Spatial structuring of soil microbial communities in commercial apple orchards 
Greg Deakin

Characterising spatial microbial community structure is important to understand and explain the consequences of continuous plantation of one crop species on the performance of subsequent crops, especially where this leads to reduced growth vigour and crop yield. We investigated the spatial structure, specifically distance-decay of similarity, of soil bacterial and fungal communities in two long-established orchards with contrasting agronomic characteristics. A spatially explicit sampling strategy was used to collect soil from under recently grubbed rows of apple trees and under the grassed aisles. Amplicon-based metabarcoding technology was used to characterise the soil microbial communities. The results suggested that (1) most of the differences in soil microbial community structure were due to large-scale differences (i.e. between orchards), (2) within-orchard, small-scale (1–5 m) spatial variability was also present, but spatial relationships in microbial community structure differed between orchards and were not predictable, and (3) vegetation type (i.e. trees or grass and their associated management) can significantly alter the structure of soil microbial communities, affecting a large proportion of microbial groups. The discontinuous nature of soil microbial community structure in the tree stations and neighbouring grass aisles within an orchard illustrate the importance of vegetation type and allied weed and nutrient management on soil microbial community structure.

Unweighted (A: fungi, C: bacteria) and weighted (B: fungi, D: bacteria) UniFrac distance (β diversity indices - between samples calculated from a neighbour joining tree of phylogenetic distance between OTUs), illustrating between-orchard difference is much greater (darker in the heatmap) than within-orchard differences. The heatmaps have top left to bottom right diagonal symmetry, and samples have been ordered on both axis by the orchard and their physical location in each orchard.

https://www.sciencedirect.com/science/article/pii/S0929139317308442#!

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