候选门级辐射类群

候选门级辐射类群
Drawing of a CPR bacterium from a "GWB1" sample.
科学分类
域：	细菌域 Bacteria
（未分级）：	地位未定 incertae sedis
（未分级）：	细菌候选门 Bacteria candidate phyla
下界：	候选门级辐射类群 Candidate phyla radiation
異名
Patescibacteria

候选门级辐射类群（英語：candidate phyla radiation，简称CPR group）是细菌的一个演化辐射分支，其中的物种大多数尚未被培养，只能从宏基因组和单细胞测序得知其存在。由于它们的体积只有纳米级，与其他细菌相比极为微小，因而也被称为“纳米细菌”（英語：nanobacteria，纳米细菌也可以指一类曾被认为是细菌的纳米级大小的矿物，二者没有直接关系）或“超小细菌”（英語：ultra-small bacteria）。

在研究早期（2016年前后），候选门级辐射类群被认为可能含有70多个门，代表了细菌中15%的门级多样性，^[1] 然而，根据基于相对演化分歧的基因组分类数据库（英语：Genome Taxonomy Database）（GTDB），认为它只是一个单一的门，^[2]早期的高估是源于核糖体蛋白的快速进化。^[3]通常来说，候选门级辐射类群的细菌基因组较小，缺少几种生物合成途径以及核糖体蛋白。因此人们猜测它是专性共生生物。^[4][5]

早期研究中，学者将现属于本类群的几个门归类为一个超门，命名为Patescibacteria，^[6]因此，这个名称也被视为候选门级辐射类群的一个异名，^[7]现在GTDB中仍在使用这个名称，因为本类群在该数据库中被视为一个门。^[2]

特征

尽管有一些例外，本类群的成员基本上缺少一些氨基酸和核苷酸的生物合成通路。目前为止，没有基因组证据可以证明它们能产生一些细胞套膜（英语：Cell envelope）形成时必须的脂质。^[5]此外，它们往往还缺乏完整的三羧酸循环和电子传递链复合体，包括三磷酸腺苷合酶。这些通路在大多数自由生活的原核生物中广泛存在，该类群缺少这些通路可能说明该类群可能主要由专性发酵共生生物组成。^[8]

本类群的成员一般难以培养，因此在依赖培养的研究方法中会被遗漏。此外，它们有一些独特的核糖体特征，因此在依赖16S rRNA的研究中也会被遗漏。它们的rRNA基因似乎负责编码蛋白质，并且含有自我剪接内含子（英语：Group_I_catalytic_intron），这些特征在细菌中很少见，不过之前也有发现过。^[9]由于这些内含子，本类群的成员在16S rRNA的研究中无法被检测到；此外，所有成员都缺乏L30核糖体蛋白质（英语：60S ribosomal protein L7），这是一种在营共生生活的细菌中常见的特征。^[8]

它们的许多特征与DPANN（英语：DPANN）类古菌相似或类似。^[5]

进化

2016年的一个基于核糖体蛋白的生命之树。^[4]

基于核糖体蛋白和RNA聚合酶亚基的细菌和古细菌的系统发育^[10]

早期的一些基于核糖体蛋白和蛋白家族的系统发育研究认为候选门级辐射类群是细菌中最早分化的谱系，以下是各个门（正常字体）和超门（粗体）之间的系统发育关系：^[5][4]

细菌域（Bacteria）	其它细菌类群   候选门级辐射 类群（CPR）   Wirthbacteria         Dojkabacteria       Katanobacteria     Microgenomates             Berkelbacteria     解糖微小寄生菌门（Saccharibacteria）           Peregrinibacteria       Absconditabacteria     Gracilibacteria         Parcubacteria

然而，一些最近的研究认为，候选门级辐射类群属于大地菌类，与绿弯菌门关系较近，^[11][12][13]根据这些研究，候选门级辐射类群与相关细菌类群的进化关系如下：

细菌域（Bacteria）	薄壁菌门（Gracilicutes）   大地菌（Terrabacteria）   DST       蓝菌/黑水仙菌（Cyanobacteria/Melainabacteria）         芽孢杆菌门（Bacillota）及软壁菌门（Mycoplasmatota）     放线菌门（Actinomycetota）           装甲菌门（Armatimonadota）     Eremiobacteraeota         候选门级辐射类群（CPR）       Dormibacteraeota     绿弯菌门（Chloroflexota）

