Elevated atmospheric CO2 concentrations caused a shift of the metabolically active microbiome in vineyard soil

Abstract

Background: Elevated carbon dioxide concentrations (eCO₂), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO₂ enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO₂ or ambient CO₂ (aCO₂).

Results: Diversity indices and redundancy analysis (RDA) demonstrated that eCO₂ changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO₂. Moreover, under eCO₂ conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N₂ fixation and NO₂^- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO₂ conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions.

Conclusions: The results of this study demonstrate that eCO₂ concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.

Keywords: Active soil bacterial community; CO2; Carbon cycle; FACE; Nitrogen cycle; Vineyard; mRNA quantification; rRNA.