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Understanding the Micro-Environments of Diazotrophs and their Associated Activities in Rice

Final Report Summary - DIAZOASSOCRICE (Understanding the Micro-Environments of Diazotrophs and their Associated Activities in Rice)

For over 3 billion people, rice is the primary food source yet the production is limited by nitrogen availability to the plants. Rice is mainly produced on flooded fields (i.e. paddy soils), which is estimated to encompass 11% of the area used for agriculture worldwide. In order to maintain the production of rice, the extensive use of industrially produced fertilizers is necessary. Unfortunately, the production of such fertilizers is not only costly, but generates downstream environmental hazards such as nitrogen leaching from soils and subsequent contamination of groundwater with nitrate. Biologically, soil nitrogen pools can be replenished by the conversion of atmospheric dinitrogen gas to ammonia via biological nitrogen fixation without cost or environmental hazard. This enzymatic process is carried out by a phylogenetically diverse group of microorganisms within the Bacteria and Archaea, the diazotrophs. Biological nitrogen fixation can alleviate nitrogen shortage in rice cultivation, and the potential of diazotrophs to supply rice with fixed nitrogen is estimated to account for up to 25% of the total demand of the plants. However, our knowledge on the diversity and the in situ nitrogen fixation activity of diazotrophs in rice fields is still fragmentary. As the human population worldwide continues to increase, we need to better understand the full potential of biological nitrogen fixation in rice plant cultivation and the microbial drivers of the nitrogen fixation activities.

This project seeks to increase the understanding of diazotroph diversity, activity, and their respective contribution to biological nitrogen fixation in rice systems. A better understanding of the colonization patterns and micro-niches of diazotrophs associated with soil-plant interfaces is needed to unravel the interactions and nitrogen transfer processes between diazotrophs and the rice plant on a biologically meaningful micro-scale. The objectives of our research are: (1) to investigate the factors (soil types, rice genotypes, micro-environments) influencing the community composition of diazotrophs based on nifH amplicon sequencing; (2) the in situ analysis of spatial distribution and colonization patterns of native diazotrophs associated with soil-grown rice roots via fluorescence in situ hybridization (FISH); and (3) to assess the in situ activity of diazotrophs associated with soil-root micro-environments by 15N2 incubations and isotope analysis (IRMS, NanoSIMS). This project combines molecular methods, biogeochemical assays, and single-cell isotope analysis to address questions regarding the N2 fixation by plant-associated diazotrophs on a biologically relevant submicron scale.

We successfully analyzed the community composition of nitrogen fixation microorganisms in two soils of different geographical origin that were cultivated with two rice genotypes in greenhouse experiments. We found that the communities of potentially active nitrogen-fixing archaea and bacteria were mainly influenced by the microbial seed bank of the soil and small-scale biotic factors present in plant-soil interfaces. Both plant genotypes assembled a comparable community in both soils. Diazotrophs were shown to be actively fixing atmospheric nitrogen in all micro-environments, even in the bulk soil compartment that is generally regarded as the portion of rice field soil with lowest nitrogen fixation capacity. Our results strongly indicate that a variety of members of nitrogen-fixing archaea and bacteria may be involved in the process of making atmospheric nitrogen readily available to rice plants. Single-cell localization of target groups of interest allowed us to better understand the niches of nitrogen-fixing microorganisms in rice fields. The interplay of abiotic and biotic parameters in the soil-microbe-plant interfaces of paddy soils drive a differentiation of diazotroph communities on much smaller scales than generally assumed. We advocate the study of this globally relevant process on a biologically meaningful micro-scale in order to understand the processes and fluxes occurring on an ecosystem level. Understanding the drivers of nitrogen fixation activity in agronomically important systems such as rice fields will lead to the identification of the most powerful diazotrophs that support rice plants with naturally available atmospheric nitrogen. We were able to identify and isolate target strains from soil and root samples that are currently analyzed for their capacity to support rice plants with nitrogen. These strains could represent promising new candidates for an application in sustainable agriculture, a practice that helps feeding the world’s population while reducing the amounts of fossil fuels burnt by the production of nitrogen fertilizers as well as diminishing those hazardous downstream effects fertilization has on natural ecosystems.

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Contact details
Dr. Hannes Schmidt
University of Vienna
Department of Microbiology and Ecosystem Science
Division of Microbial Ecology
Althanstr. 14
A-1090 Vienna
Phone: +43 1 4277 76603