临时分类

根据{{tsl|en|International Code of Nomenclature of Prokaryotes|国际原核生物命名法规]]，原核生物类群必须有纯培养物才能获得正式名称，而候选门级辐射类群的绝大多数物种无法满足这个资格。然而，一些临时名称或候选名称（英语：Candidatus）已经得到公认。^[6][14]到2017年为止，本类群下有Parcubacteria和Microgenomates两个超门得到承认。^[1]候选门级辐射类群下的门包括：

Patescibacteria的系统发育[15][16][17]

"Wirthbacteria" (CG2-30-54-11)       "Microgenomates"   "Dojkabacteria"       "Katanobacteria" (WWE3)     "Microgenomatia"     cluster       "Saccharibacteria"   "Berkelbacteria" (UBA1384)       "Kazanbacteria" (Kazan)       "Howlettbacteria" (CPR2) ^[與來源不符]     "Saccharimonadia"       cluster     "Gracilibacteria"   "Absconditabacteria" (JAEDAM01)     "Gracilibacteria"   cluster "Parcubacteria"   "Doudnabacteria"       "Andersenbacteria"         "Torokbacteria" (GCA-2792135)     ABY1       "Paceibacteria"       cluster

Microgenomatia的系统发育[15][16][17]

"Woykebacterales" (CG2-30-54-11)       "Curtissbacterales"     "Daviesbacterales"             "Roizmanbacterales" (UBA1406)       "Gottesmanbacterales" (UBA10105)     "Levybacterales"           GWA2‑44‑7   "Amesbacteraceae"       "Blackburnbacteraceae" (UBA10165)     "Woesebacteraceae" (UBA8517)             "Shapirobacterales" (UBA12405)     "Chazhemtobacteriales"   "Beckwithbacteraceae" (CG1-02-47-37)         "Collierbacteraceae" (UBA12108)     "Chazhemtonibacteraceae"         "Chisholmbacteraceae"       "Cerribacteraceae" (UBA12028)     "Pacebacteraceae" (PJMF01)

Gracilibacteria的系统发育[15][16][17]

"Absconditabacteria"   "Ca. Altimarinus" {BD1-5: UBA6164}     "Absconditicoccaceae" {"Absconditabacterales"}     "Gracilibacteria"   "Abawacabacteriales" (RBG-16-42-10)       "Peregrinibacterales" (UBA1369)       "Fallacibacteriales" (UBA4473)     "Peribacterales"

ABY1的系统发育[15][16][17]

"Kerfeldbacterales" (SBBC01)         "Jacksonbacterales" (UBA9629)       "Komeilibacterales" (UBA1558)     "Kuenenbacterales" (UBA2196)             "Veblenbacterales"       "Magasanikbacterales"     "Uhrbacterales" (SG8-24)           "Buchananbacterales"       "Falkowbacterales" (BM507)     "Moisslbacterales" (UBA2591)

Paceibacteria的系统发育[15][16][17]

"Moranbacterales"       UBA6257   "Brennerbacteraceae"       "Jorgensenbacteraceae" (GWB1-50-10)       "Wolfebacteraceae" (UBA9933)       "Colwellbacteraceae" (UBA9933)       "Harrisonbacteraceae" (WO2-44-18)     "Liptonbacteraceae" (2-01-FULL-56-20)                       "Spechtbacterales"     "Terrybacterales"         "Parcunitrobacterales" (GWA2-38-13b)       "Portnoybacterales"     "Paceibacterales"   "Wildermuthbacteraceae" (UBA10102)       "Gribaldobacteraceae" (CG1-02-41-26)       "Paceibacteraceae" ("Parcubacteria")       "Nealsonbacteraceae" (PWPS01)     "Staskawiczbacteraceae"                       "Azambacterales" (UBA10092)       "Yanofskybacterales" (2-02-FULL-40-12)       "Sungbacterales"       "Ryanbacterales"       "Giovannonibacterales" (UBA11713)       "Niyogibacterales" (HO2-45-28)       "Tagabacterales"     UBA9983   "Vogelbacteraceae" (XYD1-FULL-46-19)       "Yonathbacteraceae" (UBA1539)       "Nomurabacteraceae" (UBA9973)         "Adlerbacteraceae" (SBAW01)     "Kaiserbacteraceae" (UBA2163)         "Campbellbacteraceae" (UBA12079)       "Taylorbacteraceae" (PALSA-1337)     "Zambryskibacteraceae"

