Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

Area of Science:

• Microbial evolution
• Archaea genomics
• Biogeochemical cycles

Background:

• Ammonia-oxidizing archaea (AOA) are crucial for the global nitrogen cycle.
• Their evolutionary history and adaptation mechanisms are poorly understood.
• AOA inhabit diverse marine and terrestrial environments.

Purpose of the Study:

• To reconstruct the evolutionary history of Thaumarchaeota, focusing on AOA.
• To understand the role of environmental changes, particularly oxygenation, in AOA evolution.
• To identify key genetic adaptations enabling AOA's expansion into marine habitats.

Main Methods:

• Construction of a comprehensive phylogenomic tree of Thaumarchaeota.
• Molecular dating to correlate evolutionary events with geological timescales.
• Comparative genomic analysis to identify gene gains and losses associated with transitions.

Main Results:

• Three major evolutionary events identified: terrestrial origin, shallow ocean colonization, and deep ocean expansion.
• These events correlate with the Great Oxygenation Event and subsequent ocean oxygenation.
• Key adaptations include gaining aerobic ammonia oxidation, cobalamin/biotin pathways, K+ transporter, and ectoine; losing anaerobic pathways and DNA repair systems.

Conclusions:

• Oxygen availability was a primary driver for AOA's terrestrial origin and marine expansion.
• AOA acquired genes from other domains (Euryarchaeota, Bacteria) to adapt to environmental stressors.
• This study provides a framework for understanding archaeal evolution in response to planetary changes.