Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem

Area of Science:

• Microbiology
• Environmental Science
• Biotechnology

Background:

• Understanding microbial community dynamics is key for engineering stable microbiomes.
• Pit mud, used in Chinese liquor fermentation for centuries, represents an aged, engineered ecosystem.

Purpose of the Study:

• To investigate prokaryotic evolution and community shifts in pit mud over time.
• To identify the factors driving microbial adaptation in this unique environment.

Main Methods:

• Metagenomic analysis of 120 pit mud samples from different aging periods.
• Analysis of taxonomic composition, functional potential (hydrolytic and metabolic), and environmental drivers.

Main Results:

• A clear transition from generalist-dominated to specialist-enriched prokaryotic communities was observed with pit mud age.
• Hydrolytic potential decreased, while organic acid metabolism, particularly short-chain fatty acid turnover via syntrophy, methanogenesis, and carbon chain elongation, increased.
• Key taxonomic shifts included decreases in Proteiniphilum and Petrimonas, and increases in Methanobacterium and Caproicibacter.
• Nutrient availability influenced early community structure, while environmental stress dominated mature systems.

Conclusions:

• Long-term prokaryotic adaptation in pit mud leads to specialized, stable microbial communities.
• These findings provide insights for designing resilient microbial consortia for biotechnological applications.