Soils harbor a huge diversity of microorganisms, which are dominated by bacteria and fungi. These soil microorganisms, collectively termed as the soil microbiome, are major contributors to soil biodiversity and play essential roles in soil functions (e.g. soil fertility and plant nutrition, organic matter degradation and nutrient cycling, and soil formation). Therefore, many studies in recent decades have explored soil microbial diversity in order to unravel driving forces of its variations. Hence, this thesis reports on spatial and temporal variations of the soil microbiome in response to site specificities, i.e. local climate as well as soil physico-chemistry, and host tree parameters. To avoid effects of intraspecific genetic variations, the pedunculate oak clone DF159 (Quercus robur L.) generated by the project TrophinOak-PhytOakmeter of the Soil Ecology Department at the Helmholtz Centre for Environmental Research (UFZ) was used as phytometer system. In the PhytOakmeter project of which this thesis is a part, saplings regenerated from microcuttings of DF159 were out-planted in grassland, forest and urban field sites in Central Germany and along a European North-South transect. The overall goal of the project is to analyze how the clone adapts to and performs under different regional climatic contexts and changing environment conditions. Pedunculate oak was chosen as a model tree species because it is engaged in highly complex and diverse multitrophic interactions, including soil microorganisms. Q. robur displays an endogenous rhythmic growth with alternating growing flushes in shoot and root, which can be repeated two to four times along a vegetation period. These alternating flushes have been shown to impact on variations of biological activities in soil zones close to the tree roots. Based on the above-described background, the current PhD study investigated changes in the soil microbial communities associated to the pedunculate oak phytometer outplanted in grassland sites at two different spatial scales: (1) the local scale by comparing the soil microbiomes associated to the phytometer in sites located within a close geographic space of Central Germany with similar climatic conditions; and (2) continental scale by making a similar comparison among sites along a European North-South transect, which encompasses a wide range of climatic and soil physico-chemical conditions. Moreover, temporal scale was considered, whereby the variability of the microbiomes intra-annually along a vegetation period was analyzed. Soil samples were taken not only in the tree root zone (RZ), i.e. soil zone containing living roots of the tree, but also in the tree root-free zone (RFZ), i.e. soil zone out of reach of any tree roots, but within the same field plot, to access also the local microbial pools. The analyses used a PCR-based Illumina MiSeq amplicon sequencing approach targeting bacteria and fungi, to assess their diversity, community structure and functionality after assignment of their OTUs to functional groups. In addition to Chapter 1, which introduces the whole work of this PhD research, the findings are presented within Chapters 2-4, of which two studies were already published in international peer-reviewed journals, while another study was published as a conference paper. The thesis is closed by the synopsis Chapter 5 that integrates discussion of all the publication chapters together with an outlook section. Chapter 2 “Tree root zone microbiome: exploring the magnitude of environmental conditions and host tree impact” published in Frontiers in Microbiology investigates the relative contribution of abiotic environmental and host tree parameters among four sites characterized by homogeneous climatic conditions in Central Germany, two years after the tree out-plant. We first compared at each field site the composition of the bacterial and fungal communities between the RZ of the oak clone, called PhytOakmeter in this chapter, and the tree RFZ. The chapter further evaluates the diversity and structure of the microbial communities within the tree RZ among the sites. The results revealed different microbial compositions between the tree RZ and RFZ, whereby the tree RZ-associated microbiome included numerous ectomycorrhizal fungi of the genera Hebeloma, Exophiala, Scleroderma, Tomentella, Trichophaea, and Tuber. This quick recruitment of specific beneficial microbial taxa from the local microbial pool seems to be among the tree strategies to acclimate to local site conditions. However, the overall tree contribution to shape soil microbial communities was lower than the impact of abiotic environmental parameters. The results revealed also a similar level of microbial diversity within the tree RZ among the sites for both the bacteria and fungi, an outcome attributed to the homogeneous climatic conditions within the sites and the common genetic identity of the host trees. In contrast, structure of the microbial communities was site-specific. Chapter 3 “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” published in Environmental Microbiology, also examines the relative impact of geographic, soil physico-chemical, and pedunculate oak clone parameters on the variability