Leveraging microbiome rediversification for the ecological rescue of soil function

Area of Science:

• Soil microbiology
• Ecosystem science
• Agricultural science

Background:

• Global biodiversity loss threatens ecosystem services and soil functions.
• Agricultural soils often experience microbial diversity depletion, impacting functions like nitrification.
• Restoring soil microbial communities is crucial for maintaining ecosystem health and services.

Purpose of the Study:

• To investigate the impact of soil microbial diversity loss and rediversification on nitrification.
• To quantify changes in ammonium and nitrate pools following diversity manipulation.
• To assess the restoration of bacterial, fungal, and functional gene composition.

Main Methods:

• Used a dilution-to-extinction approach to manipulate microbial diversity in agricultural and forest soils.
• Performed microbiome rediversification experiments by re-introducing lost microorganisms.
• Analyzed nitrification, bacterial/fungal composition (16S rRNA, ITS sequencing), and functional genes (shotgun metagenomics).

Main Results:

• Nitrification disruption correlated with microbial diversity loss.
• High-diversity inocula successfully rescued nitrification in rediversification experiments.
• Metagenomics revealed loss and subsequent rescue of nitrogen metabolism genes and associated taxa.

Conclusions:

• Diverse microbiome additions can rescue depleted soil functions, contrary to some previous findings.
• The concentration of the microbial inoculum is a critical factor in successful restoration.
• Understanding rediversification impacts enhances tools for managing microbial communities and restoring soil functions.