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.

Fig. 1

Diversity analysis of VineyardFACE experiment. a Alpha diversity metrics. aCO₂, ambient CO₂ conditions; eCO₂, elevated CO₂ conditions. * p < 0.05. b, c Principal Components Analysis (PCA) calculated based on Aitchison community dissimilarity distance matrix of axis 1–2 (left) and axis 1–3 (right) of green inter-rows from ambient and elevated CO₂ rings, d, e Principal Components Analysis (PCA) calculated based on Aitchison community dissimilarity distance matrix of axis 1–2 (left) and axis 1–3 (right) of open inter-rows from ambient and elevated CO₂ rings. A, ambient CO₂ rings; E, elevated CO₂ rings; aCO₂, ambient CO₂ conditions; eCO₂, elevated CO₂ conditions

Fig. 2

Environmental parameters effect on VineyardFACE experiment bacterial composition. a, b Redundancy Analysis (RDA) based on Aitchison community dissimilarity distance matrix of green inter-rows (left) and open inter-rows (right) from ambient (blue) and elevated (red) CO₂ rings. WHC, Water holding capacity; CO₂ Conc., CO₂ concentration; Soil resp., Soil basal respiration; C, Total carbon concentration; N, Total nitrogen concentration; C:N, Carbon–nitrogen ratio; NH₄⁺, Ammonium concentration. c, d Multidimensional scaling (MDS) with a grid of ammonium concentration expressed as (µM NH₄*g⁻¹), using Aitchison community dissimilarity distance matrix of green and open inter-rows from ambient CO₂ rings (left), green and open inter-rows from elevated CO₂ rings (right). e, f Soil microbial respiration expressed as CO₂ production rate under the addition of different carbon substrates of green inter-rows from ambient and elevated CO₂ rings (left), and open inter-rows from ambient and elevated CO₂ rings (right). Error bars are expressed as variance of mean values

Fig. 3

Differential abundances of core bacterial composition of green inter-rows soil under elevated and ambient CO₂ of (a) Bacterial ASVs and (b) Bacterial genera. ALDEx2 results of features with an ALDEx2 effect size > 0.5 using centered log ratio (clr) transformation and the geometric mean abundance of all features

Fig. 4

Co-occurrence analysis of features from green inter-rows. a Network analysis of core ASVs from aCO₂ rings and b eCO₂ rings. Features with an absolute ALDEx2 effect size > 0.5 were utilized for SpiecEasi analysis applying the Meinshausen & Bühlmann (mb) method with a number of subsamples of 50, n-lambda of 100 and lambda minimum ratio of 0.1; blue and red edges indicate positive and negative co-occurrence respectively; size of the nodes is proportional to the number of ASV reads. Partial correlation analysis of genera with an absolute ALDEx2 effect size > 0.1 from c aCO₂ and d eCO₂ green inter-rows using SpiecEasi and SPRING. SpiecEasi run applying the Meinshausen & Bühlmann (mb) method and SPRING with a modified centered log ratio (mclr). Both analyses utilized a number of subsamples of 99, a lambda minimum ratio of 0.1 and the Stability Approach to Regularization Selection (StARS) using co-occurences with a threshold of < -0.5 and > 0.5

Fig. 5

qPCR Boxplots of 16S rRNA, nifH, amoA, nirS, nirK and nosZ genes from aCO₂ rings green inter-rows (a-green), aCO₂ rings open inter-rows (a-open), eCO₂ rings green inter-rows (e-green), eCO₂ rings open inter-rows (e-open). Significance codes: *** p < 0.001, ** p < 0.01, * p < 0.05

Fig. 6

Model diagram of N cycle of VineyardFACE soil under (a) aCO₂ conditions and (b) eCO₂ conditions

Fig. 7

(a) Air view of VineyardFACE experimental site. E: elevated CO₂ ring, A: ambient CO₂ ring. Google Earth Pro Image (2021). (b) Design of a VineyardFACE-ring with the two grape varieties Riesling (R) and Cabernet Sauvignon (CS). The vertical lines represent the seven rows per ring of vine plants. Green-colored inter-rows represent the area within the ring with cover crop (green inter-rows) and brown-colored inter-rows represent the areas within the ring where the soil is periodically ploughed (open inter-rows)