A Microbial Marriage Forged in Nitrate

Home , Ciliate, Endosymbiont, Eukaryote, Hydrogenosome

atmospheric composition on Earth today Evolutionary microbiology differ markedly from those that existed when life first emerged on this planet more than four billion years ago. During what is known as the Great Oxidation Event, around 2.1 bil- A microbial marriage lion years ago5, oxygen accumulated in the atmosphere and oceanic waters, a develop- forged in nitrate ment that had a major bearing on the course of life on Earth. Oxygen is toxic to most organ- William H. Lewis & Thijs J. G. Ettema isms that thrive in environments devoid of it. However, some microorganisms learnt to Symbiotic interactions between organisms have aided harness oxygen’s chemical properties, using major evolutionary transitions. The interaction between it as an electron acceptor in energy-generating two microorganisms has parallels with the evolution of pathways. This type of oxygen-dependent process, called aerobic respiration, is much more mitochondria — key organelles in eukaryotic cells. See p.445 energy-efficient than fermentation, a form of non-oxygen-dependent energy metabolism of ancient origin, which enables many anaerobic In the vast diversity of microbial life, numerous an endosymbiosis in which a host cell belong- organisms to survive without oxygen. examples exist of symbiosis — a process ing to a group of single-celled organisms called Eukaryotic cells probably arose sometime whereby different organisms maintain a stable Asgard archaea2,3 took up a type of bacterial cell after the Great Oxidation Event6, and their relationship with one another. Such inter that belonged to the phylum Proteobacteria 4. ability to perform aerobic respiration was actions generally offer some form of benefit Mitochondria in eukaryotic cells are consid- acquired through the mitochondrial endo- to one or more of the organisms involved. Graf ered to be the direct descendants of these once- symbiont. The capacity for efficient energy et al.1 report on page 445 the discovery of an free-living proteobacterial endosymbionts. production that this provided is thought to intriguing example of symbiosis between Graf and colleagues describe an intriguing have conferred selective advantages during microorganisms. This finding might shed light bacterial endosymbiont that they discov- eukaryotic evolution, although the exact con- on the types of process that led to the evolu- ered living in a ciliate, a type of eukaryotic, tribution to, for example, the emergence of tion of mitochondria, the energy-producing single-celled microbe. Although associa- cellular complexity is debated7. organelles found in eukaryotic cells (those tions between these types of organism are not Current evidence6 indicates that early eukar- containing a nucleus). uncommon, this particular case has some of yote evolution and diversification occurred In some cases, symbiotic partners can the hallmarks of the type of endosymbiosis under conditions in which oxygen was pres- become integrated in such a way that one part- that gave rise to mitochondria. That includes ent. However, some groups of eukaryotes ner is taken up into the cell of the other part- the production of energy in the form of ATP nevertheless thrive in environments devoid ner by a process called endosymbiosis (Fig. 1). molecules by the energy-generating process of oxygen. These anaerobic eukaryotes are Endosymbiotic interactions have enabled key known as respiration. This process is also con- thought to have evolved from aerobic mito- transitions during the history of life on Earth. A nected to a mechanism by which ATP might be chondrion-bearing ancestors. prime example of this is thought to be the inter exported from the endosymbiont to provide In the absence of oxygen, the anaerobic action that gave rise to the first eukaryotic cell. the host with energy. eukaryotes use a fermentation-based metab- This ancestral eukaryote probably formed from The environmental conditions and olism, which subjects them to more-stringent

a b Last ciliate c Anaerobic common ancestor ciliate

Hydrogenosome Asgard ATP Ciliate from Last eukaryotic O2 archaeal + H2O ATP common ancestor H+ Lake Zug host cell Aerobic respiration + H2 Mitochondrion using an ETC Fermentation ATP H+ + H2 ATP Eukaryotic Endosymbiosis O2 ATP + H2O diversification Endosymbiosis Nitrate + N Aerobic respiration 2 Anaerobic respiration using an ETC Other using an ETC Free-living lineages proteobacterial Free-living ancestor of mitochondria Gammaproteobacterium

