ERP118007 PRJEB35017 ena-STUDY-INRES Molecular Biology of the Rhizosphere-22-10-2019-06:57:35:267-152 Influence of cropping history on the soil and rhizosphere microbiota of rice and maize Rice and maize are main staples, but as freshwater will become more limited in the future, alternative cropping strategies for rice cultivation are required like crop rotation between maize and rice. Changes in crop rotation lead to the question how microbial communities change if paddy soils become temporary upland soils or upland soils become paddy soils for the first time. In this study, we conducted greenhouse experiments over 3 months with soils from two neighboring fields, where rice and maize were grown in monoculture for over 30 years. DNA was extracted from rhizosphere and bulk soil samples to perform 16S rRNA gene and fungal ITS region amplicon analysis. Flooding affected also the evenness of the microbiota, while cropping history affected mainly the richness. Fungal and bacterial communities were mainly affected by cropping history and first-time flooding, while the impact of the cultivated crop was less evident. Flooding significantly increased the relative frequency of different unclassified fungi in both soils compared to soils with long-term as well as first maize cultivation. Non-flooding especially favours candidate phylum Saccharibacter. In conclusion, our study shows that flooding and cropping history are the major drivers and therefore provide the framework for soil microbial community composition, while the introduced plant specifically shapes the rhizosphere microbiota. The high number of still unknown fungal species in paddy rice fields indicates that in flooded soils different, still little known fungi are obviously important, which requires more in-depth studies to understand their role and function under flooded conditions. Rice-maize Rice and maize are main staples, but as freshwater will become more limited in the future, alternative cropping strategies for rice cultivation are required like crop rotation between maize and rice. Changes in crop rotation lead to the question how microbial communities change if paddy soils become temporary upland soils or upland soils become paddy soils for the first time. In this study, we conducted greenhouse experiments over 3 months with soils from two neighboring fields, where rice and maize were grown in monoculture for over 30 years. DNA was extracted from rhizosphere and bulk soil samples to perform 16S rRNA gene and fungal ITS region amplicon analysis. Flooding affected also the evenness of the microbiota, while cropping history affected mainly the richness. Fungal and bacterial communities were mainly affected by cropping history and first-time flooding, while the impact of the cultivated crop was less evident. Flooding significantly increased the relative frequency of different unclassified fungi in both soils compared to soils with long-term as well as first maize cultivation. Non-flooding especially favours candidate phylum Saccharibacter. In conclusion, our study shows that flooding and cropping history are the major drivers and therefore provide the framework for soil microbial community composition, while the introduced plant specifically shapes the rhizosphere microbiota. The high number of still unknown fungal species in paddy rice fields indicates that in flooded soils different, still little known fungi are obviously important, which requires more in-depth studies to understand their role and function under flooded conditions. ENA-FIRST-PUBLIC 2020-03-29 ENA-LAST-UPDATE 2019-10-22