Introduction of crop rotation and rice straw application in a former flooded rice system and their impact on the microbial community in bulk soil and the rhizosphere of <em>Zea mays</em>

Abstract

Rice is one of the most important staple foods The constant flooding of rice fields results in anoxic conditions in soil, providing an optimal habitat for methane producing Archaea. The produced methane is the main substrate for methanotrophic bacteria that oxidize it to carbon dioxide (CO2) and therefore represent a methane sink within rice fields. <br /> To decrease water consumption and minimize methane emissions, an altered crop rotation by introducing plants such as maize cultivated under upland conditions, is considered. However previous studies observed, that such crop rotation promotes the development of desiccation cracks and due to that a leaching of carbon and nitrogen, whereby an increase emission of nitrous oxide was also observed. To prevent these losses, rice straw can be applied as mulch to conserve the soil moisture content and stabilize soil aggregates.<br /> How the microbial community response on the introduction of crop rotation and straw application is a central question in this thesis. Furthermore, the analysis of microbial community could indicate whether a combination of these two agricultural management practises solve the problem of high methane emissions. <br /> We analysed the microbial communities in rice fields in comparison to rice-maize crop rotation soils. <br /> The microbial community of paddy soil is well studied and characterized by an appearance of methanogens and methanotrophs. We additionally focussed on the rice phyllosphere and could isolated methanotrophs that are potentially able to consume methane emitted by rice plants. To have a closer look at the impact of crop rotation on bacteria, archaea and fungi, we analysed the microbial communities during maize cultivation in rice monoculture soils, rice-maize crop rotation soils and, as a control, in a maize monoculture soils, via amplicon sequencing. This revealed that microbial communities in crop rotation soils have a higher similarity to those in rice soils than in maize soil. However, differences between the communities in rice soils compared to crop rotation soils were mainly due to a depletion of anaerobic microbes in crop rotation soils. <br /> We investigated the active straw degrading bacterial and fungal community in detail in a crop rotation soil by applying highly labelled 13C-rice straw to the bulk soil and rhizosphere of maize. The results showed that straw degradation was performed by aerobic microorganisms in crop rotation soil, which underwent a clear temporal succession. In the rhizosphere we detected partly different microorganisms as labelled than in bulk soil, indicating that host plant specific taxa benefit from straw in the rhizosphere. Nevertheless, the lower label intensity in the rhizosphere indicates that rhizosphere organisms use straw as additional carbon source with lower efficiency besides the rhizodeposits. To investigate specifically the root exudate consuming microorganisms in the rhizosphere, we conducted a labelling experiment of maize with 13CO2 and subsequent phospholipid fatty acid stable isotope probing. The results confirm that the addition of straw impacts the uptake of root exudates. Obviously, a simultaneous use of root exudates and straw takes place, because straw addition results in a decreased uptake of root exudates.<br /> This thesis provides evidence that the introduction of crop rotation leads to an altered microbial community in bulk soil and in the rhizosphere of maize. The depletion of methanogens leads to the assumption that a crop rotation of rice, followed by maize, and straw addition during the dry season is a promising strategy to reduce methane emissions.