Soil microbial ecology through the lens of metatranscriptomics

Metatranscriptomics uncovers the dynamic expression of functional genes in soil environments, providing insights into the intricate metabolic activities within microbial communities. mRNA enrichment from soil samples remains a formidable challenge due to the presence of inhibitory compounds, low RNA yields, and sample heterogeneity. Soil metatranscriptomics unravels the expression levels of genes involved in the real-time molecular dialogues between plants and rhizobionts, uncovering the dynamics of nutrient exchange, symbiotic interactions, and plant-microbe communication. Metatranscriptomics unlocks the active expression of the soil resistome, elucidating the mechanisms of resistance dissemination under anthropogenic activities. Metatranscriptomics provides comprehensive data regarding the identification, quantification, and evolutionary history of RNA viruses. Metatranscriptomics is a cutting-edge technology for exploring the gene expression by, and functional activities of, the microbial community across diverse ecosystems at a given time, thereby shedding light on their metabolic responses to the prevailing environmental conditions. The double-RNA approach involves the simultaneous analysis of rRNA and mRNA, also termed structural and functional metatranscriptomics. By contrast, mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles, but requires either deep sequencing or effective rRNA depletion. In this review, we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics. In particular, we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields, such as rhizobiomes, antibiotic resistomes, methanomes, and viromes. Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.