Unveiling Microbial Profiles in Disease Suppressive Soils Using Long-read Shotgun Metagenomics

Abstract

Soil microbial communities are crucial in agricultural ecosystems, particularly in plant disease suppression. A notable phenomenon in this context is soil-borne legacy (SBL), where microbial communities recruited by plants under disease pressure enhance resistance in subsequent generations. Understanding the microbial mechanisms underlying SBL is crucial for sustainable agriculture. Metagenomics, as an increasingly sophisticated approach, can provide deep insights into the composition of soil microbial communities and uncover their functional potential in shaping plant-microbe interactions. However, the complexity of soil presents significant challenges for metagenomic analysis. Traditional short-read sequence (SRS) methods, such as Illumina, offer high accuracy but are limited by short-read lengths, making genome assembly, taxonomic classification, and functional annotation challenging. In recent years, long-read sequence (LRS) technologies, including Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), have rapidly advanced, emerging as powerful alternatives. This study explores the advantages and limitations of long-read shotgun metagenomics in uncovering microbial diversity and functional potential in disease-suppressive soils. We discuss how LRS overcomes key obstacles in traditional short-read metagenomics. Recent advancements have significantly improved the accuracy of LRS, bringing it close to that of short-read technologies, while challenges such as high cost remain barriers to widespread adoption. Additionally, we discuss hybrid sequencing approaches that integrate short- and long-read data to optimize metagenomic analysis. Our findings highlight the transformative role of LRS in soil microbiome research, offering a novel approach to elucidating the microbial mechanisms underlying SBL and paving the way for microbiome-based strategies in sustainable agriculture.