Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time

Abstract

Heterotrophic microbial eukaryotes play a pivotal role in aquatic and terrestrial ecosystems, contributing to carbon and nutrient cycles. These microorganisms, capable of phagocytosis, act as predators of bacterial communities and other microeukaryotes, occupying a significant position in complex food webs. The timing of the origin and diversification of heterotrophic microeukaryotes remain unclear. Fossil evidence and molecular data suggest that the emergence of predatory microeukaryotes and the transition to a eukaryote-dominant marine environment occurred around 800 million years ago (mya). Vase-shaped microfossils (VSMs), the fossil record linked to Arcellinida testate amoebae, represent the oldest known evidence of heterotrophic microeukaryotes in marine environments and terrestrial habitats. In this study, we investigate the early divergence and diversification of Arcellinida and related amoebozoan taxa using a relaxed molecular clock approach. Phylogenomic reconstructions reveal a well-resolved tree of amoebozoan testate amoebae, including a monophyletic Arcellinida with three suborders and five infraorders. Through calibration using fossils and rigorous clock models, we estimate the timing of diversification of Arcellinida during the early Neoproterozoic (886 - 764 mya), shedding light on the expansion of life during this period. Our results suggest an established biological complexity in shallow marine ecosystems, involving both phototrophic and heterotrophic microeukaryotes during the Neoproterozoic, followed by an invasion of freshwater systems potentially during Cryogenian and subsequent diversification of Arcellinida in the Phanerozoic. Overall, these findings provide valuable insights into heterotrophic microeukaryotes’ evolutionary history and ecological significance in Earth’s ecosystems.Significance StatementArcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record, the vase-shaped microfossils (VSMs). Here we generated time-calibrated trees by combining additional phylogenomic sampling of the extant group and the VSM fossil record. Our results bring to light key events in the history of microeukaryotes, including: i) the diversification of heterotrophic eukaryotes in marine ecosystems alongside red-algae in the Precambrian; ii) a Cryogenian establishment of complex terrestrial habitats; iii) a marine mass extinction during late Devonian, and; iv) a post-Silurian explosion of life on terrestrial (including freshwater) habitats. These findings corroborate recent discoveries regarding Precambrian history of eukaryotic protosteranes. Our results provide valuable insights into the evolution of life in marine and terrestrial ecosystems throughout geological time.