A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field

Abstract

Plant associated microbial communities have recently received a lot of attention because thought to play a fundamental role in plant health and development. Focusing on cultivated crops, optimized farming practices must consider the role of these communities when aiming at reducing the impact of pathogens and increasing yields. Typical inhabitants of plant’s phyllosphere are bacteria and microscopic fungi, some of them pathogenic for the plant and dangerous for the consumers, due to the production of toxins. In order to efficiently manage the microbiome, the natural drivers regulating community assembly must be clearly understood. In our study we investigated the within field variation of the phyllosphere mycobiome of wheat ears by metabarcoding of the fungal internal transcribed sequence 1 (ITS1). We selected a field characterized by a high topographic heterogeneity, which is reflected in differences in plant productivity and fitness across it. Samples were taken from 30 sampling points laid across the field where data-loggers were placed, measuring the productivity driven under canopy microclimate. The microclimatic conditions were tested as a source of potential environmental variance. Further independent spatial structures were tested using spatial eigenvector maps (MEMs). Results show considerable differences in the phyllosphere composition across the field. The local under canopy environmental conditions at each point were strong predictors of the community composition. Independent spatial effects given by the geographical position of the sampling points showed also a weaker but significant effect. Moreover we observed different spatial responses from different fungal phyla, with results resembling those described in studies done at a regional scale. This study is the first one to investigate the spatial variation of the phyllosphere mycobiome of a commercial crop within the same field. It contributes to the study of the epidemiology and community assembly dynamics of wheat phyllosphere fungi, showing how in-field community variations are the results of different environmental and spatial processes acting simultaneously. It also shows how heterogeneous fields are a smart and useful system to investigate the ecological mechanisms regulating plant microbiome composition.