Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Area of Science:

• Microbiology
• Evolutionary Biology
• Genomics

Background:

• Phylogenetic analyses have clarified many ancient archaeal relationships, but the deep-branching DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Worarchaeota) super-phylum, including Nanohaloarchaea, remains debated.
• Nanohaloarchaea, discovered in 2012, are nanosized archaea requiring high salt concentrations, representing one of only two known extreme halophilic archaeal lineages alongside Halobacteria.
• The phylogenetic placement of Nanohaloarchaea is contentious, with proposals placing them as sister to Halobacteria or within the DPANN super-phylum.

Purpose of the Study:

• To resolve the phylogenetic position of Nanohaloarchaea and Halobacteria within the archaeal domain.
• To understand the evolutionary origins of extreme halophily in archaea.
• To investigate the validity of the DPANN super-phylum based on robust phylogenetic evidence.

Main Methods:

• Comparative genomic approaches were employed to identify 258 reliable phylogenetic marker genes.
• Phylogenetic inference strategies were utilized to minimize the impact of potential biases.
• Analysis focused on disentangling deep evolutionary relationships within Archaea.

Main Results:

• Phylogenetic analyses revealed that Nanohaloarchaea and Halobacteria are two independent lineages.
• Both lineages originated from distinct, yet related, methanogen Class II ancestors.
• The study suggests that adaptation to high salinity evolved independently twice in Archaea.

Conclusions:

• The independent evolution of extreme halophily in Nanohaloarchaea and Halobacteria provides new insights into archaeal adaptive processes.
• The placement of Nanohaloarchaea within the DPANN super-phylum is likely an artifact of tree reconstruction, challenging the super-phylum's existence.
• Resolving these deep evolutionary divergences is crucial for a comprehensive understanding of archaeal history and genome evolution.