Dating Alphaproteobacteria evolution with eukaryotic fossils

Abstract

Elucidating the timescale of the evolution of Alphaproteobacteria, one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth’s systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria, based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

“…The tree in Figure 1 shows an 'Alphaproteobacteria-sister' to mitochondria topology that is equivalent to that initially reported using 24 concatenated proteins, including NuoL and many marine MAGs [11]. The same clustering has been recently reproduced with different taxonomic samplings of either Alphaproteobacteria or mitochondria [26,33]. However, the most common topology of phylogenetic trees combining Alphaproteobacterial and mitochondrial proteins shows the mitochondrial clade nested within the early branching part of the trees, often in a sister position to the Rickettsiales order [2,4,11,26].…”

“…Then, a series of minor orders of predominantly marine taxa, such as Sneathiellales, separates clade b from clade c, which includes all major lineages of Alphaproteobacteria, from Rhizobiales to Rhodobacterales (Figure 1). An equivalent three-clades sequence can be discerned in the branching order of phylogenetic trees reported earlier, for example in studies on Alphaproteobacteria only [3,5,13], as well as in studies focusing on the Alphaproteobacterial ancestry of mitochondria [11,26,33]. Indeed, clade c fundamentally corresponds to the 'Core alphaproteobacteria' group reported by Martijn et al, 2018 [11].…”

Bacterial glycyl tRNA synthetase offers glimpses of ancestral protein topologies

“…With the hypothesis described above, we calculated a phylogenetic tree (Figure 7) using the sequences of the available babb duplicated topologies of archaea and bacteria domains. Notably, we could use the Archaeal, CCA-adding enzyme sequences to obtain a rooted tree (Figure 7), that yields information consistent with the widely accepted taxonomy, like the overall, Gracilicutes vs Terrabacteria division (Coleman et al, 2021), the general Firmicutes phylogeny division of Limnochordales, Halanaerobiales, Negativicutes (Taib et al, 2020), or the placement of Magnetococcales as an Alpha proteobacteria outgroup (Wang & Luo, 2021). It also proposes that Methanopyrus is the closest Archaea related to bacteria (Long et al, 2020); to divide Deltaproteobacteria in four phyla that do not belong to proteobacteria (Waite et al, 2020).…”

Microbial habitability of early Mars lacustrine environments sustained by iron redox cycling

“…In an evolutionary context, Alpha-and Delta-proteobacteria like R. palustris and G. sulfurreducens, respectively, probably did not arise on Earth until well after (<2-3 GYA; Marin et al, 2017;Wang and Luo, 2021) Gale crater was formed in the Late Noachian (Fig. 1C).…”