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

Abstract

Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.

Features of bacterial and fungal communities in the rhizosphere of Gastrodia elata cultivated in greenhouse for early harvest

“…DNA was extracted from each collected sample using the GeneAll Exgene Soil DNA isolation kit (GeneAll, Seoul, South Korea), following the manufacturer’s instructions ( Dutta et al, 2022 ). The quality and quantity of the isolated DNA were analyzed using a BioTek, Epoch Spectrometer (Agilent Technologies, Santa Clara, California, United States) and 1% agarose gel electrophoresis.…”

“…Bacterial libraries were generated by amplifying the V3–V4 region of the 16S rRNA gene using the universal primers including 341F and 805R ( Dutta et al, 2022 ). Fungal libraries were produced by amplifying the ITS region using the forward primer ITS3-F and reverse primer ITS4-R ( White et al, 1990 ).…”

“…These primers appended with the nextera concensus and sequencing adaptor at the 5′ end ( Fadrosh et al, 2014 ). The PCR products were cleaned up and used for further amplification with primers containing Illumina dual indices and sequencing adapter ( Dutta et al, 2022 ). The PCR cycling conditions were a denaturation step at 95°C for 3 min; 25 cycles (1st PCR) and 8 cycles (2nd PCR) of 30 s denaturation at 95°C, 30 s annealing at 55°C, 30 s extension at 72°C; and a 5 min final extension at 72°C.…”

“…Sequenced data were analyzed using EzBioCloud, 1 a public pipeline that provides quality control, merging paired-end reads, sequence processing, taxonomic classification, and diversity analysis for operational taxonomic units (OTUs), operated by CJ Bioscience, Inc. (Seoul, South Korea), as described by Dutta et al (2022) . Taxonomic assignments were implemented by searching reference databases using the USEARCH program for the 16S rRNA of bacteria and the UNITE 2 database for the ITS2 of fungi.…”

Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae)

“…Additionally, Edaphobacter has shown associations with smut resistance in sugarcane [75]. In the context of plant endophytes, Edaphobacter was found to be more abundant in the roots than in the bulk soil and rhizosphere of cultivated Allium ulleungense [76]. Niastella is categorized within the Bacteroidota class, specifically in the Chitinophagaceae.…”