Soil-specific responses of methanotrophic communities in the rice rhizosphere to genotype and nitrogen fertilisation
Sandy Jan Labarosa1, Katharina Frindte2, Michael Frei3, Claudia Knief4
1University of Bonn, Inst. of Crop Science and Resource Conservation (INRES), Germany
One of the most significant agricultural sources of the greenhouse gas methane is lowland rice production. An approach to reduce methane flux from the rice field is to develop rice varieties that support methane oxidation in the roots and surrounding rhizosphere by methanotrophs. However, the effect of different genotypes on methanotrophic communities in comparison to other influence factors such as soil or nitrogen fertilisation management is still poorly understood. We conducted pmoA amplicon sequencing of root and rhizosphere samples collected from planted (Kasalath, Nipponbare, IR64, and O. rufipogon) and unplanted (as a control) paddy soil microcosms. The microcosms contained either Italian or Philippine paddy soil and were either fertilised with additional N (50 kg/ha) or not. 2,865 amplicon sequence variants were identified across 171 samples. Beta diversity analysis based on Aitchison distance and ANOSIM suggests that the two soils had significantly different (R=0.66, P=0.001) methanotrophic communities, while effects of genotype (R=-0.01, P=0.86) and N fertilisation scheme (R=0.09, P=0.09) were essentially absent. However, on a per soil basis, the effect of genotype became significant in Philippine soil (R=0.1, P=0.001), where Kasalath has a similar community with Nipponbare and IR64 with O. rufipogon. Additionally, the two fertilisation schemes resulted in significantly different methanotrophic communities in Italian soils (R=0.04, P=0.01) only. Our findings indicate that community assembly of methanotrophs in the rice root and rhizosphere depends mainly on the native population present in the soil and that plant-genotype effects and nitrogen fertilisation-responses are soil specific. Despite being phylogenetically closer, i.e. Nipponbare to O. rufipogon and Kasalath to IR64, they established different methanotrophic communities, which indicates that the relatedness of the plants is not necessarily reflected in the preferential recruitment of dis-/similar methanotrophic communities.
Keywords: Greenhouse gas, methane, methanotrophs, microcosm, PmoA, rhizosphere, rice, rice variety
Contact Address: Sandy Jan Labarosa, University of Bonn, Inst. of Crop Science and Resource Conservation (INRES), Bonn, Germany, e-mail: sandyjanlabarosagmail.com