In the great diversity of microbial life, there are several examples of symbiosis – a process in which different organisms maintain a stable relationship with each other. Such interactions generally provide some form of benefit to one or more of the organisms involved. Entering Nature, Graf et al.1 reports the discovery of an intriguing example of symbiosis between microorganisms. This finding may shed light on the types of processes that led to the development of mitochondria, the energy-producing organelles found in eukaryotic cells (those that contain a nucleus).
In some cases, symbiotic partners can be integrated in such a way that one partner is taken up into the other partner’s cell by a process called endosymbiosis (Fig. 1). Endosymbiotic interactions have enabled important transitions during the history of life on Earth. A good example of this is thought to be the interaction that gave rise to the first eukaryotic cell. This ancestral eukaryote is probably formed by an endosymbiosis in which a host cell belonging to a group of single-celled organisms called Asgard archaea2,3 took a type of bacterial cell belonging to the phylum Proteobacteria4. Mitochondria in eukaryotic cells are considered the direct descendants of these once free-living proteobacterial endosymbionts.
Graf and colleagues describe an exciting bacterial endosymbiont that they discovered living in a ciliate, a type of eukaryotic, single-celled microbe. Although connections between these types of organisms are not uncommon, this particular case has some of the characteristics of the type of endosymbiosis that gave rise to mitochondria. It includes the production of energy in the form of ATP molecules by the energy-generating process known as respiration. This process is also associated with a mechanism by which ATP can be exported from the endosymbiont to provide the host with energy.
The environmental conditions and atmospheric composition of the Earth today differ markedly from those that existed when life first appeared on this planet more than four billion years ago. During what is known as the Great Oxidation Event, about 2.1 billion years ago5, oxygen accumulated in the atmosphere and oceanic waters, a development that had a major impact on the course of life on Earth. Oxygen is toxic to most organisms that thrive in environments that are devoid of it. However, some microorganisms learned to exploit the chemical properties of oxygen by using it as an electron acceptor in energy-producing pathways. This type of oxygen-dependent process, called aerobic respiration, is much more energy efficient than fermentation, a form of non-oxygen-dependent energy metabolism of ancient origin that allows many anaerobic organisms to survive without oxygen.
Eukaryotic cells probably emerged sometime after the major oxidation event6and their ability to perform aerobic respiration was acquired through mitochondrial endosymbiont. The capacity for efficient energy production provided by this is believed to have provided selective benefits during eukaryotic development, although the exact contribution to, for example, the emergence of cellular complexity is discussed.7.
Current evidence6 indicates that early eukaryotic evolution and diversification took place under conditions where oxygen was present. However, some groups of eukaryotes nevertheless thrive in an oxygen-free environment. These anaerobic eukaryotes are thought to have evolved from aerobic mitochondrial-bearing ancestors.
In the absence of oxygen, the anaerobic eukaryotes use a fermentation-based metabolism, which exposes them to stricter energy regimes than aerobic eukaryotes. This type of metabolism has occurred in different types of anaerobic eukaryotes and is associated with the development of mitochondria to organelles called hydrogenosomes8. All hydrogenosomes have to some extent lost mitochondrial pathways to aerobic respiration, generating hydrogen rather than carbon dioxide and water as an end product of their energy-generating pathways. Ciliates are exceptionally effective at adapting to oxygen-depleted environments, and mitochondrial-to-hydrogenosome transitions have occurred independently several times in this group of organisms.9.
Graf and colleagues studied an anaerobic ciliate belonging to the class Plagiopylea, found in the deepest layers of Lake Zug in Switzerland. This environment lacks oxygen and contains relatively high levels of nitrate. An initial assessment by microscopy revealed that these ciliates unusually have a bacterial endosymbiont (belonging to the class of Gamma proteobacteria) rather than an archaeal endosymbiont that produces methane, which is the more typical type of endosymbiont present in anaerobic ciliates.
DNA sequencing data for seawater samples revealed the presence of genes indicating that the ciliate cells have hydrogenosomes. In addition, the sequencing data indicate that the bacterial endosymbionts have an electron transport chain – a collection of protein complexes for respiration that allow energy to be produced by a process called oxidative phosphorylation. Graph et al. suggest that the electron acceptor in this chain is nitrate, rather than the oxygen used by aerobic organisms. Consistent with this model, the authors report that rates of denitrification (the microbial process that converts nitrate to nitrogen) were higher in seawater samples where ciliates were present than in those from which ciliates had been removed.
In particular, the genome of endosymbiont identified by Graf and colleagues is smaller than the genomes of most endosymbionts of microbial eukaryotes, which contain only 310 protein-coding genes. Among them, the authors identified a gene encoding a potential transporter protein for ATP, which they suggest is used to export ATP from endosymbiont to its host, allowing the ciliate to use endosymbiont for energy production by ‘breathing’ nitrate. This finding represents a unique example of an endosymbiont that has contributed to the respiratory capacity (albeit by using nitrate instead of oxygen as an electron acceptor) to a eukaryote that apparently preserves organelles of mitochondrial lineage (hydrogenosomes) – whose ancestral versions once performed respiratory functions .
Interestingly, several parallels can be drawn between the cellular partnership discovered by Graf and colleagues and the development of mitochondria in eukaryotes. In both cases, the respiration capacity was acquired by an anaerobic host cell through metabolic integration of a proteobacterial endosymbiont, and mechanisms can be identified for energy exchange between symbiont and host cell. In addition, a significant reduction in the endosymbiont genome is observed, although mitochondrial genomes are typically either much smaller than the endosymbiont genome observed by Graf and colleagues or have been completely lost (as is the case for several hydrogenosomes).10).
Despite these fascinating similarities, there are also remarkable differences. Mitochondrial endosymbiosis was a much older event in which an archaeal host cell was employed rather than a modern eukaryotic cell. Mitochondria, although now reduced from their original form, or even lost from some contemporary eukaryotes11became an integral part of eukaryotic cells. Genes inherited from the original mitochondrial endosymbiont were often targeted to the nuclear genome, and some of the proteins encoded by these genes adopted different functions throughout the cell. A similar level of integration is unlikely for the bacterial endosymbionts of the ciliates studied.
Nevertheless, it would be interesting to investigate whether there has been any relocation or rearrangement of genes between the host and endosymbiont, and the extent to which a typical mitochondrial function, such as ATP production, has been replaced or maintained in the hydrogenosomes of the ciliate. Evidence that the ATP transporter identified by Graf and colleagues can export ATP to the ciliate host will help confirm the proposed symbiotic interaction. Further discovery and exploration of similarly surprising symbiotic interactions in poorly explored parts of the microbial world is certainly an intriguing perspective for the future.