Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities

Background Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce. Methods Here, we assessed the effect of temperate agroforestry on the abundance, diversity and composition of soil bacterial communities at three paired poplar-based alley cropping and conventional monoculture cropland systems using real-time PCR and Illumina sequencing of bacterial 16S rRNA genes. Two of the three systems grew summer barley (Hordeum vulgare); one system grew maize (Zea mays) during the sampling year. To capture the spatial heterogeneity induced by the tree rows, soil samples in the agroforestry systems were collected along transects spanning from the centre of the tree rows to the centre of the crop rows. Results Tree rows of temperate agroforestry systems increased the abundance of soil bacteria while their alpha diversity remained largely unaffected. The composition of the bacterial communities in tree rows differed from those in arable land (crop rows of the agroforestry systems and conventional monoculture croplands). Several bacterial groups in soil showed strong association with either tree rows or arable land, revealing that the introduction of trees into arable land through agroforestry is accompanied by the introduction of a tree row-associated microbiome. Conclusion The presence of tree row-associated bacteria in agroforestry increases the overall microbial diversity of the system. We speculate that the increase in biodiversity is accompanied by functional diversification. Differences in plant-derived nutrients (root exudates and tree litter) and management practices (fertilization and tillage) likely account for the differences between bacterial communities of tree rows and arable land in agroforestry systems.