![]() According to theories, a bacterial species merged with another host microbe, presumably an archaeon, giving rise to eukaryotes. While the idea of endosymbiotic origin of organelles has emerged early in the twentieth century, it was a little more than 50 years ago that Lynn Margulis has established the prokaryotic ancestry of mitochondria and plastids and the endosymbiotic origin of eukaryotes. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy. This assumption is twice fallacious: ( i) endosymbioses are known to evolve from exploitative interactions and ( ii) cooperativity does not necessarily lead to stable mutualism. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria–host cooperation. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost–benefit budget, and the types of benefits, investments, and controls. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote–prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote–prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. ![]() The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. Endosymbiosis and organellogenesis are virtually unknown among prokaryotes.
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