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Doctoral thesis, 2015

Ecology and genomics of microorganisms reducing the greenhouse gas N₂O

Graf, Daniel


Nitrous oxide (N₂O) is a potent greenhouse gas and the major ozone depleting substance in the stratosphere. One major source of N₂O is incomplete denitrification, whereas the only known tropospheric sink of N₂O is the microbial enzyme nitrous oxide reductase. Denitrification is defined as the stepwise reduction of nitrite to dinitrogen via nitric oxide and N₂O by facultative anaerobic microorganisms. This thesis aims to elucidate the phylogenetic diversity of the N₂O reductase encoding gene nosZ and its context in microbial genomes in relation to other genes in the denitrification pathway, as well as the relative influence of plants and soil on the activity, abundance and structure of N₂O-reducing communities in the rhizosphere. Phylogenetic analysis of publicly available nosZ gene sequences revealed that its genetic diversity is divided into two distinct clades termed clade I and clade II, the latter having not been accounted for in previous studies. Newly developed molecular tools revealed that it is abundant in a wide range of environments. Analysis of microbial genomes showed that co-occurrence patterns of nosZ with other denitrification genes were neither randomly distributed among taxonomic units nor among habitats. Many genomes had truncated pathways as organisms possessing nosZII often lacked other genes involved in denitrification, suggesting these organisms may act as N₂O-sinks in the environment. Pot experiments with sunflower and barley indicated a niche differentiation between the two nosZ gene variants, as nosZI showed an affinity for plant roots while nosZII was more abundant in the surrounding soil. However, denitrification and N₂O-production activity in soil were controlled by edaphic factors. Moreover, an intercropping experiment with cocksfoot and lucerne showed that intercropping had a negative influence on nosZII abundances on cocksfoot roots which in conjunction with phylogenetic placement of sequencing reads indicated the presence of organisms with only nosZ lacking a denitrification pathway. In conclusion, the development of new molecular tools combined with comparative genomic analysis sheds new light on the ecology of biological N₂O reduction in the rhizosphere.


nitrous oxide; nosZ; nirS; nirK; microbial genomes; community assembly; rhizosphere; intercropping

Published in

Acta Universitatis Agriculturae Sueciae
2015, number: 2015:109
ISBN: 978-91-576-8416-5, eISBN: 978-91-576-8417-2
Publisher: Department of Microbiology, Swedish University of Agricultural Sciences

Authors' information

Graf, Daniel (Graf, Daniel )
Swedish University of Agricultural Sciences, Department of Microbiology

UKÄ Subject classification

Bioinformatics (Computational Biology)
Environmental Sciences related to Agriculture and Land-use
Soil Science

URI (permanent link to this page)