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Archaea: why science is so interested in this ancient life form

Roxane Lestini
Professor of Biology at École Polytechnique (IP Paris)
Béatrice Clouet-d'Orval
Research Director at Centre de Biologie intégrative de l'Université de Toulouse
Key takeaways
  • Archaea are a form of life that is genetically distinct from bacteria and eukaryotes: they make up a new category of life.
  • However, they share common traits with both bacteria and eukaryotes, prompting researchers to study the relationship between these forms of life.
  • Metagenomics reveals that archaea are present in all types of environments: volcanic, oceanic, terrestrial and even human.
  • Studying archaea would make it possible to improve bioindustrial production systems or to imagine life forms found beyond Earth.

As soon as you read the name ‘archaea’ you may feel like you are talk­ing about a spe­cialised sub­ject… But it is just anoth­er form of life, like bac­te­ria. So why all the fuss? The answer is found in both the way they were dis­cov­ered and because of the role they might have played in our evo­lu­tion­ary history.

An unusual life form

“At first, we referred to them as Archae­bac­te­ria, but this led to some con­fu­sion,” says Rox­ane Les­ti­ni, a pro­fes­sor at École Poly­tech­nique (IP Paris). We need to go back to the dis­cov­ery of this cell form to appre­ci­ate the misunderstanding. 

Béa­trice Clou­et-d’Or­val, a CNRS researcher at the Cen­tre for Inte­gra­tive Biol­o­gy in Toulouse, agrees. “When they were dis­cov­ered 40 years ago, we thought they were a spe­cial type of bac­te­ria… They are the same size, have the same type of mor­phol­o­gy and their DNA is not enclosed in a nucle­us.” Like bac­te­ria, archaea are only found in sin­gle cell form: they are not mul­ti­cel­lu­lar organisms. 

These obser­va­tions led sci­en­tists to believe that they were relat­ed to bac­te­ria and not to the oth­er known type of cells: eukary­otes. The lat­ter group includes all ani­mals and plants, which are made from cells that are com­part­men­talised and with DNA trapped inside a nucle­us. Biol­o­gists at the time not­ed some pecu­liar­i­ties in archaea, such as the com­po­si­tion of their cel­lu­lar mem­brane, which was made up of ethers and not esters like bac­te­ria, with­out this call­ing into ques­tion its clas­si­fi­ca­tion. At the very least, they were not ordi­nary bac­te­ria: per­haps prim­i­tive bacteria?

With the study of genomes, we realised that these were not bacteria.

This hypoth­e­sis was swept away by the first analy­ses of genet­ic mate­r­i­al, car­ried out by the Amer­i­can biol­o­gists Carl Woese and George Fox in 19771. “With the study of genomes, and in par­tic­u­lar the one that codes for ribo­so­mal RNA, which is an essen­tial cel­lu­lar machin­ery for life, we under­stood that these were not bac­te­ria,” explains Béa­trice Clou­et-d’Or­val. The dif­fer­ences between the sequences revealed that we need to con­sid­er not two but three areas of life: bac­te­ria, eukary­otes, and archaea. 

Bacteria, eukaryotes, archaea… what connects these life forms?

How are these three life forms relat­ed?  In 2015, this ques­tion is mak­ing progress. “A sam­pling study car­ried out in under­wa­ter vol­ca­noes off the coast of Nor­way2 uncov­ered archaea with pro­teins that were only pre­vi­ous­ly known in eukary­otes, for exam­ple mol­e­cules that go from the nucle­us to the cyto­plasm,” says Rox­ane Les­ti­ni. This is sur­pris­ing for cells with­out a nucle­us! “This was very con­tro­ver­sial, many thought it was an anom­aly,” says the researcher. 

But oth­er stud­ies have con­firmed these find­ings. “We now know that their cel­lu­lar mech­a­nisms – repli­some, ribo­some, genome main­te­nance sys­tems, tran­scrip­tion mech­a­nisms and so on – are very sim­i­lar to those of eukary­otes. This is why it is assumed that archaea are involved in the evo­lu­tion of eukary­otes,” explains Béa­trice Clouet-d’Orval.

There are thus two hypothe­ses to describe the his­to­ry of the first liv­ing cells, start­ing with LUCA (Last Uni­ver­sal Com­mon Ances­tor). In the first hypoth­e­sis, eukary­otes are derived from archaea. In the sec­ond, archaea and eukary­otes are derived from a com­mon ances­tor that is not known.

