16S and ITS amplicon sequences of bulk apple soils exposed to elevated CO2 and increased temperature from an organic and conventional orchard in South East England

Aim We assessed the effect of exposing apple orchard soil to different temperatures and CO2 levels on the resident microbiome of soils at two different depths from a conventionally managed and an organically managed apple orchard. The key difference between these two orchards was that synthetic fertilizers and pesticides are routinely used in the former one. Methods and Results To investigate the effect of CO2 and temperature soil samples from each site and depth were exposed to elevated temperature (29 oC) at either 5,000 or 10,000 ppm for 5 weeks or exposed to control conditions (25 oC + 400 ppm). Both bacterial and fungal communities were profiled with amplicon-sequencing. The differences between the two orchards were the most significant factor affecting both bacterial and fungal communities contributing to 53.7% and 14.0% of the variance in Bray-Curtis ß diversity respectively. The effects of both elevated CO2 concentrations and increased temperature affected organic fungal and bacterial diversity more than in conventional soils. A number of candidate beneficial and pathogenic microorganisms include Pseudoxanthomonas, Janthinobacterium, Nocardioides, Pseudomonas, Variovorax, Massilia, Streptomyces, Burkholderia, Mucilaginibacter, and Trichoderma had differential abundance when temperature and CO2 were elevated. The effect on the plant is unclear. Conclusions This study has highlighted that microbial communities in bulk soils are most significantly influenced by crop management practice compared to the climate conditions used in the study. The studied climate conditions had a limited effect on conventionally managed soil microbial communities than organic soils, but may significantly influence the relative abundance of microbial communities, including both beneficial and phytopathogenic microbes. Significance and Impact of Study The study showed that climate change scenarios can have a significant impact on the microbiome of soils, with agronomic factors being particularly important. This study highlights the buffering capacity of conventionally managed soils compared to organically managed soils to elevated temperature and CO2. It also identifies beneficial microorganisms sensitive to climate conditions as candidates for soil amendment and potential emerging pathogens in bulk soil. This study provides the basis for further work on the relative impact of changes in climatic conditions and plant development influences on the soil microbiome.