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Abstract

The potential of crop associated microbiota research is realized and being harnessed essentially for the benefit of plant/crop. In this scenario the need for optimized amplicon sequencing protocols is there for complex samples like phyllosphere endophytes which could face the problem of host originated sequences. Endophyte research usually consists of processes like surface sterilization to remove epiphytes and freezing of samples for storage. Also, in this regard, no systematic research has been done to evaluate how the sequence of freezing and sterilization effects the host associated microbiome identification. In this study, I have developed optimized protocols to profile the bacterial and fungal endophytic communities associated with matured wheat leaves in the field. Also I have studied the effect of timing/sequence of surface sterilization and freezing on the structure of endophytic microbial community data of wheat phylloplane. As a third objective I have analyzed the impact of field sites on alpha and beta diversities of bacterial and fungal communities. It was found that first frozen (FF) samples have higher fungal diversity while first sterilized (FS) samples have more bacterial diversity but not significant. Within the field, bacterial communities are more diverse than between the fields. While fungal communities are more different between the fields compared to within field diversity. This difference is also found to be statistically not significant. Zymoseptoria and Blumeria are significantly abundant in the samples from fungicide free plot of Karkendamm compared to the samples of Hohenschulen field.