Multi-omics resolved integration reveals microbial niche separation in soil aggregates

Area of Science:

• Soil Science
• Microbiology
• Environmental Science

Background:

• Soil is a complex matrix of aggregates, varying in size and properties.
• Aggregate size creates unique microhabitats influencing microbial communities and functions.
• Homogenized soil studies often miss microscale spatial variability.

Purpose of the Study:

• Investigate microbial taxonomy, functional genes, and metabolic products across soil aggregate size fractions.
• Understand how soil management practices influence these microbial characteristics.
• Determine the role of aggregate size in shaping soil microbial ecology.

Main Methods:

• Collected soil aggregates from agricultural fields under two management practices.
• Analyzed four aggregate size fractions (8 mm to <53 μm).
• Utilized metagenomic sequencing for taxonomic and functional gene profiling, and metabolomics.

Main Results:

• Functional gene composition significantly differed across aggregate sizes.
• Macroaggregates showed higher gene abundance for plant compound degradation; smaller fractions for biomass recycling.
• Metabolome composition varied significantly, correlating with aggregate size, but enzyme activities did not.
• Ammonia-oxidizing archaea were more abundant in macroaggregates, with genomes suggesting niche adaptation.

Conclusions:

• Soil microbial communities and functions are demonstrably shaped by soil aggregate size.
• Resource availability differences between macro- and microaggregates likely drive these microbial patterns.
• Aggregate size is a critical factor influencing soil microbial ecology and biogeochemical processes.