Open access publications in the SLU publication database

Abstract

Denitrification is a biogeochemical process of major importance for nitrogen loss from
ecosystems. This four-step pathway is modular, as organisms can have different subsets
and variants of the genes involved in each step. The last step is the only known biological
sink of nitrous oxide, a potent greenhouse gas and ozone depleting substance. The aim
of this thesis was to assess whether specific environmental conditions favour certain
denitrifying and nitrous oxide reducing genotypes. The effects of nitrogen, carbon and
oxygen availabilities, as well as habitat type and diversity were examined in studies of
denitrifying and nitrous oxide reducing microorganisms in pure cultures, enrichment
cultures and natural communities from coastal sediments. By utilizing molecular
techniques and directly targeting functional genes encoding for nitrite and nitrous oxide
reductases, this work explores the link between genetic potential and functionality of
denitrifying and nitrous oxide reducing microbial communities.

Microorganisms harbouring genes for complete denitrification dominated in coastal
marine sediments, irrespective of oxygen regime and habitat type, which suggests they
have an important role not only for nitrogen removal, but also nitrous oxide reduction in
coastal ecosystems. However, oxygen affected the nitrous oxide reducing communities.
The results indicate niche differentiation between nitrous oxide reducers in relation to
oxic/anoxic conditions, as specific lineages within the nitrous oxide reductase gene
phylogeny were favoured by certain oxygen regimes. In enrichment cultures, complete
denitrifiers were competitive nitrous oxide reducers and could outcompete organisms
only capable of nitrous oxide reduction when subjected to carbon and nitrous oxide
limitation. For denitrifiers, functional difference between the genes nirS and nirK
encoding two structurally different nitrite reductases within the same organism was
observed, corroborating that closely related and almost identical genotypes differ in their
denitrification activity. Furthermore, primers targeting nitrite reducing communities
harbouring either nirS or nirK were re-evaluated and clade-specific primers are
suggested. Finally, a framework for primer evaluation using metagenomes is suggested.

These results highlight the importance of accounting for the genetic potential of
denitrifying and nitrous oxide reducing communities to better understand overall
ecosystem constraints and how environmental factors might control this potential.