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Diversity of functional genes in the aquatic nitrogen cycle


Kim,  Ok-Sun
Department Ecophysiology, Max Planck Institute for Limnology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Kim, O.-S. (2007). Diversity of functional genes in the aquatic nitrogen cycle. PhD Thesis, Christian-Albrechts-Universität, Kiel.

In this PhD thesis the diversity of functional bacterial genes in the nitrogen cycle was investigated with molecular methods in the lakes Plußsee and Schöhsee, and the Baltic Sea. The diversity of ammonia-oxidizing bacteria (AOB) was studied by diversity of specific 16S rDNA and amoA genes. Dominant sequences from Baltic Sea water column and Schöhsee 1 m were related to different Nitrosospira clusters. Sequences from Plußsee 7 m, Schöhsee 12 m and sediment of both lakes were clustered into a purely environmental cluster with no cultivated representatives. Two groups of amoA sequences from Baltic Sea sediment were related to environmental clusters from brackish and marine habitats. The diversity of the evolutionarily related genes for ammonia monooxygenase (AMO) and particulate methane monooxygenase (pMMO) was analyzed. A higher frequency of pmoA sequences, mainly belonging to methane oxidizing bacteria of the gamma subgroup of proteobacteria (γ-MOB), was detected. Dominant amoA sequences were related to ammonia oxidizing bacteria of the beta subgroup of proteobacteria (β-AOB), no sequences related to amoA of the γ-AOB were detected. The deduced amino acid sequences of some clones from lake sediments were distantly related to PmoA from Crenothrix polyspora, a filamentous methane oxidizer with an unusual methane monooxygenase. The distribution of denitrifying bacteria was studied by the nitrite reductase genes nirK and nirS. The dominant sequences of nirK from all clone libraries belonged to two distinct phylogenetic clusters, while nirS sequences from both lakes were scattered over several clusters throughout the complete phylogenetic tree, and only few sequences from Baltic Sea overlapped. In the Baltic Sea, nirK-denitrifiers were diverse throughout the water column, while nirS-denitrifiers were dominant in the sediment and almost absent in the water column. In Plußsee the community composition was inverted: nirK-denitrifiers were more diverse in the water column and nirS-denitrifiers in the sediment. In Schöhsee nirS-denitrifiers were highly diverse in water and sediment samples. For nirK and nirS the sequences of the protein were less conserved than those of the gene while the amoA and pmoA protein were conserved, which might be an indication of a differential selection pressure.