Host selection shapes crop microbiome assembly and network complexity

Area of Science:

• Microbiology
• Ecology
• Plant Science
• Agricultural Science

Background:

• Plant microbiomes are crucial for host health and agricultural productivity.
• The ecological processes governing crop microbiome assembly remain incompletely understood.
• Understanding microbiome assembly is key to sustainable agriculture and crop management.

Purpose of the Study:

• To investigate bacterial community assembly across soil and plant compartments in a maize-wheat/barley rotation system.
• To determine the influence of compartment niche, host species, site, and fertilization on crop microbiome structure.
• To identify potential microbial sources and enrichment processes within the soil-plant continuum.

Main Methods:

• Collected 684 samples from soil (rhizosphere, bulk soil) and plant niches (rhizoplane, root endosphere, phylloplane, leaf endosphere).
• Analyzed bacterial communities in a maize-wheat/barley rotation system under varied fertilization at two sites.
• Employed source tracking to infer microbial origins and enrichment pathways.

Main Results:

• Microbiome assembly was predominantly driven by compartment niche and host species, overriding site and fertilization effects.
• Host selection pressure increased sequentially from soil to endosphere, reducing bacterial diversity and network complexity.
• Bacilli and Methylobacteriaceae were identified as key biomarker taxa for wheat/barley and maize, respectively.

Conclusions:

• Crop microbiomes are primarily derived from soil and are filtered and enriched across plant compartments.
• Host species exert a strong selective pressure, particularly in the leaf endosphere.
• Findings provide empirical evidence for microbiome assembly dynamics, informing strategies for sustainable agriculture.