The ISME Journal (2012) 6, 227–230 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej COMMENTARY Spotlight on the

C Brochier-Armanet, S Gribaldo and P Forterre

The ISME Journal (2012) 6, 227–230; doi:10.1038/ismej. In fact, many lineages of uncultivated have 2011.145; published online 10 November 2011 been reported based on 16S rRNA sequences (Prosser and Nicol, 2008), some of them belonging to the Thaumarchaeota (for example, group I.1c, 1A/ pSL12, ThAOA/HWCG III, SAGMCG-I, SCG and Over the last two decades, many new groups of FSCG, etc.) (Pester et al., 2011). However, the deeply branching uncultivated archaea have been situation is less clear for a few other uncultivated unveiled by molecular screening of 16S rRNA lineages (for example, HWCG I, Miscellaneous . Among these, Thaumarchaeota (Brochier- Crenarchaeotic Group, Marine Benthic Group B) Armanet et al., 2008) are now known to represent whose position is unresolved in rRNA phylogenies. a highly diversified and ancient present Regarding HWGC I, Nunoura and coworkers have in a wide variety of , including marine recently reconstituted the of one of its and fresh waters, soils and also hot environ- members, ‘Ca. Caldiarchaeum subterraneum’, using ments (Pester et al., 2011). The Thaumarchaeota a metagenomic library prepared from a geothermal have rapidly gained much attention after the water stream collected in a subsurface gold discovery that some of them are able to oxidize mine (Nunoura et al., 2011). Based on the ana- aerobically, providing the first example lysis of the genome sequence, they proposed of in the Archaea and therefore extend- that ‘Ca. C. subterraneum’ represents a novel ing the range of microorganisms capable of this archaeal phylum, which was tentatively called important , which was previously ‘’. However, in contrast to rRNA trees, thought to be restricted to a few proteobacterial ‘Ca. C. subterraneum’ appears robustly grouped lineages (Konneke et al., 2005). The interest raised with Thaumarchaeota in -based phylogenies by Thaumarchaeota is witnessed by the growing (Brochier-Armanet et al., 2011, Nunoura et al., availability over the last 4 years of isolated 2011). This suggests that HWCG I might represent representatives (or enrichment cultures) and of a basal thaumarchaeal lineage, although more data genomic data. This opens up a whole new perspec- from additional representatives is surely necessary tive on the diversity of Archaea and on ancient to clarify the issue. evolution. Further exploration of Thaumarchaeota—including uncultivated subgroups—will be essential to deline- ate more precisely this phylum from a biological, A diverse and ancient phylum ecological and evolutionary point of view. For instance, it will be interesting to know if crenarch- Isolates or enrichment cultures from groups I.1a aeol, a specific lipid identified in the membranes of ( symbiosium and various Thaumarchaeota and recently proposed to maritimus), I.1b (‘Ca. viennensis’) be renamed thaumarchaeol (Pester et al., 2011), is a and ThAOA/HWCG III (‘Ca. Nitrosocaldus yellow- specific feature of the whole phylum. Similarly, it stonii’) have now been reported. In addition, will be important to explore all thaumarchaeal complete genome sequences are now available from lineages for the presence of members capable of three Thaumarchaeota belonging to the marine ammonia oxidation. Indeed, it is possible that not all group I.1a (C. symbiosium, N. maritimus and Thaumarchaeota are ammonia oxidizers, and a key ‘Candidatus (Ca.) Nitrosoarchaeum limnia’), and question will be to understand whether this partial genome data has been released from a important metabolism is ancestral in the phylum, moderately thermophilic strain from soil, ‘Ca. or rather appeared later during its diversification. ’ (group I.1b) (see Brochier- For example, the ‘Ca. C. subterraneum’ composite Armanet et al. (2011) and references therein). genome seems to lack the genes coding for ammo- Importantly, these sequence data have confirmed nia-oxidation enzymes. This might suggest that the genomic features and phylogenetic distinctive- ammonia oxidation appeared in Thaumarchaeota ness of the Thaumarchaeota (Spang et al., 2010). after the divergence of HWCG I, but further data Currently available genomic data are, however, far from additional HWCG I representatives and from from covering the whole diversity of this phylum. other deeply branching uncultivated thaumarchaeal Commentary 228 lineages are required to conclude about this cellular systems, sometimes shared either with important issue. Moreover, the exploration of the Bacteria or Eucarya, appears to be a common feature biology and ecological diversity of Thaumarchaeota in Archaea (Brochier-Armanet et al., 2011). The is expected to continue revealing a high diversity of availability of genomic data from the Thaumarch- cellular forms and lifestyles. For example, marine aeota has allowed making this phenomenon all the giant