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The protistan microbiome of German grassland soils
High throughput next generation sequencing (NGS) is a method used in ecological impact studies and biomonitoring to survey large sample numbers. When studying very small unicellular protists, this methodology is most optimally used in combination with morphological culture-based or other molecular techniques, to compensate the shortcomings of each method. In most studies to date, it was however used as a standalone method – therefore the biases and inclusion criteria of the NGS results become important. For this reason, we applied an own pipeline and very conservative criteria to be most inclusive (include all Unique Individual Reads – UIRs), but also very conservative (cluster to Operational Taxonomic Units - OTUs) within sequence pairwise similarity cut-offs to the closest reference sequence in the Protist Ribosomal Reference (PR2) database. The results were comparable to other similar studies, but very unique in that a detailed analysis of the true sequences was possible, and pyrotags could be compared to environmental sequences of other studies to compare the biogeography of the unknown diversity. While only a very few sequences (~1%) strictly matched protist reference sequences, pairwise identity inclusion cut-offs identified a large hidden diversity with no representatives in the PR2 database. In this dissertation, the first taxa-area relationship for protists in the mesoscale (1 – 1000 km between sampling sites) is described, being unexpectedly more similar to large animal and plant species than to other micro-organisms (fungi and bacteria). Taxa-area relationship of species overlap was discovered to decrease with increased land-use intensity (LUI – grazing livestock, mowing and fertilization). Combining the protist dataset for the 150 grassland sites in the mesoscale with georeferenced data for altogether 12 below- and aboveground trophic groups, true multitrophic homogenization could be measured as diversity changes with land-use intensification. A major conclusion of this multitrophic diversity ...
The protistan microbiome of German grassland soils
High throughput next generation sequencing (NGS) is a method used in ecological impact studies and biomonitoring to survey large sample numbers. When studying very small unicellular protists, this methodology is most optimally used in combination with morphological culture-based or other molecular techniques, to compensate the shortcomings of each method. In most studies to date, it was however used as a standalone method – therefore the biases and inclusion criteria of the NGS results become important. For this reason, we applied an own pipeline and very conservative criteria to be most inclusive (include all Unique Individual Reads – UIRs), but also very conservative (cluster to Operational Taxonomic Units - OTUs) within sequence pairwise similarity cut-offs to the closest reference sequence in the Protist Ribosomal Reference (PR2) database. The results were comparable to other similar studies, but very unique in that a detailed analysis of the true sequences was possible, and pyrotags could be compared to environmental sequences of other studies to compare the biogeography of the unknown diversity. While only a very few sequences (~1%) strictly matched protist reference sequences, pairwise identity inclusion cut-offs identified a large hidden diversity with no representatives in the PR2 database. In this dissertation, the first taxa-area relationship for protists in the mesoscale (1 – 1000 km between sampling sites) is described, being unexpectedly more similar to large animal and plant species than to other micro-organisms (fungi and bacteria). Taxa-area relationship of species overlap was discovered to decrease with increased land-use intensity (LUI – grazing livestock, mowing and fertilization). Combining the protist dataset for the 150 grassland sites in the mesoscale with georeferenced data for altogether 12 below- and aboveground trophic groups, true multitrophic homogenization could be measured as diversity changes with land-use intensification. A major conclusion of this multitrophic diversity ...
The protistan microbiome of German grassland soils
Venter, Paul Christiaan (Autor:in)
18.01.2018
Venter, Paul Christiaan (2018). The protistan microbiome of German grassland soils. PhD thesis, Universität zu Köln.
Hochschulschrift
Elektronische Ressource
Deutsch , Englisch
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