It is not easy to dif­fer­en­ti­ate between these two hypothe­ses. “There are no fos­sils for sin­gle-cell struc­tures,” insists Béa­trice Clou­et-d’Or­val. “It is pos­si­ble that eukary­otes are in fact archaea. What’s more, we are increas­ing­ly find­ing archaea that are very sim­i­lar to eukary­ot­ic cells, such as Asgards that have been dis­cov­ered in the deep ocean. Their bio­chem­istry seems to cre­ate a bridge between the first archaea dis­cov­ered and mod­ern eukary­ot­ic cells3.” 

From there, it is easy to believe that these archaea could have giv­en rise to the first eukary­ot­ic cell… a step quick­ly tak­en by some biol­o­gists. But Rox­ane Les­ti­ni points out, “noth­ing is cer­tain because with uni­cel­lu­lar organ­isms, hor­i­zon­tal gene trans­fers [the pas­sage of a piece of DNA from one cell to anoth­er, from one species to anoth­er, with­out any rela­tion­ship of descent] are fre­quent and con­fuse the evo­lu­tion­ary analy­sis of uni­cel­lu­lar organ­isms”. There is still much con­tro­ver­sy around this subject.

Archaea, everywhere

Beyond the ques­tion of ori­gins, the mol­e­c­u­lar prox­im­i­ty between archaea and eukary­otes is of great inter­est to biol­o­gists. Rox­ane Les­ti­ni points out that “they are good mod­els of eukary­ot­ic cells, close but less com­plex”. But they are still quite dif­fi­cult to manip­u­late. Béa­trice Clou­et-d’Or­val adds, “archaea are dif­fi­cult to cul­ti­vate. For a long time, this was an obsta­cle to their study, but today we have more and more strains adapt­ed to the laboratory.”

It was also their nat­ur­al envi­ron­ment that had to be revis­it­ed. “Ini­tial­ly, they were only found in extreme envi­ron­ments, such as ocean­ic rifts and vol­ca­noes. But recent metage­nom­ic tools show that they are present in all types of envi­ron­ments,” explains Béa­trice Clou­et-d’Or­val. Metage­nomics makes it pos­si­ble to under­take a blind analy­sis of life forms in an envi­ron­ment by detect­ing fun­da­men­tal mol­e­cules and asso­ci­at­ing them with data­bas­es of liv­ing organisms. 

Recent metage­nom­ic tools show that archaea are present in all types of environments.

This tech­nique has also made it pos­si­ble to reveal that archaea even live… in us, in our micro­bio­ta, with­in the microbes that pop­u­late our intestines, but also our skin, our nasal cav­i­ties and the uterus4. “There is a great phe­no­typ­ic vari­ety in archaea, and they are present in many eco­log­i­cal habi­tats,” says Béa­trice Clou­et-d’Or­val. So, should we be con­cerned about these lit­tle-known microbes? “They have nev­er been iden­ti­fied as path­o­gen­ic,” reas­sures the Toulouse researcher.

Under­stand­ing the role of these life forms in their ecosys­tems is anoth­er grow­ing field of research. “We know, for exam­ple, that they play an impor­tant role in the nitri­fi­ca­tion of soils,” explains Rox­anne Lestini. 

As for their bio­log­i­cal and chem­i­cal prop­er­ties, they are draw­ing the inter­est of indus­tri­al­ists and biotech­nol­o­gy spe­cial­ists. They are being stud­ied to devel­op new PCR tech­niques, improve bioin­dus­tri­al pro­duc­tion sys­tems and make ster­ile pro­duc­tion safer. They are even good can­di­dates for imag­in­ing life forms beyond Earth.

Agnès Vernet
1CR Woese, GE Fox, PNAS (1977) 74, 5088–90 
2Spang, A. et al. Nature (2015) 521, 173–179 
3K. Zarem­ba-Niedzwiedz­ka et al., Nature (2017) 54, doi:10.1038/nature21031
4R. Moham­madzadeh et al. Cur­rent Opin­ion in Micro­bi­ol­o­gy 2022, https://​doi​.org/​1​0​.​1​0​1​6​/​j​.​m​i​b​.​2​0​2​2​.​1​02146

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