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. Bulk apple soil exposed to climate change conditions

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 β 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.

研究目的：本研究旨在探究将苹果园土壤暴露于不同温度与二氧化碳（CO₂）浓度条件下，对常规管理与有机管理苹果园两个不同土层深度的原位土壤微生物组的影响。两个果园的核心差异在于：常规管理果园常规施用合成肥料与农药。

材料与方法及结果：为探究CO₂浓度与温度的影响，本研究将两个果园各土层的土壤样品分别置于29℃、5000 ppm或10000 ppm CO₂浓度下培养5周，同时设置对照组（25℃、400 ppm CO₂）。采用扩增子测序（amplicon-sequencing）对细菌与真菌群落进行表征分析。结果显示，两个果园的管理方式差异是影响细菌与真菌群落的最显著因素，分别解释了Bray-Curtis β多样性（Bray-Curtis β diversity）总方差的53.7%与14.0%。相较于常规管理土壤，有机管理土壤的真菌与细菌多样性对CO₂浓度升高与温度上升的响应更为显著。当温度与CO₂浓度升高时，包括假黄色单胞菌属（Pseudoxanthomonas）、詹森杆菌属（Janthinobacterium）、诺卡氏菌属（Nocardioides）、假单胞菌属（Pseudomonas）、贪铜菌属（Variovorax）、马西利亚菌属（Massilia）、链霉菌属（Streptomyces）、伯克霍尔德菌属（Burkholderia）、黏纤维菌属（Mucilaginibacter）以及木霉菌属（Trichoderma）在内的多种潜在有益与病原微生物的丰度均发生显著变化。本研究中气候变化对植物的影响尚不明确。

研究结论：本研究表明，相较于本研究所设置的气候条件，农田管理方式对原状土壤微生物群落的影响更为显著。相较于有机管理土壤，本研究设置的气候条件对常规管理土壤微生物群落的影响相对有限，但可显著改变有益与植物病原微生物的相对丰度。

研究意义与影响：本研究证实，气候变化情景可对土壤微生物组产生显著影响，其中农艺管理因素尤为关键。本研究凸显了常规管理土壤相较于有机管理土壤对温度与CO₂浓度升高的缓冲能力。同时，本研究筛选出对气候条件敏感的有益微生物作为土壤改良候选菌剂，并明确了原状土壤中潜在的新兴病原微生物类群。本研究为后续探究气候条件变化与植物生长对土壤微生物组的相对影响奠定了研究基础。