Soil microbial biogeography: from maps to blueprints

Abstract

Soil microorganisms are the biological engines of terrestrial ecosystems. The development of molecular technologies has overturned the ‘everything is everywhere’ paradigm, revealing that at the strain-level, soil microbes exhibit distinct biogeographical patterns governed by environmental selection, dispersal, diversification, and drift. In this review, we first summarize the major progresses in soil microbial biogeography. Then, we discuss the potential limitations, including the constraints of space-for-time substitution, the disconnect between statistical correlation and ecological causality, and the inherent challenges in mapping and scaling microbial distributions. Finally, we propose a strategic framework centered on three directions: (1) Enhancing prediction, by integrating microbial traits into Earth System Models to forecast the responses of soil microbes and their associated functions to global change; (2) Deciphering mechanisms, by bridging multi-omics approaches with rigorous experimental validation to establish causality between structure and function; and (3) Achieving manipulation, by leveraging synthetic ecology and core taxa to engineer microbiomes for practical application in One Health initiatives. Moving from pattern description to mechanistic understanding and functional manipulation will enable soil microbial biogeography to provide actionable solutions for sustainability in a rapidly changing world.

Graphical abstract

Keywords

soil microbial biogeography / community assembly / functional traits / microbiome engineering

Highlight

	● Reveals key progress in soil microbial biogeography.
	● Identifies major conceptual and methodological limitations.
	● Proposes a framework linking prediction, mechanism, and manipulation.
	● Highlights the role of microbes in sustainability under global change.

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