Article] [PubMed]
    [Google Scholar]
19. Zhang X, Liu Z, Xu W, Pan J, Huang Y et al. Genomic insights into versatile lifestyle of three new bacterial candidate phyla. Sci China Life Sci 2022; 65:1547–1562 [View Article] [PubMed]
    [Google Scholar]
20. Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM et al. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol 2019; 42:54–66 [View Article]
    [Google Scholar]
21. Begmatov S, Beletsky AV, Dedysh SN, Mardanov AV, Ravin NV. Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism. Front Microbiol 2022; 13:951761 [View Article]
    [Google Scholar]
22. Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK et al. Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature 2017; 552:400–403 [View Article] [PubMed]
    [Google Scholar]
23. Rodriguez‐R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol 2020; 22:3394–3412 [View Article] [PubMed]
    [Google Scholar]
24. Ward LM, Cardona T, Holland-Moritz H. Evolutionary implications of anoxygenic phototrophy in the bacterial phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 2019; 10:1658 [View Article]
    [Google Scholar]
25. Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM et al. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. ISME J 2016; 10:2352–2364 [View Article]
    [Google Scholar]
26. Xie R, Wang Y, Huang D, Hou J, Li L et al. Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. Sci China Life Sci 2022; 65:818–829 [View Article]
    [Google Scholar]
27. Jungbluth SP, Amend JP, Rappé MS. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci Data 2017; 4:170037 [View Article] [PubMed]
    [Google Scholar]
28. Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat Microbiol 2018; 3:328–336 [View Article] [PubMed]
    [Google Scholar]
29. Schwank K, Bornemann TLV, Dombrowski N, Spang A, Banfield JF et al. An archaeal symbiont-host association from the deep terrestrial subsurface. ISME J 2019; 13:2135–2139 [View Article] [PubMed]
    [Google Scholar]
30. Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL et al. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015; 17:4929–4941 [View Article] [PubMed]
    [Google Scholar]
31. Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Boone DR, Castenholz RW, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 1 New York: Springer; 2001 pp 213–235
    [Google Scholar]
32. Youssef NH, Farag IF, Hahn CR, Premathilake H, Fry E et al. Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst Appl Microbiol 2019; 42:85–93 [View Article]
    [Google Scholar]
33. Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun 2016; 7:10476 [View Article] [PubMed]
    [Google Scholar]
34. Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521:173–179 [View Article]
    [Google Scholar]
35. Bulzu P-A, Andrei A-Ş, Salcher MM, Mehrshad M, Inoue K et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019; 4:1129–1137 [View Article] [PubMed]
    [Google Scholar]
36. Yadav A, Vilcáez J, Farag IF, Johnson B, Mueller K et al. Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA. Syst Appl Microbiol 2020; 43:126057 [View Article]
    [Google Scholar]
37. Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ et al. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 2016; 1:16170 [View Article] [PubMed]
    [Google Scholar]
38. Dick GJ, Baker BJ. Omic approaches in microbial ecology: charting the unknown. Microbe Magazine 2013; 8:353–360 [View Article]
    [Google Scholar]
39. Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW et al. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ 2015; 3:e740 [View Article]
    [Google Scholar]
40. Barnum TP, Figueroa IA, Carlström CI, Lucas LN, Engelbrektson AL et al. Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities. ISME J 2018; 12:1568–1581 [View Article] [PubMed]
    [Google Scholar]
41. Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017; 541:353–358 [View Article] [PubMed]
    [Google Scholar]
42. Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 2015; 523:208–211 [View Article] [PubMed]
    [Google Scholar]
43. Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF. Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. Sci Rep 2017; 7:40101 [View Article] [PubMed]
    [Google Scholar]
44. Rinke C, Rubino F, Messer LF, Youssef N, Parks DH et al. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J 2019; 13:663–675 [View Article]
    [Google Scholar]
45. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219 [View Article]
    [Google Scholar]
46. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 2013; 31:533–538 [View Article] [PubMed]
    [Google Scholar]
47. Farag IF, Zhao R, Biddle JF. “Sifarchaeota,” a novel Asgard phylum from Costa Rican sediment capable of polysaccharide degradation and anaerobic methylotrophy. Appl Environ Microbiol 2021; 87:e02584-20 [View Article]
    [Google Scholar]
48. Kadnikov VV, Mardanov AV, Beletsky AV, Rakitin AL, Frank YA et al. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Syst Appl Microbiol 2019; 42:67–76 [View Article] [PubMed]
    [Google Scholar]
49. Cui G, Zhou Y, Li W, Gao Z, Huang J et al. A novel bacterial phylum that participates in carbon and osmolyte cycling in the Challenger Deep sediments. Environ Microbiol 2021; 23:3758–3772 [View Article] [PubMed]