• ?"Elulimicrobiota" Rodriguez-R et al. 2020
• Clade "Patescibacteria" Rinke et al. 2013
  • "Wirthbacteria" Hug et al. 2016
  • Microgenomates Cluster
    • "Dojkabacteria" Wrighton et al. 2016 (WS6)
    • "Katanobacteria" Hug et al. 2016b (WWE3)
    • Superphylum Microgenomates
      • "Woykebacteria" Anantharaman et al. 2016 (RIF34)
      • "Curtissbacteria" Brown et al. 2015
      • "Daviesbacteria" Brown et al. 2015
      • "Roizmanbacteria" Brown et al. 2015
      • "Gottesmanbacteria" Brown et al. 2015
      • "Levybacteria" Brown et al. 2015
      • "Shapirobacteria" Brown et al. 2015
      • Clade GWA2-44-7
        • ?"Genascibacteria" He et al. 2021
        • "Amesbacteraceaeia" Brown et al. 2015
        • "Blackburnbacteria" Anantharaman et al. 2016 (RIF35)
        • "Woesebacteria" Brown et al. 2015 (DUSEL-2, DUSEL-4)
      • Clade "Chazhemtobacteriales" Pallen, Rodriguez-R & Alikhan 2022 [UBA1400]
        • "Beckwithbacteria" Brown et al. 2015
        • "Collierbacteria" Brown et al. 2015 (MFAQ01)
        • "Chazhemtonibacteraceae" corrig. Kadnikov et al. 2020
        • "Chisholmbacteria" Anantharaman et al. 2016 (RIF36)
        • "Cerribacteria" Kroeger et al. 2018
        • "Pacebacteria" Brown et al. 2015 (PJMF01)
  • Gracilibacteria Cluster
    • Clade "Absconditabacteria"
      • "Absconditabacteria" Hug et al. 2016b (SR1)
      • "Ca. Altimarinus" Rinke et al. 2013 {BD1-5: UBA6164} (GN02)
    • Superphylum "Gracilibacteria"
      • "Abawacabacteria" Anantharaman et al. 2016 (RIF46)
      • "Peregrinibacteria" Brown et al. 2015 (PER)
      • "Fallacibacteriota" Dudek et al. 2017 ["Fertabacteria" (sic)] (DOLZORAL124_38_8)
      • "Peribacteria" Anantharaman et al. 2016
  • Saccharibacteria Cluster
    • "Berkelbacteria" Wrighton et al. 2014 (ACD58)
    • "Kazanbacteria" Jaffe et al. 2020 (Kazan)
    • "Howlettbacteria" Probst et al. 2018 (CPR2)^{[與來源不符]}
    • "Saccharibacteria" Albertsen et al. 2013 (TM7)
  • Parcubacteria Cluster
    • "Andersenbacteria" Anantharaman et al. 2016 (RIF9)
    • "Doudnabacteria" Anantharaman et al. 2016 (SM2F11)
    • "Torokbacteria" Probst et al. 2018
    • Clade ABY1
      • ?"Brownbacteria" Danczak et al. 2017
      • "Kerfeldbacteria" Anantharaman et al. 2016 (RIF4)
      • "Jacksonbacteria" Anantharaman et al. 2016 (RIF38)