of the soil microbiome, but at a larger spatial scale from Lapinjärvi (Finland) to Bordeaux (Southwestern France), which is characterized by a broad range of geographic and soil physico-chemical conditions. In addition to the tree RFZ total microbiome and the tree RZ total microbiome, this chapter introduces a new sub-microbiome called tree RZ affine microbiome. The latter was defined as a subset of the RZ bacteria and fungi, significantly enriched in this zone compared to the tree RFZ. The results demonstrated an interplay among abiotic environmental and host tree parameters in shaping bacterial and fungal communities of the tree RZ along the European transect. These parameters showed a descending order of magnitude of their impact on the tree RZ total microbiome: geographic > soil physico-chemical > host tree parameters. However, for the variability of the RZ affine microbiome alone, the impact of the abiotic environmental parameters decreased, while the tree influence was strongly increased, particularly for fungi. Another important result was the highest proportion of the tree RZ affine microbial OTUs shared among all four sites, which was here designated as the tree “core” microbiome. These bacteria and fungi with significant affinity to the host tree, and shared by all the sites because of their ability to cope with diverging environmental conditions across the transect, may be playing a crucial role in supporting the wide distribution of Q. robur across Europe. Interestingly, we found no members of the RZ affine microbiome to be exclusive of only one particular site. Chapter 4 “Temporal changes and alternating host tree root and shoot growth affect soil microbiomes” published in Proceedings as conference paper after “The 1st International Electronic Conference on Microbiology”, considers a temporal scale, and here the variability of the tree RZ and RFZ total microbiomes was analyzed along a vegetation period in two sites of Central Germany. The soil was sampled at different time points coinciding with the tree alternating root and shoot growth, and the fall senescence that concludes the vegetation period. The results show a directional change over time along a vegetation period for the bacterial communities. However, the fungal communities did not show such temporal changes; they rather displayed a fine spatial scale partitioning closely linked to host plant individuals. In addition to the effect of temporal succession, deeper analyses of the generated data set will enable us to specify the impact of the alternating root and shoot growth characteristic of the tree endogenous rhythmic growth in the near future. These further analyses will include for example zooming in the tree RZ affine microbiome and in individual microbial functional groups. The results presented in this thesis evidence the quick impact of pedunculate oak tree clone on the soil microbiome within a two-year time span after the tree out-plant. Also, to different extents, geographic, soil physico-chemical, and host tree concurrently shape the soil bacterial and fungal communities. This thesis shows different spatial and temporal responses to the abiotic environmental and tree parameters between the soil bacterial and fungal communities. The use of tree clonal phytometer to study the tree-related parameters on soil microbiomes was proved to be a promising tool, to unravel the hierarchy of different abiotic and biotic factors in shaping the soil microbiome associated to long live trees. Finally, this work represents a first step toward establishing a long term monitoring of the dynamics of soil microbiomes associated to trees, as a strategy to unravel how these microorganisms participate to the long term acclimation of these long live plants to diverse and changing environments.

The aim of the diploma thesis was to evaluate the content of soil organic carbon in the area of Novohradsko. Soil organic carbon was monitored in its stable (SOC) and labile (WSOC) form, followed by the total organic carbon stock (Cpool). These soil parameters were determined in soils of different land cover types (forest, arable land, grassland) in the area formed by the catchments of Pasecký, Bedřichovský, Váčkový and Veverský stream. Data obtained in 2001, 2007 and 2014 were statistically analysed and the comparison of the data from different catchments was conducted. The results show the impact of different land use on the amount of soil organic carbon. In general, a higher amount of soil organic carbon were found in soils of grassland and forest soils, whereas a lower amounts were found in arable land. The comparison and the time development analysis show that there is a trend of the increase in quantity of stable fraction of soil organic carbon in all categories of land cover over the whole monitored period. The opposite trend of a continuous decrease over the whole of the monitored period in all categories of land cover was observed in amounts of labile fraction of soil organic carbon. It can be said that there is an increase in the stock of a stable fraction of soil organic carbon due to lower losses of the labile fraction of soil organic carbon in forest soils, arable soils and soils of grassland.

