Features of Bacterial Microbiota in the Wild Habitat of Pulsatilla tongkangensis, the Endangered “Long-Sepal Donggang Pasque-Flower Plant,” Endemic to Karst Topography of Korea

Abstract

Microbes associated with plants significantly influence the development and health of the plants. The diversity and function of microbiomes associated with the long-sepal Donggang pasque-flower (DPF) plant, an endemic and endangered species in karst ecosystems, remain unexplored. In this study, we investigated the features of bacterial communities associated with the rhizosphere and roots of DPF plants and their functions in plant growth promotion. The DPF plants were collected from natural and cultivated habitats, and their 16S rDNA was sequenced to assess the bacterial community structures. The bacterial microbiota was more diverse in wild than in cultivated plants. The core bacterial microbiota commonly functioned as endophytes in both wild and cultivated DPF plants, although there were some differences. The identified bacterial strains benefited plants through nitrogen fixation, phosphate solubilization, or phytohormone production, inducing measurable growth differences in Arabidopsis thaliana. To the best of our knowledge, this study is the first to report the bacterial community structures associated with the rhizosphere soil and roots of DPF plants in karst ecosystems. The bacterial strains isolated in this study could be used to aid sustainable growth and restoration of rare plants in karst ecosystems. Our systematic research on the microbiomes associated with these endangered plants will contribute to their conservation as well as development of better cultivation.

Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress

“…From the plant collection areas, two individual Ulleung-sanmaneul ( Allium ulleungense H. J. Choi & N. Friesen; U-SMN) plants (spaced 30 cm apart) were randomly dug out with intact roots along with soil from 5 cm outside of the root zone and combined to form one biological replicate and stored in sterile plastic bags at 4 °C. The samples were brought to the laboratory and separated into bulk soil, rhizosphere soil, and endosphere (root) samples 47 . Bulk soil was collected from the root system by gentle shaking, and the detached particles were then sieved through a 2-mm sieve.…”

“…EzBioCloud ( https://www.ezbiocloud.net/ ), an in-house pipeline developed by ChunLab Inc. (Seoul, South Korea) 47 , 49 was used to analyze the sequenced data. The pipeline is used for quality control, merging of forward and reverse paired-end reads, sequence processing and taxonomic classification, and diversity analysis of OTUs.…”

“…The bacterial diversities were analyzed and compared using CL community™ v3.43 (ChunLab, Seoul, South Korea) 47 , 56 . Rarefaction curves, alpha diversity analysis, abundance-based coverage estimator (ACE), Chao1, Shannon, Simpson, and phylogenetic diversity indices were calculated.…”

“…The following were the cutoff values for other reference sequences: (x = similarity), genus (97% > x ≥ 94.5%), family (94.5% > x ≥ 86.5%), order (86.5% > x ≥ 82%), class (82% > x ≥ 78.5%), and phylum (78.5% > x ≥ 75%) 55 . The bacterial diversities were analyzed and compared using CL community™ v3.43 (ChunLab, Seoul, South Korea) 47,56 . Rarefaction curves, alpha diversity analysis, abundance-based coverage estimator (ACE), Chao1, Shannon, Simpson, and phylogenetic diversity indices were calculated.…”