Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Abstract

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

Keywords: PhytOakmeter; core and site-specific microbiomes; environmental conditions; microbial diversity; microbial recruitment.

FIGURE 1

(A) Distribution overview of bacterial and fungal phyla between PhytOakmeter root and root-free zones within and among the field sites, (B) Shannon diversity index for bacteria and fungi within soils from PhytOakmeter root zone and the tree root-free zone of the respective field sites. Different letters above boxplots indicate significant differences (p < 0.05) according to Tukey-HSD post hoc test. n.s., not significantly different.

FIGURE 2

Non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity displaying bacterial (stress = 0.07) and fungal (stress = 0.09) communities’ structure within field sites, and significantly correlated soil chemical parameters (p < 0.05).

FIGURE 3

Non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity displaying bacterial and fungal communities’ structure within respective field sites, and differentiating between the samples of PhytOakmeter root and root-free zones. p and statistic R values within respective sites are given by the analysis of similarities (ANOSIM) permutation test (999 permutations).

FIGURE 4

Overlap of bacterial and fungal OTUs between PhytOakmeter root zone and the tree root-free zone.

FIGURE 5

Venn diagrams showing an overlap of OTUs exclusive to PhytOakmeter root zone among the field sites.

FIGURE 6

Differential abundance test for bacterial and fungal genera using Phyloseq and DESeq2. The graphs represents log₂_fold change of the microbial genera with significantly different abundance (p < 0.05) in the PhytOakmeter root zone compared to the tree root-free zone. A positive value signifies higher abundance while a negative value means lower abundance of the respective genera within the PhytOakmeter root zone compared to the tree root-free zone.

FIGURE 7

Variance partitioning analysis of the respective impacts of soil chemistry, weather, and host tree growth parameters on variations within bacterial and fungal communities. Soil chemistry included pH and soil organic matter content (SOC, TN, C/N, CWC, CWN, CWC/CWN, HWC, and HWN). Weather data included annual precipitations as well as monthly mean atmospheric and soil temperatures in the period of January 2014–September 2016. Tree growth-related parameters were height at the outplanting time, height increases in 2015 and 2016, shoot flushes produced in 2016 vegetative period, height of 2016 first shoot flush (SF1) as well as fresh and dry matter weight of SF1 leaves produced in 2016. Each circle represents the portion of variation accounted by each factor. Shared variance is represented by the intersecting portions of the circles. Values ≤ 0 are not shown. The calculations were done by using all the OTUs found within the host tree root zone.