Thaumarchaeota forming multicellular fila- more evident. For instance, the analysis of thau- ments possibly associated with bacterial ectosym- marchaeal has revealed a unique combina- bionts have been recently reported from sulfide rich tion of features shared either with , environments of a mangrove tropical swamp (Muller or (Figure 1). A striking et al., 2010). Finally, the availability of genomic data example is the presence of components of two very from a wide variety of thaumarchaeal lineages will different cell division systems: Cdv, previously provide material for the establishment of a detailed thought to be present only in some Crenarchaeota, classification of Thaumarchaeota, and will help and FtsZ, so far thought to be specific of Euryarch- clarifying their phylogenetic relationships with the aeota and Korarchaeota (see Makarova et al. (2010) other major archaeal phyla. and references therein). A major question to be addressed is how these two cell division systems coexist and function in Thaumarchaeota. Interest- A hot-loving ancestor? ingly, the major partner of FtsZ in Bacteria, MinD, is present in Euryarchaeota (Gerard et al., 1998) The presence of Thaumarchaeota, not only in but not in Thaumarchaeota (unpublished observa- mesophilic but also in thermophilic environments tions), suggesting a different role for FtsZ in (de la Torre et al., 2008), confirms the wide range of these two archaeal phyla. The forthcoming avail- phenotypes present in this phylum. It is worth ability of genomic sequence data from basal un- noting that the deepest thaumarchaeal branches are cultured groups will likely confirm the cellular composed of uncultivated groups from various hot systems in the Archaea. As an example, a eukar- environments (de la Torre et al., 2008). This yotic-like ubiquitin modifier system has been found observation, together with the presence of a in the genome of ‘Ca. C. subterraneum’ that is very reverse gyrase in the genome of Ca. C. subterraneum different from those recently identified in prokar- (Nunoura et al. 2011), suggests that the ancestor of yotes (Nunoura et al., 2011), and a eukaryotic-like Thaumarchaeota and ‘Aigarchaeota’ was at least actin has been discovered in Korarchaeota, some , and that mesophily in some thau- Crenarchaeota (Makarova et al., 2010) and more marchaeal lineages is a derived character. The recently in ‘Ca. C. subterraneum’ (Brochier-Armanet analysis of environmental sequences from Thau- et al., 2011) (Figure 1). The distribution of these marchaeota indicates that adaptation to mesophily components may result from horizontal trans- may have been helped through horizontal gene fers between Archaea and Eucarya, Archaea and transfer from bacteria or from mesophilic archaea Bacteria or among Archaea, but may also represent (Lopez-Garcia et al., 2004). Because secondary ancient traits that were present in the common adaptations to mesophily are also observed in ancestor of Archaea and were subsequently lost in Euryarchaeota, this would be consistent with the different archaeal lineages. Investigating further the hypothesis of multiple independent adaptations to great plasticity of archaeal cellular systems, their mesophily in the Archaea from thermophilic or origin and function, will surely provide important hyperthermophilic ancestors. This scenario is also information on the evolutionary paths and adap- supported by recent inferences of ancestral archaeal tive strategies followed by Archaea along their rRNA and protein sequences (Groussin and Gouy, diversification. 2011). The growing availability of genomic data Besides providing insights into the early evolu- from Thaumarchaeota will now allow studying in a tion of cellular features, the discovery of Thau- more precise way such adaptations from thermo- marchaeota is also crucial for understanding the phily to mesophily, for example, whether they have nature of ancient microbial communities. For followed similar or different evolutionary paths example, bacterial nitrification appears to be a with respect to the Euryarchaeota. recent feature because it is present only in a few late-emerging subgroups of g- and b-proteobacteria (Konneke et al., 2005). Therefore, it is tempting A new perspective on archaeal biology to speculate that the very ancient traces of nitri- and ancient evolution fication recently suggested by isotopic records from the late Archaean (Garvin et al., 2009) may The discovery of Thaumarchaeota opens up new have been produced by the activity of ancient perspectives on the biological diversity and ammonia-oxidizing Thaumarchaeota. In order to evolution of the Archaea, along with the relation- test this hypothesis, it will be essential to establish ships of this of life with Bacteria and whether nitrification is widespread in Thaumarch- Eucarya. An uneven distribution among archaeal aeota and whether it is an ancestral ability in this lineages of components involved in important phylum.

