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Evolutionary Relationships vs Chemical
Arguments
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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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