Figure 1 | Organelle evolution. a, Eukaryotic cells, those with a nucleus adapted to thrive in environments without oxygen. The mitochondria of these (nucleus not shown), probably arose when a type of single-celled host called ciliates have evolved into organelles called hydrogenosomes. Anaerobic ciliates an Asgard archaeal cell2,3 took up a proteobacterial cell in a process called carry out fermentation, a process in which ATP is generated and hydrogen ions 4 + 1 endosymbiosis . The proteobacterium evolved to form mitochondrial (H ) gain electrons to form hydrogen (H2). Graf et al. report the discovery of an organelles in the last common ancestor of all eukaryotes. Through the anaerobic ciliate with a gammaproteobacterial endosymbiont. This bacterium’s

process of aerobic respiration, in which oxygen (O2) is consumed and water is genome encodes the components needed to generate ATP by converting nitrate

formed as electrons are transferred along an electron-transport chain (ETC), a to nitrogen (N2) using anaerobic respiration, and to export ATP to the host. mitochondrion produces energy in the form of ATP molecules. b, Eukaryotes This finding reveals how anaerobic ciliates can regain the ability to carry out diversified, and only some lineages, such as the last common ancestor of respiration using an ETC. These features are similar to processes associated with organisms called ciliates, retained mitochondria. c, Some lineages of ciliate mitochondrial evolution.

