The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment

Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2

Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO₂ (eCO₂) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO₂ directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO₂ enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO₂ with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N₂O reductase, involved in the last step of the denitrification process, which explains the increase of N₂O emissions in the Gi-FACE. Also, a shift in nitrate (NO3-) metabolism occurred, with an increase in transcript abundance for the dissimilatory NO3- reduction to ammonium (NH4+) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO42-) assimilation under eCO₂ conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO₂ conditions. The results exhibited the effects of eCO₂ on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO₂ and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.

Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.

Microbial functional genes commonly respond to elevated carbon dioxide

Atmospheric CO₂ concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO₂ enrichment (FACE) experimental sites have shown significant impacts of elevated CO₂ (eCO₂) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO₂ environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO₂, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO₂. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO₂ environment.

Seasonal and Agricultural Response of Acidobacteria Present in Two Fynbos Rhizosphere Soils

The Acidobacteria is one of the most abundant phyla in most soil types. Fynbos plants are endemic to South Africa, and these soils provide the ideal habitat for Acidobacteria, because of its low pH and oligotrophic properties. However, little is known about their distribution in the fynbos biome and the impact of cultivation of plants on Acidobacterial diversity. Therefore, the aim of this study was to determine the effect of seasonal changes and cultivation on the relative abundance and diversity of Acidobacteria associated with Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush). This study was based on rhizosphere soil. A total of 32 and 31 operational taxonomic units (OTUs) were identified for honeybush and rooibos, respectively. The majority of these were classified as representatives of subdivisions 1, 2, 3, and 10. Significant differences in community compositions were observed between seasons for both honeybush and rooibos, as well as between the cultivated and uncultivated honeybush. Acidobacteria had a significantly positive correlation with pH, C, Ca2+, and P. In this study, we have shown the effect of seasonal changes, in summer and winter, and cultivation farming on the relative abundance and diversity of Acidobacteria present in the soil of rooibos and honeybush.

Bacterial community response to a preindustrial-to-future CO2 gradient is limited and soil specific in Texas Prairie grassland

Rising atmospheric CO₂ concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO₂ enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO₂ gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO₂ gradient (R²  = 0.01, p > 0.05). CO₂ gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO₂ gradient (p < 0.001) among three soils. Similarly, CO₂ gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO₂ effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO₂ gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO₂ gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO₂ enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.

Soil Conditions Rather Than Long-Term Exposure to Elevated CO2 Affect Soil Microbial Communities Associated with N-Cycling

Continuously rising atmospheric CO₂ concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO₂ (eCO₂) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N₂O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO₂ (aCO₂). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO₂ effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO₂ on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO₂ and aCO₂, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO₂ differed only slightly from soil under aCO₂. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO₂ level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO₂ had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N₂O emissions under eCO₂ and future studies should aim at exploring the active members of the soil microbial community.