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Dependence of soil microbial community structure and function on land use types and management regimes

dc.contributor.advisorDaniel, Rolf Prof. Dr.
dc.contributor.authorKaiser, Kristin
dc.titleDependence of soil microbial community structure and function on land use types and management regimesde
dc.contributor.refereeDaniel, Rolf Prof. Dr.
dc.description.abstractengSoil microbial communities are the most diverse assemblages of organisms on earth. They play key roles in nutrient cycling and help prevent soil erosion. Soil microbial communities also harbor many potentially plant-associated microorganisms. Plant-associated microbes inhabit the rhizosphere or phyllosphere, or live endophytic within plants. Despite the increasing number of studies on both soil and plant-associated microbial communities, the response of microbial communities towards land use intensification is still not fully understood. The aim of this thesis was to provide insights into the structure, diversity and function of soil and plant-associated microbial communities by amplicon-based analyses with regard to potential abiotic, biotic and anthropogenic drivers. The first study investigated the effect of different nucleic acid extraction methods on the abundance and diversity of 16S rRNA genes and transcripts derived from different soils. Quality and yields of nucleic acids varied considerably between the different extraction methods applied, as well as between the different soils. Furthermore, abundances of dominant soil taxa varied by a factor up to ten by applying different extraction methods. Therefore, it is of high importance to choose an extraction method that is able to reproduce diversity and composition of the soil microbial community over a range of differing soils. This is crucial when soils from the entire study area should be compared, as they might differ in their properties. The second study presented a large-scale analysis of soil bacterial communities in temperate grasslands and forests. Therefore, 300 samples were taken in May 2011 in a joint sampling campaign of the German Biodiversity Exploratory project. Metagenomic DNA was extracted and the V3-V5 regions of the bacterial 16S rRNA gene were amplified and pyrosequenced, to assess bacterial community structure and diversity. Additionally, a functional profile was predicted based on the taxonomic profile. The bacterial community structure was driven by edaphic properties with pH as the major driver while land use intensification represented by different management regimes exhibited only minor effects. However, tree species notably affected soil bacterial community structure, with distinct bacterial communities in soils beneath broadleaved and coniferous trees. Edaphic properties were significantly different between grassland and forest soils, resulting in distinct bacterial community structures. Biogeographic variation of edaphic properties also resulted in regional patterns of bacterial community structure. Bacterial diversity was additionally strongly dependent on soil pH. Furthermore, the functional profile of the bacterial communities was shaped by the same drivers as community structure and diversity. Because of the strong impact of soil pH, genes involved in the acid tolerance response (ATR) were in the focus of the analyses of the functional profiles. Genes involved in alkali production, biofilm formation and attributed to two component systems were more abundant in profiles from low pH soils. The functional profiles of grassland and forests soils were significantly different. The investigation of different key enzyme-encoding genes involved in nutrient cycling revealed that certain functions are either more abundant in grassland (e.g. PAH degradation, alkaline phosphatase, urease, chitinase) or forests soils (e.g. acid phosphatase, methane oxidation, nitrous oxide-reductase, nitrogenase). The third study investigated soil bacterial and fungal communities beneath beech and spruce trees, and their changes with increasing distance to the tree trunks, soil depth and season. Community structure was driven by edaphic properties (pH, clay content) and the tree species. Seasonal changes as well as depth-related changes were observed for community structure of both bacteria and fungi. Additionally, bacterial community structure and diversity was affected by the distance from the trunk beneath spruce trees. The following two studies synthesized the effects of land use intensification on different taxonomic groups. The fourth study investigated species abundance distributions (SADs) of 10 aboveground and belowground taxonomic groups in grasslands under different management regimes. SADs are a powerful tool to investigate community changes, as they not only capture overall changes in community structure, but also indicate whether these changes are driven by abundant or rare species. Species richness was largely unaltered by increasing land use intensification. In addition, belowground organisms (bacteria and arbuscular mycorrhizal fungi) were not significantly affected by land use intensity. The fifth study analyzed the effects on biodiversity by management regimes (even-aged or uneven-aged forests) in European beech forests. Gamma-, beta-, and alpha-diversity of 15 taxonomic groups were analyzed. Gamma diversity of bacteria and fungi as well as of plant and animals was higher in even-aged forests than in uneven-aged forests. These differences were driven by a higher beta-diversity in even-aged forests. The last three studies focused on plant-associated microbial communities. In the sixth study bacterial endophyte communities in three agriculturally important grasses (Lolium perenne, Festuca rubra and Dactylis glomerta) in response to fertilization and mowing in two subsequent years (2010 and 2011) were analyzed. Diversity was highest in D. glomerta, and community structure was significantly shaped by the host plants. Fertilization only affected endophytic community structure and diversity in 2010, while mowing had no effect in both years. In studies seven and eight, a wheat/faba bean intercropping experiment investigated soil archaeal and soil and plant-associated bacterial and fungal communities, respectively. Soil archaeal but not bacterial or fungal community structure was affected by plant species and cropping regime. Bacterial and fungal community structure was similar in bulk soil and rhizosphere, and bacterial communities were distinct in the endosphere of roots and leaves. Fungal communities did not follow this trend. In conclusion, soil microbial communities in soils are affected by edaphic properties. These effects most likely overrule effects of land use intensification. Plant-associated microbial assemblages are mainly shaped by the host plant and plant compartment. Nevertheless, agricultural management such as intercropping, alters archaeal community structure and therefore potentially affects microbial community structure on long-term
dc.contributor.coRefereeHoppert, Michael PD Dr.
dc.affiliation.instituteBiologische Fakultät für Biologie und Psychologiede
dc.subject.gokfullBiologie (PPN619462639)de

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