Denitrification: from genes to ecosystems

Sammanfattning: Denitrification is a part of the global nitrogen cycle in which fixed nitrogen in the biosphere is returned to the atmosphere, which is mediated by diverse communities of microorganisms. This thesis seeks to gain a greater understanding of the ecology of denitrifying microorganisms by examining the pathway from four different aspects; gene, population, community, and ecosystem. A combination of bioinformatic analysis of denitrification genes in pure cultures and environmental samples as well as experimental work with denitrifying bacterial cultures and soil microcosms was performed to understand the relationship between genes and ecosystems in denitrification. Analysis of the phylogeny of genes involved in key steps in the denitrificaiton pathway revealed a different evolutionary pattern for each gene, as processes such as horizontal gene transfer, duplication/divergence, and lineage sorting have contributed differentially to the evolution of each gene. However, genetic variation is not easily translated into an extended phenotype for a population of denitrifiers, as the denitrification phenotype of a set of closely related denitrifying Bacillus soil isolates was variable depending on pH. Yet, the genetic community structure was shown to be an important factor in determining denitrification rates and end product ratios, as denitrifying communities in soil microcosms showed differential response to altered ratios of organisms with an without the ability to reduce nitrous oxide. Finally, patterns of nirS and nirK sequences suggested that community assembly of both denitrifier types was largely driven by niche-based processes, as community structure varied among habitats with different salinities. However, nirS and nirK denitrifiers were not ecologically equivalent, as patterns of phylogenetic clustering among co-existing nirS and nirK type denitrifying communities along the same environmental gradient were not comparable. In conclusion, denitrification is a complex ecological function that is regulated by the interaction between gene and environmental processes, and evolutionary processes that underlying the diversification and distribution of denitrification genes may have direct consequences on the denitrification unction in ecosystems.