The ISME Journal Commentary 229

THAUMARCHAEOTA

C. symbiosum N. maritimus Ca. N. gargensis ‘Aigarchaeota’ Korarchaeota Crenarchaeota Euryarchaeota Translation: S25e (COG4901/arCOG04327); S26e (COG4830/arCOG04305); S30e (COG4919/arCOG04293) L13e (COG4352/arCOG01013) L14e (COG2163/arCOG04167)*; L34e (COG2174/arCOG04168) L38e (arCOG04057) L29p (COG0255/arCOG00785)* LXa (COG2157/arCOG04175) L39e (COG2167/arCOG04177)

Transcription: RpoA (COG0086/arCOG04256)* RpoA split (COG0086/arCOG04256) RpoB (COG0085/arCOG01762)* RpoB split (COG0085/arCOG01762) RpoG/Rpb8 (arCOG04271) MBF1 (COG1813/arCOG01863) ELF1 (COG4888/arCOG04136) Replication:

DNA pol D small + large subunits (COG1311/arCOG04455 + COG1933/arCOG04447) Euryarchaeota-like RPA (COG1599/arCOG01510) RPA/SSB single OB-fold (COG1599/arCOG01510) Many PCNA homologues (COG0592/arCOG00488)*

Topoisomerases: Topoisomerase IA (COG0550/arCOG01527)* Topoisomerase IB (COG3569)* Reverse gyrase (COG1110/arCOG01526)* Gyrase subunits A+B (COG0187/arCOG04371 + COG0188/arCOG04367)*

Cell division: CdvB/ESCRT-III/Snf7 (COG5491/arCOG00452) CdvC/ Vsp4 (COG0464/arCOG01307) CdvA Eukaryotic-like actin (COG5277/arCOG05583) FtsZ (COG0206/arCOG02201)* Smc (COG1196/arCOG00371)* ScpA (COG1354/arCOG02610)* + ScpB (COGarCOG02613)

Histones: Histones H3/H4 (COG2036/arCOG02144)

Repair: ERCC4-type nuclease (COG01948/arCOG04206)* F ERCC4-type helicase (COG1111/arCOG00872)* RadB (COG0468/arCOG00417)* RadA (COG0468/arCOG00415)* DnaK (COG0443/arCOG03060)*; GrpE (COG0576/arCOG04772)*; DnaJ (COG0484)* uvrA (COG0178/arCOG04694)*; uvrB (COG0556/arCOG04748)*; uvrC (COG0322/arCOG04753)*

Figure 1 Distribution of information-processing and cell division components in Archaea. Data were extracted from Spang et al. (2010) and Brochier-Armanet et al. (2011). Note that this list is susceptible to evolve with the availability of new archaeal genome sequences. The relationships among main archaeal lineages are still unclear apart from the grouping of Thaumarchaeota and ‘Aigarchaeota’ in agreement with Brochier-Armanet et al. (2011) and Nunoura et al. (2011). Black and empty squares indicate the presence or absence of the corresponding gene in a given lineage, whereas hashed squares indicate the presence in only a few members. ‘F’ indicates that the corresponding genes are fused. The genes that are also present in Eucarya are underlined, whereas those present also in Bacteria are indicated by asterisks.