      • "Komeilibacteria" Anantharaman et al. 2016 (RIF6)
      • "Kuenenbacteria" Brown et al. 2015
      • "Veblenbacteria" Anantharaman et al. 2016 (RIF39)
      • "Magasanikbacteria" Brown et al. 2015
      • "Uhrbacteria" Brown et al. 2015 (SG8-24)
      • "Buchananbacteria" Anantharaman et al. 2016 (RIF37)
      • "Falkowbacteria" Brown et al. 2015
      • "Moisslbacteria" Probst et al. 2018
    • Superphylum Parcubacteria
      • ?"Montesolbacteria " He et al. 2021
      • "Moranbacteria" Brown et al. 2015 (OD1-i)
      • Clade UBA6257
        • "Brennerbacteria" Anantharaman et al. 2016 (RIF18)
        • "Jorgensenbacteria" Brown et al. 2015
        • "Wolfebacteria" Brown et al. 2015
        • "Colwellbacteria" Anantharaman et al. 2016 (RIF41)
        • "Harrisonbacteria" Anantharaman et al. 2016 (RIF43)
        • "Liptonbacteria" Anantharaman et al. 2016 (RIF42)
      • "Spechtbacteria" Anantharaman et al. 2016 (RIF19)
      • "Terrybacteria" Anantharaman et al. 2016 (RIF13)
      • "Parcunitrobacteria" Castelle et al. 2017 (GWA2-38-13b)
      • "Portnoybacteria" Anantharaman et al. 2016 (RIF22)
      • Clade "Paceibacteria"
        • "Wildermuthbacteria" Anantharaman et al. 2016 (RIF21)
        • "Gribaldobacteria" Probst et al. 2018
        • "Paceibacteria"
        • "Nealsonbacteria" Anantharaman et al. 2016 (RIF40)
        • "Staskawiczbacteria" Anantharaman et al. 2016 (RIF20)
      • "Azambacteria" Brown et al. 2015
      • "Yanofskybacteria" Brown et al. 2015
      • "Sungbacteria" Anantharaman et al. 2016 (RIF17)
      • "Ryanbacteria" Anantharaman et al. 2016 (RIF10)
      • "Giovannonibacteria" Brown et al. 2015
      • "Niyogibacteria" Anantharaman et al. 2016 (RIF11)
      • "Tagabacteria" Anantharaman et al. 2016 (RIF12)
      • Clade UBA9973
        • ?"Hugbacteria" Danczak et al. 2017
        • ?"Llyodbacteria" Anantharaman et al. 2016 (RIF45)
        • "Vogelbacteria" Anantharaman et al. 2016 (RIF14)
        • "Yonathbacteria" Anantharaman et al. 2016 (RIF44)
        • "Nomurabacteria" Brown et al. 2015
        • "Adlerbacteria" Brown et al. 2015
        • "Kaiserbacteria" Brown et al. 2015
        • "Campbellbacteria" Brown et al. 2015
        • "Taylorbacteria" Anantharaman et al. 2016 (RIF16)
        • "Zambryskibacteria" Anantharaman et al. 2016 (RIF15)

