Eukaryogenesis
Presently, it is understood that there are three domains of life. There is the eukarya, which is the domain consisting of the highest degree of complexity per cell and constitutes organisms such as plants, animals, and fungi. The other two are sub-branches of the prokarya, wherein the individual cells are less complex than the eukarya, and these are the bacteria and the archaea. Archaea, specifically, are a relatively new discovery (in terms of the scientific timescale) as their existence was first reported by Dr. Carl Woese in 1977.
Over time, the tree of life has undergone many changes, but the current most popular form is the below image, which was published in Nature Microbiology in 2016 and is based on 16S rRNA sequences (these ribosomal RNAs are ubiquitous in all life, and thus are a solid candidate for tracking evolutionary lineages)
There are two interesting features of this tree. The first is the upper right branch, which consists entirely of candidatus bacterial species. Candidatus indicates the the organism has been identified, but it has not been isolated and grown in a homoculture. Some species may never escape this category as it stands as some are obligate syntrophs, meaning that they cannot be grown without a co-culture that provides necessary nutrients. The second feature is the bottom right corner, in which the archaea and eukarya are located on the same arm, with the eukaryotes branching off just after the Asgard archaea.
An interesting feature of archaeal species is that they are a sort-of middle ground between the bacteria and the eukarya. What I mean by this is that, despite being prokaryotes like bacteria, they contain proteins that are more eukaryote-like. Additionally, the rRNA of some Asgard archaea actually contains elongation segments, something previously considered a trait exclusive to eukaryotes.
With these cursory points in mind, a current hypothesis for an aspect of eukaryogenesis (the origin of eukarya), specifically the aquisition of the mitochondria and/or the chloroplast, is that an archaeal species and a bacterial species were closely symbiotic to the point that the archaea engulfed the bacteria and fully incorporated it into its metabolism and replication cycle. This hypothesis is called "endosymbiosis."
Evidence for the mitochondria and chloroplast having their origins as bacterial species is the presence of a double membrane (one would have been the bacteria's, and one would have been the proto-eukaryote's), their own distinct ribosomes, and their own DNA.
How exactly this occurred is hotly debated, but two methods of engulfment include standard phagocytosis, and the other involves filaments of cytoplasm-containing membrane called "blebs" that could slowly build up around the symbiote. An example of the latter has been observed in the species Candidatus Prometheoarchaeum syntrophicum, strain MK-D1, which is an example of Lokiarchaeota (a subsection of the Asgard archaeota). In the paper "Isolation of an archaeon at the prokaryote-eukaryote interface" by Itachi et al. (2020), it was observed to grow blebs around its syntrophs, namely Halodesulfovibrio bacteria and Methanagenium archeaon.
As might be gathered by its classification as Candidatus, it was incapable of growth without its syntrophs due to an "incomplete" metabolism where the syntrophs covered the crucial gaps.
Based on their results, they proposed their own model for Endosymbiotic Eukaryogenesis, which they dubbed "Entangle, Engulf, Endogenize."
However, it is important to note that these cells were grown in optimized growth conditions. Originally, these cells came from a deep-sea sediment core, meaning that they are more accustomed to minimal nutrient conditions. As such, the optimized growth conditions may have resulted in the formation of these blebs as the cells struggled to self-regulate under overly nutrient-rich conditions. So, as always, more research would need to be done on these cells to make sure the bleb formation was not simply a side-product of lab growth conditions. Furthermore, this only accounts for one aspect of eukaryogenesis and does not account for the formation of the nucleus.
