Longitudinal variations in soil microbiome diversity and microbial activity in a grassland ecosystem under a climate change scenario

Several experiments have assessed how elevated CO₂ (eCO₂) affects the soil microbiome. Nonetheless, there are still gaps in our knowledge of how eCO₂ and warming combined influence soil microorganisms. The soil microbiome's responses to eCO₂ and warming are diverse, highly ecosystem/location specific, and also time dependent. Reductions in microbial biomass, fungal abundance, and shifts in microbial communities have been described.

In this context, this study aims to longitudinally determine the combined effects of eCO₂ and warming on the diversity of the soil microbiome and the microbial activity of a temperate grassland ecosystem.

To achieve the aforementioned, soil samples were taken in 2019, 2021, and 2023 at the Giessen Thermo FACE experiment on a permanent grassland site near Giessen, Germany, which combines eCO₂ and warming alongside a soil water gradient. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and data were processed with QIIME2 and R software. Physiochemical soil parameters, soil respiration, and greenhouse gas fluxes were determined. Machine Learning (ML) algorithms and Linear Mixed Models (LMM) were created to assess correlations among microbiome diversity, microbial metabolic activity, and experiment environmental conditions.

ML and LMM results demonstrated that soil microbiome and microbial activity are highly time-dependent. However, warming and soil water content are the main drivers of soil microbiome alpha diversity (p<0.05), whereas eCO₂ has little influence. Moreover, increments in soil microbial respiration rates positively correlated with increased CO₂ concentrations and elevated temperature (p<0.05). Besides, our results showed a negative correlation between alpha diversity and respiration rates. ML applied to taxa selection and correlation identified 30 bacterial ASVs positively associated with warming. Regarding soil greenhouse gas fluxes, LMM results demonstrated that higher CO₂ and N₂O emissions positively correlated with warming and eCO₂. In conclusion, our results indicate that the soil microbiome has been affected under a climate change scenario, mainly driven by warming and soil water content, and to a lesser extent, eCO₂, which was reflected in an increment in soil microbial alpha diversity and microbial activity, accompanied by higher emission levels of greenhouse gases such as CO₂ and N₂O.