目前的系统发育结果基于核糖体蛋白。^[4]其他方法，包括蛋白家族和16S 核糖体RNA，得到的结果类似但分辨率较低。^[18][1]

参见

• 细菌分类表

参考资料

1. Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ. Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. Microbiome. September 2017, 5 (1): 112. PMC 5581439 . PMID 28865481. doi:10.1186/s40168-017-0331-1 . 
2. Parks, Donovan; Chuvochina, Maria; Waite, David; Rinke, Christian; Skarshewski, Adam; Chaumeil, Pierre-Alain; Hugenholtz, Philip. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology. 27 August 2018, 36 (10): 996–1004 [13 January 2021]. PMID 30148503. S2CID 52093100. doi:10.1038/nbt.4229. 
3. Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria; Chaumeil, Pierre-Alain; Woodcroft, Ben J.; Evans, Paul N.; Hugenholtz, Philip; Tyson, Gene W. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology. November 2017, 2 (11): 1533–1542. PMID 28894102. doi:10.1038/s41564-017-0012-7 . 
4. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nature Microbiology. April 2016, 1 (5): 16048. PMID 27572647. doi:10.1038/nmicrobiol.2016.48 . 
5. Castelle CJ, Banfield JF. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell. March 2018, 172 (6): 1181–1197. PMID 29522741. doi:10.1016/j.cell.2018.02.016 . 
6. Rinke C; et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013, 499 (7459): 431–7. Bibcode:2013Natur.499..431R. PMID 23851394. doi:10.1038/nature12352 . hdl:10453/27467 . 
7. Beam, Jacob P.; Becraft, Eric D.; Brown, Julia M.; Schulz, Frederik; Jarett, Jessica K.; Bezuidt, Oliver; Poulton, Nicole J.; Clark, Kayla; Dunfield, Peter F.; Ravin, Nikolai V.; Spear, John R.; Hedlund, Brian P.; Kormas, Konstantinos A.; Sievert, Stefan M.; Elshahed, Mostafa S.; Barton, Hazel A.; Stott, Matthew B.; Eisen, Jonathan A.; Moser, Duane P.; Onstott, Tullis C.; Woyke, Tanja; Stepanauskas, Ramunas. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Frontiers in Microbiology. 2020, 11: 1848. PMC 7507113 . PMID 33013724. doi:10.3389/fmicb.2020.01848 . 
8. Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria (PDF). Nature. July 2015, 523 (7559): 208–11. Bibcode:2015Natur.523..208B. OSTI 1512215. PMID 26083755. S2CID 4397558. doi:10.1038/nature14486. 
9. Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. Prokaryotic introns and inteins: a panoply of form and function. Journal of Bacteriology. July 1995, 177 (14): 3897–903. PMC 177115 . PMID 7608058. doi:10.1128/jb.177.14.3897-3903.1995. 
10. Martinez-Gutierrez CA, Aylward FO. Phylogenetic signal, congruence, and uncertainty across bacteria and archaea. Molecular Biology and Evolution. 2021, 38 (12): 5514–5527. PMC 8662615 . PMID 34436605. doi:10.1093/molbev/msab254. 
11. Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA. A rooted phylogeny resolves early bacterial evolution. Science. 2021, 372 (6542). PMID 33958449. S2CID 233872903. doi:10.1126/science.abe0511. hdl:1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 . 
12. Martinez-Gutierrez CA, Aylward FO. Phylogenetic signal, congruence, and uncertainty across bacteria and archaea. Molecular Biology and Evolution. 2021, 38 (12): 5514–5527. PMC 8662615 . PMID 34436605. doi:10.1093/molbev/msab254. 
13. Taib N, Megrian D, Witwinowski J, Adam P, Poppleton D, Borrel G, Beloin C, Gribaldo S. Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition (PDF). Nature Ecology and Evolution. 2020, 4 (12): 1661–1672. PMID 33077930. S2CID 224810982. doi:10.1038/s41559-020-01299-7. 
14. Sayers. Patescibacteria group. National Center for Biotechnology Information (NCBI) taxonomy database. [2021-03-20]. 
15. GTDB release 09-RS220. Genome Taxonomy Database. [10 May 2024]. 
16. bac120_r220.sp_labels. Genome Taxonomy Database. [10 May 2024]. 
17. Taxon History. Genome Taxonomy Database. [10 May 2024]. 
18. Méheust, Raphaël; Burstein, David; Castelle, Cindy J.; Banfield, Jillian F. The distinction of CPR bacteria from other bacteria based on protein family content. Nature Communications. 13 September 2019, 10 (1): 4173. Bibcode:2019NatCo..10.4173M. PMC 6744442 . PMID 31519891. doi:10.1038/s41467-019-12171-z . 

外部链接

• Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there. by Ed Yong, April 12, 2016, atlantic.com.
• Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You; on: SciTechDaily; July 21, 2020; source: Forsyth Institute
• McLean, Jeffrey S.; Bor, Batbileg; Kerns, Kristopher A.; Liu, Quanhui; To, Thao T.; Solden, Lindsey; Hendrickson, Erik L.; Wrighton, Kelly; Shi, Wenyuan; He, Xuesong. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Reports. 2020, 32 (3): 107939. PMC 7427843 . PMID 32698001. bioRxiv 10.1101/258137 . doi:10.1016/j.celrep.2020.107939. 
• Bokhari, RH; Amirjan, N; Jeong, H; Kim, KM; Caetano-Anollés, G; Nasir, A. Bacterial Origin and Reductive Evolution of the CPR Group. Genome Biology and Evolution. 1 March 2020, 12 (3): 103–121. PMC 7093835 . PMID 32031619. doi:10.1093/gbe/evaa024 .