    [Google Scholar]
50. Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee J-H et al. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939 [View Article] [PubMed]
    [Google Scholar]
51. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ et al. A new view of the tree of life. Nat Microbiol 2016; 1:16048 [View Article] [PubMed]
    [Google Scholar]
52. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007; 450:560–565 [View Article] [PubMed]
    [Google Scholar]
53. Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P. Lokiarchaea areclose relatives of euryarchaeota, not bridging the gap betweenprokaryotes and eukaryotes. PLoS Genet 2017; 13:e1006810:
    [Google Scholar]
54. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 2011; 39:3204–3223 [View Article]
    [Google Scholar]
55. Momper L, Jungbluth SP, Lee MD, Amend JP. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J 2017; 11:2319–2333 [View Article] [PubMed]
    [Google Scholar]
56. Meng J, Xu J, Qin D, He Y, Xiao X et al. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J 2014; 8:650–659 [View Article] [PubMed]
    [Google Scholar]
57. Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J 2014; 8:1452–1463 [View Article] [PubMed]
    [Google Scholar]
58. Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO₂ concentrations. Environ Microbiol 2017; 19:459–474 [View Article] [PubMed]
    [Google Scholar]
59. De Anda V, Chen L-X, Dombrowski N, Hua Z-S, Jiang H-C et al. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404 [View Article] [PubMed]
    [Google Scholar]
60. Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC et al. Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. Microbiome 2017; 5:112 [View Article]
    [Google Scholar]
61. Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R et al. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol 2016; 18:159–173 [View Article] [PubMed]
    [Google Scholar]
62. Dudek NK, Sun CL, Burstein D, Kantor RS, Aliaga Goltsman DS et al. Novel microbial diversity and functional potential in the marine mammal oral microbiome. Curr Biol 2017; 27:3752–3762 [View Article]
    [Google Scholar]
63. Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT et al. RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME J 2016; 10:2702–2714 [View Article] [PubMed]
    [Google Scholar]
64. He C, Keren R, Whittaker ML, Farag IF, Doudna JA et al. Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol 2021; 6:354–365 [View Article] [PubMed]
    [Google Scholar]
65. Kozubal MA, Romine M, Jennings R deM, Jay ZJ, Tringe SG et al. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J 2013; 7:622–634 [View Article] [PubMed]
    [Google Scholar]
66. Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW et al. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Sci China Life Sci 2020; 63:886–897 [View Article]
    [Google Scholar]
67. Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y et al. Potential for microbial H₂ and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J 2017; 11:1915–1929 [View Article] [PubMed]
    [Google Scholar]
68. McGonigle JM, Bernau JA, Bowen BB, Brazelton WJ. Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats. mSphere 2019; 4:e00378-19 [View Article]
    [Google Scholar]
69. L Bräuer S, Basiliko N, M P Siljanen H, H Zinder S. Methanogenic archaea in peatlands. FEMS Microbiol Lett 2020; 367:fnaa172 [View Article]
    [Google Scholar]
70. Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun 2019; 10:1822 [View Article]
    [Google Scholar]
71. Jay ZJ, Beam JP, Dlakić M, Rusch DB, Kozubal MA et al. Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nat Microbiol 2018; 3:732–740 [View Article] [PubMed]
    [Google Scholar]
72. Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2013; 2:e01102 [View Article]
    [Google Scholar]
73. Wang Y, Wegener G, Hou J, Wang F, Xiao X. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat Microbiol 2019; 4:595–602 [View Article]
    [Google Scholar]
74. Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 2015; 25:690–701 [View Article] [PubMed]
    [Google Scholar]
75. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 2012; 337:1661–1665 [View Article] [PubMed]
    [Google Scholar]
76. Fieseler L, Horn M, Wagner M, Hentschel U. Discovery of the novel candidate phylum “Poribacteria” in marine sponges. Appl Environ Microbiol 2004; 70:3724–3732 [View Article] [PubMed]
    [Google Scholar]
77. Dombrowski N, Seitz KW, Teske AP, Baker BJ. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. Microbiome 2017; 5:106 [View Article] [PubMed]
    [Google Scholar]
78. Wilson MC, Mori T, Rückert C, Uria AR, Helf MJ et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 2014; 506:58–62 [View Article] [PubMed]
    [Google Scholar]
79. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 2013; 4:2120 [View Article] [PubMed]
    [Google Scholar]
80. Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 2013; 4:1854 [View Article]
    [Google Scholar]
81. Katayama T, Nobu MK, Kusada H, Meng X-Y, Hosogi N et al. Isolation of a member of the candidate phylum “Atribacteria” reveals a unique cell membrane structure. Nat Commun 2020; 11:6381 [View Article] [PubMed]
    [Google Scholar]