Research Foci
Physiology and Genetics of Nitrifying Bacteria
Environmental Controls on N2O Production by Nitrifying Bacteria
Nitrifying Bacteria and d18O signatures of NO3- in the Ocean
Isotopic Signatures as Indicators of Nitrification & Denitrification
Sources of N2O in Past Ocean Ecosystems
Co-Evolution of Organisms and Environment

Evolutionary Relationships vs Chemical Arguments

From chemical arguments it has been suggested that nitrification preceded denitrification in evolutionary history. This is due to the need for nitrifiers to convert substantial amounts of reduced N to NO3- before denitrification could become a viable metabolic option. Arguments may also be made based on the phylogeny of particular enzymes, and I am interested in testing the "nitrification-first" hypothesis through comparison of functional genes common to nitrifying and denitrifying bacteria. The similarity of nirK (and norB) among nitrifiers and denitrifiers suggests shared ancestry for these enzymes, however the origin of nirK and norB in nitrifying and denitrifying bacteria is an open question. From the phylogenetic relationships of denitrifier nirS and nirK (nitrite reductase) sequences, it has been suggested that denitrifiers probably have obtained these genes by horizontal gene transfer and thus widespread denitrification may have evolved relatively late in evolutionary history. NirK genes in nitrifying bacteria appear to be more diverse, but closely parallel evolutionary relationships of other genes in these organisms (16S rRNA and amoA genes), suggesting early acquisition of the ability to reduce nitrite and nitric oxide. Additional sequences from nitrifying bacteria are needed to extend this argument.

Phylogenetic comparison of nirK genes with 16S rRNA and ammonia monooxygenase (amoA) gene phylogenies (Casciotti and Ward, 2001) suggests that nirK may be ancestral in nitrifying bacteria (existing in the last common ancestor of all nitrifiers), while classical denitrifying bacteria may have acquired the genes through horizontal gene transfer later in evolutionary history. The origins of nitrification and denitrification have implications for the co-evolution of the Earth's atmosphere and biosphere and the historical availability of substrates for bacterial metabolism.

 

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