Diversity and Activity of Soil Bacterial Communities under different Management Regimes
Diversity and Activity of Soil Bacterial Communities under different Management Regimes
by Sarah Herzog
Date of Examination:2015-11-20
Date of issue:2015-12-09
Advisor:Prof. Dr. Rolf Daniel
Referee:Prof. Dr. Rolf Daniel
Referee:PD Dr. Michael Hoppert
Persistent Address:
http://dx.doi.org/10.53846/goediss-5417
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Abstract
English
Bacteria are key players in nutrient cycles and energy transduction in soil. Although soil bacterial communities have been studied for several decades, our knowledge on their structure, dynamics ecosystem function is still limited. The aim of this thesis was to contribute to the understanding of these communities. In the first two studies, the impact of fertilizer treatment, two distinct aspen demes, soil properties (pH, water content, and C/N ratio), and sampling time on the total (DNA level) and the metabolic active (RNA level) bacterial community was analyzed. Thus, soil samples were collected in April, July, and September over two consecutive years. Community compositions were further assessed by pyrotag sequencing of 16S rRNA amplicons generated from environmental DNA and RNA, respectively. Additionally, functional analyses were performed based on the prediction of functional traits from taxonomic community composition. In the first study, all factors investigated influenced the bacterial community composition and diversity. Fertilizer application leaded to a diversity loss in the active bacterial community at phylum as well as at species level. Relative abundances of active bacterial community members showed a shift to bacterial groups such as Xanthomonadales, which are specialized to use nitrogen compounds as energy source. In addition, genes encoding for the uptake of nitrate/nitrite, nitrification, and denitrification steps were significantly more abundant in fertilized plots at active bacterial community level. In the second study, an influence of two different aspen demes Geismar2 and Geismar8 on soil bacterial community and diversity was observed at the active community level. The comparison of mean Shannon indices revealed a significantly higher diversity in the active soil bacterial community of aspen deme Geismar2 compared to Geismar8 at 3% and 20% genetic distance. Moreover, several of the main abundant phyla and proteobacterial classes were either more abundant in aspen deme Geismar2 or Geismar8, respectively. The effect of sampling time on bacterial community was more pronounced at active bacterial community level, indicating that the metabolic active community members responded earlier to environmental changes. This result was supported by correlation analyses of relative abundances and soil properties. Additionally, we observed more significant positive and negative correlations of soil properties at many taxonomic levels (at phylum, proteobacterial class, and order level) in the active bacterial community than in the total bacterial community. As a consequence, seasonal change has to be regarded in further studies as it might alter the effects of different grassland management regimes or aspen demes on soil bacterial communities. In the third study, the effect of management regimes, mowing frequency, sward composition, and above-ground herbivory on the bacterial community composition in the rhizosphere was investigated. For this purpose, a lysimeter experiment was established in autumn 2010. Following a two-week exposure to herbivory by grasshoppers and snails, soil samples were collected from the lysimeters in summer 2011. DNA was extracted from the collected samples and subjected to 16S rRNA gene analysis. Community structure and bacterial diversity were assessed either by DGGE analysis or pyrosequencing of 16S rRNA gene amplicons. Sward composition and lower mowing frequencies decreased the bacterial richness in the rhizosphere. Despite that differences in bacterial richness between fertilized and non-fertilized plots were not recorded, the bacterial community composition responded to different management regimes. For example, Acidobacteria were significantly more abundant in non-fertilized plots, whereas Actinobacteria were significantly more abundant in fertilized plots. In conclusion, bacterial communities in soil and in the rhizosphere are affected by different factors such as fertilizer application. Evaluating the main drivers of bacterial communities may results in a better understanding of the complex interactions between plants and bacterial communities. Furthermore, the results of this study will help to predict the impact of different factors onto bacterial communities in rhizosphere and soil and related effects on soil ecosystems.
Keywords: Soil bacteria; Metagenomics; Metatranscriptomics; Microbial ecology