Plant material and soil sampling

Dendrobium plants were artificially cultivated in the greenhouse of Anhui Tongjisheng Biotechnology Company, Lu’an, China. The original source was collected by the company from the wild after obtaining local permission. The protocols and the conditions of planting for the growth of protocorm-like bodies were described by our previous study [31]. From the grown plants of the three species of Dendrobium, two-year-old D. huoshanense, D. moniliforme and D. officinale were selected to provide eight replicates of each sample. The voucher specimens were authenticated by Professor Maoyun Yu from West Anhui University and deposited at Jiangsu Key Laboratory of Crop Genetics and Physiology in Yangzhou University, Yangzhou, China (Voucher number: 20A01, 20A02 and 20A03).

To obtain rhizosphere soil, plants were removed from flowerpots and large soil aggregates were removed by hand; soil firmly attached to roots was collected with sterile brushes and regarded as rhizosphere soil. The rhizosphere soil was sampled and sieved to remove plant debris. A part of the soil samples was put into sterile centrifuge tubes, frozen in liquid nitrogen immediately, and then stored at − 80 °C until the soil microbial composition was analyzed.