Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests

Abstract

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

“…This can be achieved through expert and accurate annotation of environmental metabarcoding (Anthony et al, 2022), metagenomics (Hagh-Doust et al, 2023, and metatranscriptomic (Auer et al, 2023;Zeng et al, 2023) datasets. The latter approach has been used to examine gene expression in ECM root tips in natural environments, including the effects of anthropogenic N deposition on ECM tree metabolism (Liao et al, 2018;Law et al, 2022;Rivera P erez et al, 2022). Anthony et al (2022) showed that tree growth was linked to the gene copy number of genes involved N uptake and assimilation in associated ECM symbionts.…”

Life at the borderlands: microbiomes of interfaces critical to One Health

“…Host–microbiome cosequencing: for host-associated microbiomes such as those found in the rhizosphere, human gut, or rumen, sequencing both host and microbial RNA can reveal networks of molecular communication between them (Law et al 2022 ).…”

A natural history of networks: Modeling higher-order interactions in geohistorical data

“…We focus on the Map Equation framework and its applications in paleobiology research because it is an increasingly popular alternative to the standard statistical approaches currently used in paleobiology research (Kocsis et al 2021; Rojas et al 2021; Pilotto et al 2022; Viglietti et al 2022). The associated software called Infomap for finding community structure in standard and higher-order networks is also widely used in natural and social sciences (Law et al 2022; Lazaridis et al 2022; Martins et al 2022). The Map Equation framework for higher-order networks combines sedimentological, ecological, morphological, taxonomic, and any other data retrieved from geohistorical records, enabling an integrated investigation of the complex interactions between plate tectonics, global climate change, and evolution of life.…”