Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome

Area of Science:

• Microbiology
• Plant Science
• Genomics

Background:

• Plant-associated microbes are vital for plant growth and survival.
• Current high-throughput amplicon sequencing methods primarily assess microbial relative abundance, not total microbial load or colonization relative to host plant tissues.

Purpose of the Study:

• To develop and validate a novel method, host-associated quantitative abundance profiling (HA-QAP), for accurately quantifying microbial load in plant roots.
• To assess the total microbial load and colonization of individual root microbiome members relative to host plants.

Main Methods:

• Developed the HA-QAP method using the copy-number ratio of microbial marker genes to the plant genome.
• Validated HA-QAP through mock experiments, perturbation experiments, and metagenomic sequencing.

Main Results:

• HA-QAP accurately measures total microbial load, overcoming limitations of relative abundance methods.
• In healthy rice and wheat, bacterial 16S rRNA gene copy-number ratios ranged from 1.07 to 6.61, and fungal ITS ratios ranged from 0.40 to 2.26.
• Increased total microbial load was observed in rice under drought stress and wheat with root rot disease, impacting microbial interaction networks.

Conclusions:

• HA-QAP provides an accurate and technically feasible approach to quantify root microbiome load.
• This method enhances understanding of genuine plant-microbe interactions and the impact of microbial load on plant health under stress and disease.