Different soil sampling designs influence the diversity and drivers of the avocado rhizosphere bacterial and fungal communities

The variability of the rhizosphere microbial community has not been well-studied in avocado plantations at the field-scale. This research aimed to determine if the bacterial and fungal communities in the rhizosphere and/or the soil physicochemical properties from two commercial avocado orchards varied with different sampling designs (grid-based, longitudinal transect, and zigzag transect), and in turn if this changed the soil physicochemical properties driving the composition of the microbial communities. There were no differences in alpha diversity of bacteria or fungi based on sampling design in either orchard, and bacterial and fungal alpha diversity showed no evidence of spatial autocorrelation. Bacterial community composition in Orchard 1 varied with sampling design, whereas no differences were observed for bacterial community composition in Orchard 2 or for fungal community composition in either orchard. In each orchard, at least 50 % of the most abundant bacterial taxa were common between the sampling designs, however, less than 40 % the most abundant fungal taxa were common between the sampling designs. Canonical correspondence analysis indicated that the edaphic drivers of bacterial and fungal communities in Orchard 1 differed based on the sampling design. These results highlight the importance of field-scale sampling design for accurately characterising avocado rhizosphere bacterial and fungal communities particularly when such data will inform orchard management decisions. Soil sampling using a random, grid-based design is recommended as a simple and reliable method for monoculture fruit tree orchards. • Bacterial community composition in Orchard 1 differed between sampling designs. • At least 40 % of the most abundant bacteria and fungi were common to all sampling designs. • Edaphic drivers of bacteria and fungi in Orchard 1 changed with the sampling design. • No spatial autocorrelation in microbial alpha diversity or in soil properties in each orchard