News & views energy regimes than those of aerobic eukar- mitochondria in eukaryotes. In both cases, res- production, has been replaced or retained in yotes. This kind of metabolism has arisen in piratory capacity was acquired by an anaerobic the ciliate’s hydrogenosomes. Evidence indicat- various types of anaerobic eukaryote, and is host cell through the metabolic integration of ing that the ATP transporter identified by Graf associated with the evolution of mitochon- a proteobacterial endosymbiont, and mecha- and colleagues can export ATP to the ciliate host dria into organelles called hydrogenosomes8. nisms can be identified for energy exchange would help to confirm the proposed symbiotic All hydrogenosomes have, to some degree, between symbiont and host cell. Furthermore, interaction. Further discovery and exploration lost mitochondrial pathways for aerobic res- a substantial reduction of the endosymbiont of similarly surprising symbiotic interactions in piration, and generate hydrogen rather than genome is observed, although mitochondrial poorly explored parts of the microbial world is carbon dioxide and water as an end product genomes are typically either much smaller than certainly an exciting prospect for the future. of their energy-generating pathways. Ciliates the endosymbiont genome observed by Graf are exceptionally effective at adapting to oxy- and colleagues, or have been lost completely William H. Lewis and Thijs J. G. Ettema are in gen-depleted environments, and mitochon- (as is the case for several hydrogenosomes10). the Laboratory of Microbiology, Wageningen drion-to-hydrogenosome transitions have Despite these fascinating similarities, there University and Research, NL-6708 WE occurred independently several times in this are also notable differences. Mitochondrial Wageningen, the Netherlands. W.H.L. is also in group of organisms9. endosymbiosis was a much more ancient the Department of Biochemistry, University of Graf and colleagues investigated an anaero- event, enlisting an archaeal host cell rather Cambridge, Cambridge, UK. bic ciliate belonging to the class Plagiopylea, than a modern eukaryotic cell. Mitochondria, e-mails: [email protected]; found in the deepest layers of Lake Zug in even if now reduced from their original form, [email protected] Switzerland. This environment lacks oxygen or even lost from some present-day eukar- 11 and contains relatively high levels of nitrate. yotes , became an integral part of eukary- 1. Graf, J. S. et al. Nature 591, 445–450 (2021). An initial assessment using microscopy otic cells. Genes inherited from the original 2. Eme, L., Spang, A., Lombard, J., Stairs, C. W. & revealed that, unusually, these ciliates have mitochondrial endosymbiont were often re Ettema, T. J. G. Nature Rev. Microbiol. 15, 711–723 (2017). 3. Zaremba-Niedzwiedzka, K. et al. Nature 541, 353–358 a bacterial endosymbiont (belonging to the targeted to the nuclear genome, and some of (2017). class Gammaproteobacteria), rather than an the proteins these genes encoded adopted var- 4. Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. archaeal endosymbiont that produces meth- ious functions throughout the cell. A similar Curr. Biol. 27, R1177–R1192 (2017). 5. Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. Nature 506, ane, which is the more typical type of endo- level of integration is unlikely for the bacterial 307–315 (2014). symbiont present in anaerobic ciliates. endosymbionts of the ciliate investigated. 6. Betts, H. C. et al. Nature Ecol. Evol. 2, 1556–1562 (2018). DNA-sequencing data for lake-water sam- Nevertheless, it would be interesting to 7. Pittis, A. A. & Gabaldón, T. Nature 531, 101–104 (2016). 8. Embley, T. M. Phil. Trans. R. Soc. B 361, 1055–1067 (2006). ples revealed the presence of genes indicating study whether there has been any relocation 9. Embley, T. M. et al. Proc. R. Soc. Lond. B 262, 87–93 (1995). that the ciliate cells have hydrogenosomes. or repurposing of genes between the host 10. Lewis, W. H. et al. Mol. Biol. Evol. 37, 524–539 (2020). Moreover, the sequencing data indicate that and endosymbiont, and to what extent a 11. Karnkowska, A. et al. Curr. Biol. 26, 1274–1284 (2016). the bacterial endosymbionts have an elec- typical mitochondrial function, such as ATP This article was published online on 3 March 2021. tron-transport chain — a collection of protein complexes for respiration that enable energy Geophysics to be produced by a process called oxidative phosphorylation. Graf et al. propose that the electron acceptor in this chain is nitrate, rather than the oxygen used by aerobic organisms. Oceanic fault zones Consistent with this model, the authors report that rates of denitrification (the microbial pro- reconstructed cess that converts nitrate into nitrogen) were higher in lake-water samples in which ciliates Garrett Ito were present than in those from which ciliates had been removed. Tectonic-plate material is generally thought to be neither The genome of the endosymbiont identi- created nor destroyed at plate boundaries called oceanic fied by Graf and colleagues is notably smaller transform faults. An analysis of sea-floor topography suggests than the genomes of most endosymbionts of microbial eukaryotes, containing a mere that this assumption is incorrect. See p.402 310 protein-encoding genes. Among those, the authors identified a gene that encodes a poten- tial transporter protein for ATP, which they At undersea structures called oceanic spread- in a several-kilometre-wide region called the suggest is used to export ATP from the endo- ing centres, two tectonic plates split apart, and transform deformation zone, the crust gen- symbiont into its host, enabling the ciliate to molten rock from volcanic activity solidifies erated at one spreading segment undergoes use the endosymbiont for energy production to produce the crust of the sea floor. These episodes of thinning and then regrowth as it by ‘breathing’ nitrate. This finding represents spreading centres are separated into indi- drifts towards and past the adjacent segment. a unique example of an endosymbiont that has vidual segments that are tens to hundreds of Grevemeyer and colleagues’ work was ena- contributed the capacity for respiration (albeit kilometres long. At the ends of the segments, bled by international collaborations that have using nitrate instead of oxygen as an electron shearing (side-by-side sliding) of the two supported decades of seagoing expeditions acceptor) to a eukaryote that seemingly plates occurs along plate boundaries known to the world’s oceanic spreading centres. The retains organelles of mitochondrial descent as oceanic transform faults. Since their dis- authors analysed sea-floor topography around (hydrogenosomes) — the ancestral versions of covery in the mid-1960s1, these faults have the intersections between spreading-segment which once performed respiratory functions. been considered as sites where plate mater ends and transform faults globally. At these Intriguingly, several parallels can be drawn ial is neither created nor destroyed. But on intersections, young crust produced at one between the cellular partnership discovered page 402, Grevemeyer et al.2 report that this spreading segment (the ‘proximal’ segment) is by Graf and co-workers and the evolution of description is too simplistic. They show that, adjacent to old crust that has been transported