Soil organic matter (OM) is a complex mixture of compounds, mainly derived from plants and microbes at various states of decay. It is part of the global carbon cycle and is important for maintaining soil quality. OM protection is mainly attributed to its association with minerals. However, clay minerals preferentially sorb specific OM structures, and clay sorption sites become saturated as OM concentrations increase. Therefore, it is important to examine how OM structures influence their association with soil minerals, and to characterize other protection mechanisms. Several techniques, which provide complementary information, were combined to investigate OM composition: Biomarker (lignin phenol, cutin-OH acid, and lipid) analysis, using gas chromatography/mass spectrometry; solid-state 13C nuclear magnetic resonance (NMR) spectroscopy; and an emerging method, solution-state 1H NMR spectroscopy. OM composition of sand-, silt-, clay-size, and light fractions of Canadian soils were compared. It was found that microbial-derived and aliphatic structures accumulated in clay-size fractions, and lignin phenols in silt-size fractions may be protected from further oxidation. Therefore, OM protection through association with minerals may be structure-specific. OM in soils amended with maize leaves, stems, and roots from a biodegradation study were also examined. Over time, lignin phenol composition, and oxidation; and aliphatic structure contribution changed less in soils amended with leaves compared to soils amended with stems and roots. Compared to soils amended with leaves and stems, amendment with roots may have promoted the more efficient formation of microbial-derived OM. Therefore, plant chemistry influenced soil OM turnover. Synthetic OM-clay complexes and soil mineral fractions were used to investigate lignin protection from chemical oxidation. Coating with dodecanoic acid protected lignin from chemical oxidation, and overlying vegetation determined the relative resistance of lignin phenols in clay-size fractions from chemical oxidation. Therefore, additional protection from chemical oxidation may be attributed to OM composition and interactions between OM structures sorbed to clay minerals. Overall, these studies suggest that while association with minerals is important, OM turnover is also influenced by vegetation, and protection through association with clay minerals was modified by OM structure composition. As well, OM-OM interaction is a potential mechanism that protects soil OM from degradation.

Soil organic matter (OM) is a complex mixture of compounds, mainly derived from plants and microbes at various states of decay. It is part of the global carbon cycle and is important for maintaining soil quality. OM protection is mainly attributed to its association with minerals. However, clay minerals preferentially sorb specific OM structures, and clay sorption sites become saturated as OM concentrations increase. Therefore, it is important to examine how OM structures influence their association with soil minerals, and to characterize other protection mechanisms. Several techniques, which provide complementary information, were combined to investigate OM composition: Biomarker (lignin phenol, cutin-OH acid, and lipid) analysis, using gas chromatography/mass spectrometry; solid-state 13C nuclear magnetic resonance (NMR) spectroscopy; and an emerging method, solution-state 1H NMR spectroscopy. OM composition of sand-, silt-, clay-size, and light fractions of Canadian soils were compared. It was found that microbial-derived and aliphatic structures accumulated in clay-size fractions, and lignin phenols in silt-size fractions may be protected from further oxidation. Therefore, OM protection through association with minerals may be structure-specific. OM in soils amended with maize leaves, stems, and roots from a biodegradation study were also examined. Over time, lignin phenol composition, and oxidation; and aliphatic structure contribution changed less in soils amended with leaves compared to soils amended with stems and roots. Compared to soils amended with leaves and stems, amendment with roots may have promoted the more efficient formation of microbial-derived OM. Therefore, plant chemistry influenced soil OM turnover. Synthetic OM-clay complexes and soil mineral fractions were used to investigate lignin protection from chemical oxidation. Coating with dodecanoic acid protected lignin from chemical oxidation, and overlying vegetation determined the relative resistance of lignin phenols in clay-size fractions from chemical oxidation. Therefore, additional protection from chemical oxidation may be attributed to OM composition and interactions between OM structures sorbed to clay minerals. Overall, these studies suggest that while association with minerals is important, OM turnover is also influenced by vegetation, and protection through association with clay minerals was modified by OM structure composition. As well, OM-OM interaction is a potential mechanism that protects soil OM from degradation.