Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Subseafloor microbial life exists in isolated, energy-limited environments.
• The genomic evolution of these long-term isolated microbes remains largely unknown.
• Subseafloor microbes have ultralow metabolic rates, potentially impacting reproduction and trait spread.

Purpose of the Study:

• To investigate the nature and extent of genomic evolution in subseafloor microbial populations.
• To understand how long-term physical isolation and energy limitation shape microbial genomes.
• To compare genomic and phenotypic characteristics of subseafloor Thalassospira with surface-isolated strains.

Main Methods:

• Culturing of Thalassospira bacterial populations from million-year-old subseafloor sediments.
• Genomic sequencing and analysis, including pangenome analysis.
• Measurement of growth rates and assessment of pseudogene accumulation and substitution patterns.

Main Results:

• Subseafloor Thalassospira genomes evolved via point mutation with low homologous recombination and high pseudogene numbers.
• Genetic drift appears to dominate subseafloor strains, indicated by substitution ratios and fewer singleton genes.
• Motility genes showed insertion-deletion events and pseudogenes, suggesting reduced importance in the subseafloor environment.
• Subseafloor isolates exhibited slower growth rates compared to surface-isolated Thalassospira xiamenensis.

Conclusions:

• Long-term physical isolation of Thalassospira leads to clonal populations with reduced genetic exchange.
• Accumulation of mutations and pseudogenes over millions of years is driven by genetic drift in isolated subseafloor populations.
• Genomic evolution in subseafloor microbes is characterized by relaxed purifying selection and adaptation to stable, resource-limited conditions.