Perspectives whereas FtsZ appears not to be and is suggested to have developed a new function in Thaumarchaeota Microbes have dominated most of the life history (Pelve EA, LindI´s AC, Martens-Habbena W, de la and are a fundamental part of the biosphere. The Torre JR, Stahl DA, Bernander R. (2011). Cdv-based study of microbial diversity and evolution is there- cell division and cell cycle organization in the fore an essential issue in Biology, and many thaumarchaeon Nitrosopumilus maritimus. Mol unexpected findings are being unveiled from the Microbiol 82: 555–566). investigation of poorly known microbial lineages. The example of Thaumarchaeota underlines the fact that the exploration of many uncultivated or unexplored microbial lineages is likely to provide Acknowledgements key information on all aspects—biological, evolu- We wish to thank three anonymous referees for their tionary and ecological—of the microbial world. useful comments, and apologize to colleagues whose work could not be directly cited due to constraints on the number of allowed references. Note added in proof While this article was in press, the group of Rolf C Brochier-Armanet at Aix-Marseille Universite´, Bernander reported experimental data showing Laboratoire de chimie bacte´rienne, CNRS, that Cdv is the main system implicated in cell UPR9043, IFR88, 31 chemin Joseph Aiguier, division in the thaumarchaeon N. maritimus, Marseille, France

The ISME Journal Commentary 230 C Brochier-Armanet is now at Universite´ Lyon 1; Pyrococcus AL585, and phylogenetic characterization CNRS; UMR5558, Laboratoire de Biome´trie et of related in the three domains of life. Gene 222: 99–106. Biologie Evolutive, 43 boulevard du 11 novembre Groussin M, Gouy M. (2011). Adaptation to environmental 1918, F-69622 Villeurbanne, France; temperature is a major determinant of molecular S Gribaldo is at Institut Pasteur, Unite´ Biologie evolutionary rates in archaea. MolBiolEvol28: Mole´culaire du Ge`ne chez les Extreˆmophiles 2661–2674. (BMGE), De´partement de Microbiologie, Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. (2005). Isolation of an 28 rue du Dr Roux, Paris, France; autotrophic ammonia-oxidizing marine archaeon. P Forterre is at Institut Pasteur, Unite´ Biologie Nature 437: 543–546. Mole´culaire du Ge`ne chez les Extreˆmophiles Lopez-Garcia P, Brochier C, Moreira D, Rodriguez-Valera F. (BMGE), De´partement de Microbiologie, (2004). Comparative analysis of a genome fragment of 28 rue du Dr Roux, Paris, France; and an uncultivated mesopelagic Crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol P Forterre is also at Univ Paris-Sud, Institut de 6: 19–34. Ge´ne´tique et Microbiologie (IGM), CNRS UMR8621, Makarova KS, Yutin N, Bell SD, Koonin EV. (2010). Orsay Cedex, France Evolution of diverse cell division and vesicle formation E-mail: [email protected]; systems in Archaea. Nat Rev Microbiol 8: 731–741. [email protected] Muller F, Brissac T, Le Bris N, Felbeck H, Gros O. (2010). First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts References in a sulfidic marine habitat. Environ Microbiol 12: 2371–2383. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, (2008). Mesophilic Crenarchaeota: proposal for a third Kazama H et al. (2011). Insights into the evolution of archaeal phylum, the Thaumarchaeota. Nat Rev Archaea and eukaryotic protein modifier systems Microbiol 6: 245–252. revealed by the genome of a novel archaeal group. Brochier-Armanet C, Forterre P, Gribaldo S. (2011). Nucleic Acids Res 39: 3204–3223. Phylogeny and evolution of the Archaea: one hundred Pester M, Schleper C, Wagner M. (2011). The Thaumarch- genomes later. Curr Opin Microbiol 14: 274–281. aeota: an emerging view of their phylogeny and de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl ecophysiology. Curr Opin Microbiol 14: 300–306. DA. (2008). Cultivation of a thermophilic ammonia Prosser JI, Nicol GW. (2008). Relative contributions of oxidizing archaeon synthesizing . archaea and bacteria to aerobic ammonia oxidation in Environ Microbiol 10: 810–818. the environment. Environ Microbiol 10: 2931–2941. Garvin J, Buick R, Anbar AD, Arnold GL, Kaufman AJ. Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, (2009). Isotopic evidence for an aerobic Tischler P, Spieck E et al. (2010). Distinct gene set in in the latest Archean. Science 323: 1045–1048. two different lineages of ammonia-oxidizing archaea Gerard E, Labedan B, Forterre P. (1998). Isolation of a supports the phylum Thaumarchaeota. Trends Micro- minD-like gene in the hyperthermophilic archaeon biol 18: 331–340.

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