Analysis of Microbial Diversity in Soil under Ginger Cultivation

Abstract

Ginger is a perennial monocotyledonous herb, which can be used as both a vegetable and a medicinal plant. However, it is susceptible to various plant pathogens. Microbial diversity in soil is related closely to the health and productivity of plant crops including ginger. In the current study, we compared microbial diversity from soil samples under ginger cultivation (disease incidence of >50% [relatively unhealthy sample] versus disease incidence of <10% [relatively healthy sample]). The bacterial and fungal taxa were analyzed by Illumina-based sequencing, with 16S and ITS identification, respectively. Both bacterial and fungal OTUs were significantly more in the healthy soil sample than the unhealthy sample. Moreover, the dominant bacterial and fungal genera were detected to be different in each sample. Rhodanobacter and Kaistobacter were the dominant bacterial genera in the healthy sample, while Rhodoplanes and Bradyrhizobium were the dominant genera in the unhealthy sample. For fungal analysis, Cladosporium, Cryptococcus, and Tetracladium were the dominant genera in the healthy sample, while Lecanicillium, Pochonia, and Rhodotorula were the dominant genera in the unhealthy sample. Collectively, the basic information of microbial diversity in ginger soil is helpful for elucidating the ginger-microbe interactions and potentially selecting suitable plant growth-promoting rhizobacteria and biocontrol agents for ginger production.

Abundance of Plant-Associated Gammaproteobacteria Correlates with Immunostimulatory Activity of Angelica sinensis

“…The advent of powerful sequencing tools has transformed the way we characterize plant-associated microbes. Microbial communities of both phyllosphere and rhizosphere have been characterized for various plants, including Arabidopsis [25,26], maize [27], basil [28], ginger [29], lettuce [30], and Korean ginseng [31]. These studies provided important new insights into plant–microbe interactions, which can be translated to agricultural applications, such as development of biocontrol agents and pathogen detection.…”

Comparative Analyses of Soil Bacterial Colonies of Two Types of Chinese Ginger after a Major Flood Disaster

“…In soil microbial sequencing, a bacterial genome’s 16S rRNA gene fragment is first amplified and sequenced, followed by studying the colony type and microorganism structure through bioinformatic analyses ( 3 , 5 , 7 , 8 ). Recently, with the development of research and technology, second-generation high-throughput sequencing (NGS) technology has emerged, which is a modification of the traditional Sanger sequencing ( 9 – 11 ).…”

“…The analysis is usually performed using 16S rRNA sequencing and bioinformatics. Based on the sequencing results, the microbial communities are classified by the degree of similarity into operational taxonomic units (OTUs) ( 3 , 7 , 12 ). Based on OTUs, researchers can perform various soil microbial characterizations, such as soil microbial analyses of localized homogeneous environmental species diversity (α-diversity analysis), principal-component analysis (PCA), and composition analyses of microbial communities ( 3 , 13 ).…”

“…Previous studies have comparatively analyzed the microbial communities of healthy and diseased ginger ( 3 , 7 ). Also, turmeric and ginger intercropping affects the proportion of dominant bacteria and increases the active ingredient contents in patchouli ( 14 ).…”

Landscape scale ecology of Tetracladium spp. fungal root endophytes

“…Furthermore they have been found associated with Equisetaceae [29,30] and Bryophytes [31][32][33][34]. Tetracladium has most frequently been described in metabarcoding studies of soil from disturbed agricultural and grassland habitats [35][36][37][38]. There are numerous reports of the genus from the Antarctic tundra [39][40][41][42] where they have also been found in unvegetated habitats including glaciers and bedrock [43][44][45].…”