Ammonia-oxidizing and denitrfying microorganisms populations in rice crop

Doctoral thesis abstract

Abstract

Worldwide, rice is an important food source. Its farming is potentially a source of greenhouse effect gases (GHG), such as CH4 and N2O. Water management and or rice cultivar selection are some of the management strategies employed to mitigate these gases. In addition, soils with different physicochemical characteristics can differ in their tendency to emit GHG. In soils N2O is biologically produced, mainly by two microbial guilds, ammonia-oxidizing microorganisms, and denitrifying microorganisms. In this thesis, it was determined the effect of water management, rice cultivar and soil type on the abundance and population structure of both guilds. These microorganisms abundance were determined by qPCR, while their population structures were determined by T-RFLP. For the ammonia-oxidizing microorganisms the amoA gene that encodes for the ammonia monooxygenase was used as the target gene; archeal and bacterial amoA gene were analyzed separately. On the other hand, nirS and nirK genes, which encode for the two kinds of the enzyme nitrite reductase, were used as the target genes to study the denitrifying microorganisms. Two greenhouse experiments were set up in two consecutive years. In the first experiment, two rice cultivars and two water managements were evaluated, while in the second experiment two soil types and two times of flooding were evaluated. Results showed that all the factors evaluated had some effect on the microbial populations, however not all the factors affected the populations equally. The soil type was the strongest factor shaping microbial populations, and had a particularly strong effect on the ammonia-oxidizing archaea.