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.

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils

“…The molecular procedure was in accordance with Habiyaremye et al . (2020). Briefly, total genomic DNA was extracted from 0.5 g of each subplot sample using the Power Soil™ DNA Isolation Kit (Qiagen Laboratories, Solana Beach, USA) following the manufacturer's instructions.…”

“…From the core soil samples for microbial analysis, the roots were sorted out by hand and soil homogenized by sieving at a 2 mm mesh size. The molecular procedure was in accordance with Habiyaremye et al (2020). Briefly, total genomic DNA was extracted from 0.5 g of each subplot sample using the Power Soil™ DNA Isolation Kit (Qiagen Laboratories, Solana Beach, USA) following the manufacturer's instructions.…”

Temporal changes and alternating host tree root and shoot growth affect soil microbiomes

“…Soil samples were taken in the tree root and root-free zone as described previously Habiyaremye, et al [9], despite the upper 0-15 cm soil 30 cm from the tree trunk that were taken. Detailed descriptions of the molecular methods, from DNA extraction to Illumina-based sequencing were also published before [9].…”

“…Soil samples were taken in the tree root and root-free zone as described previously Habiyaremye, et al [9], despite the upper 0-15 cm soil 30 cm from the tree trunk that were taken. Detailed descriptions of the molecular methods, from DNA extraction to Illumina-based sequencing were also published before [9]. Bioinformatics and processing of sequences data were conducted using the dadasnake pipeline (v0.5,) [10], a DADA2 [11] implementation in snakemake [12].…”

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North–South transect

“…The soil of RZ includes both, rhizosphere soil and nonrhizosphere soil located around the active tree roots, and is therefore expected to accommodate microbial communities strongly shaped by the respective tree (Burns et al, 2015). Studying the tree RZ soil allowed us to distinguish between the respective impacts of the host tree and local environmental conditions in shaping the soil microbial community (Weißbecker et al, 2018;Habiyaremye et al, 2020a). We also sampled the tree RFZ soil to analyse communities of the local soil microbial pools.…”