Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

Abstract

Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.

Keywords: FUNGuild; Fagus sylvatica; Illumina MiSeq sequencing; Quercus spp.; bacterial and fungal communities; deep forest soil layers; drought.

FIGURE 1

Richness and Shannon index of bacteria and fungi of soils and fine roots in the various soil layers (L1–L7) at beech and oak sites. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L3: 45–55 cm, L4: 75–85 cm, L5: 110–125 cm, L6: 140–155 cm, L7: 180–200 cm.

FIGURE 2

Canonical analysis of principal coordinates (CAP) based on Bray–Curtis dissimilarities for bacterial and fungal communities. (A) Bacterial communities in the various soil layers (L1–L7) of three forest locations. (B) Bacterial communities in the beech and oak sites of the three forest locations. (C) Bacterial communities in the soil and fine root substrates of the three forest locations. (D) Fungal communities in the various soil layers (L1–L7) of three forest locations. (E) Fungal communities in the beech and oak sites of the three forest locations. (F) Fungal communities in the soil and fine root substrates of the three forest locations.

FIGURE 3

Non-metric multidimensional scaling (NMDS) ordination based on Bray–Curtis dissimilarities for (A) bacterial and (B) fungal communities in various soil layers (L1–L6) of beech and oak sites. Soil environmental variables were projected as arrow vectors onto the NMDS ordinations. Vector arrowheads show the direction of variation of the soil variables, and vector lengths reflect the strength of the correlation of the variables with the NMDS axes. AWC: plant-available water storage capacity, BS, base saturation; C, C_org; Clay, clay content; CN, C:N ratio; Earth, fine-earth density; N, N_tot; pH, pH (CaCl₂); Root, fine-root biomass; Sand, sand content; Silt, silt content; Stone, stone content; Tree, tree genus. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L3: 45–55 cm, L4: 75–85 cm, L5: 110–125 cm, L6: 140–155 cm (for explanations see Table 3).

FIGURE 4

Differentially abundant bacteria phyla of topsoil (soil layers L1 and L2) vs. subsoil (soil layers L5 and L6). Shown are only significant log₂-fold changes (LFC) of phyla based on a significance level of p < 0.01 after false discovery rate correction. Error bars represent standard deviation. Positive LFC values indicate a higher occurrence of phyla in the topsoil, whereas negative LFC indicate a higher occurrence in the subsoil. The number of differentially abundant OTUs comprised in each phyla are indicated in brackets. Poorly known phyla are highlighted in red. Relative abundance (%): sum of the abundance of the differentially abundant OTUs belonging to the same phyla as a percentage of the total number of sequences across the compared soils. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L5: 110–125 cm, L6: 140–155 cm.

FIGURE 5

Differentially abundant bacteria genera of topsoil (soil layers L1 and L2) vs. subsoil (soil layers L5 and L6). Shown are only significant log₂-fold changes (LFC) of genera based on a significance level of p < 0.01 after false discovery rate correction. Error bars represent standard deviation. Positive LFC values indicate a higher occurrence of the taxa in the topsoil, whereas negative LFC indicate a higher occurrence in the subsoil. Only 30 genera with the highest (positive) and lowest (negative) mean LFC values were represented. The number of differentially abundant OTUs comprised in each genus, and the phyla to which they belong are indicated in brackets. Poorly known taxa are highlighted in red. Relative abundance (%): sum of the abundance of the differentially abundant OTUs belonging to the same genera as a percentage of the total number of sequences across the compared soils. Relative abundance depicted in red exceeds the abundance scale. Ac, Acidobacteria; At, Actinobacteria; Cf, Chloroflexi; F, Firmicutes; Ni, Nitrospirae; Pl, Planctomycetes; Pr, Proteobacteria; R, Rokubacteria; T, Thaumarchaeota. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L5: 110–125 cm, L6: 140–155 cm.

FIGURE 6

Differentially abundant fungal genera of topsoil (soil layers L1 and L2) vs. subsoil (soil layers L5 and L6). Shown are only significant log₂-fold changes (LFC) of genera based on a significance level of p < 0.01 after false discovery rate correction. Error bars represent standard deviation. Positive LFC values indicate a higher occurrence of the taxa in the topsoil, whereas negative LFC indicate a higher occurrence in the subsoil. Only thirty genera with the highest (positive) and lowest (negative) mean LFC values were represented. The number of differentially abundant OTUs comprised in each genus, and the phyla to which they belong are indicated in brackets. Relative abundance (%): sum of the abundance of the differentially abundant OTUs belonging to the same genera as a percentage of the total number of sequences across the compared soils. Relative abundance depicted in red exceeds the abundance scale. A, Ascomycota; B, Basidiomycota. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L5: 110–125 cm, L6: 140–155 cm.

FIGURE 7

Saprotrophs to ectomycorrhizal fungi ratio of relative abundances of fungi in soils and fine roots in the various soil layers (L1–L6) at beech and oak sites. Fungal functional guilds were analyzed by FUNGuild. Dashed lines have been drawn for better visualization. Soil layers: L1: 0–10 cm, L2: 15–25 cm, L3: 45–55 cm, L4: 75–85 cm, L5: 110–125 cm, L6: 140–155 cm.