Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales

Area of Science:

• Soil science
• Microbiology
• Biogeochemistry

Background:

• Soil ecosystems harbor complex microbial communities essential for nutrient cycling and plant growth.
• Microorganisms predominantly reside within soil aggregates, which are small, stable clusters of minerals and organic matter.
• Understanding microbial interactions at the micro-scale within aggregates is vital for predicting soil biological activities, as bulk soil analysis is insufficient.

Purpose of the Study:

• To review the current knowledge of soil aggregate microbial communities.
• To identify research opportunities for studying soil ecosystems at a cell-relevant scale.
• To present a framework for understanding aggregate communities as interconnected "microbial villages".

Main Methods:

• Review of existing literature on soil aggregate microbial communities.
• Proposal of a framework viewing aggregates as "microbial villages" connected by wetting events.
• Discussion of top-down and bottom-up research strategies, including model systems, field observations, and studying underrepresented members like viruses.

Main Results:

• Soil microorganisms form distinct communities within soil aggregates.
• Wetting events facilitate periodic connections between these aggregate communities, enabling exchange of genetic material, metabolites, and viruses.
• Aggregate-based approaches are critical for a predictive understanding of soil microbial ecology.

Conclusions:

• Studying soil microbial communities within aggregates, rather than bulk soil, is essential for understanding biogeochemical processes.
• A combined approach using model systems, field studies, and investigation of all community members (including viruses) is necessary.
• Aggregate-based research represents a crucial advancement for predicting soil microbial community structure and function.