Microbial Assemblages Associated with the Soil-Root Continuum of an Endangered Plant, Helianthemum songaricum Schrenk

Abstract

The microbial network of the soil-root continuum plays a key role in plant growth. To date, limited information is available about the microbial assemblages in the rhizosphere and endosphere of endangered plants. We suspect that unknown microorganisms in roots and soil play an important role in the survival strategies of endangered plants. To address this research gap, we investigated the diversity and composition of the microbial communities of the soil-root continuum of the endangered shrub Helianthemum songaricum and observed that the microbial communities and structures of the rhizosphere and endosphere samples were distinguishable. The dominant rhizosphere bacteria were Actinobacteria (36.98%) and Acidobacteria (18.15%), whereas most endophytes were Alphaproteobacteria (23.17%) as well as Actinobacteria (29.94%). The relative abundance of rhizosphere bacteria was higher than that in endosphere samples. Fungal rhizosphere and endophyte samples had approximately equal abundances of the Sordariomycetes (23%), while the Pezizomycetes were more abundant in the soil (31.95%) than in the roots (5.70%). The phylogenetic relationships of the abundances of microbes in root and soil samples also showed that the most abundant bacterial and fungal reads tended to be dominant in either the soil or root samples but not both. Additionally, Pearson correlation heatmap analysis showed that the diversity and composition of soil bacteria and fungi were closely related to pH, total nitrogen, total phosphorus, and organic matter, of which pH and organic matter were the main drivers. These results clarify the different patterns of microbial communities of the soil-root continuum, in support of the better conservation and utilization of endangered desert plants in Inner Mongolia. IMPORTANCE Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment. Therefore, the profound study of the microbial diversity of rare desert plants can provide important data to support the protection and utilization of rare desert plants. Accordingly, in this study, high-throughput sequencing technology was applied to study the microbial diversity in plant roots and rhizosphere soils. We expect that research on the relationship between soil and root microbial diversity and the environment will improve the survival of endangered plants in this environment. In summary, this study is the first to study the microbial diversity and community structure of Helianthemum songaricum Schrenk and compare the diversity and composition of the root and soil microbiomes.

Keywords: Helianthemum songaricum; diversity; endangered plants; high-throughput sequencing; soil-root continuum microbial community.

FIG 1

Distributions of bacterial (A) and fungal (B) communities in each sample at the class level. The width of the bar for each phylum indicates the class relative abundance for that sample.

FIG 2

LDA effect size (LEfSe) of the bacterial (A) and fungal (B) communities with an LDA score of >4.0 (P < 0.05). Microbial lineages and plant compartment associations are displayed by cladogram phylogenetic distributions. Phylogenetic levels from phylum to species are represented by circles. Different-colored nodes represent microbial groups that are significantly enriched in the corresponding groups and have a significant influence on the differences between groups. The light-yellow nodes represent microbial groups that have no significant difference between groups or have no significant effect on the differences between groups.

FIG 3

LDA bar graphs indicating the communities of bacteria (A) and fungi (B) with an LDA score of >4.0.

FIG 4

Species correlation and cooccurrence network analyses at the class level between the Helianthemum songaricum Schrenk soil and root communities of bacteria (A and C) and fungi (B and D). The cooccurrence network diagram visually displays the cooccurrence relationships of species in different samples. The nodes in the network represent sample nodes or species nodes, and the lines between the sample nodes and species nodes represent the species contained in the samples. Species with an abundance (number of sequences) of >50 are displayed by default.

FIG 5

Phylogenetic relationships and genera of the top 50 most abundant bacterial (A) and fungal (B) taxa. The phylogenetic evolutionary tree is on the left. Each branch in the evolutionary tree represents a species. The branches are colored according to the advanced taxonomic level to which the species belongs. The bar chart on the right shows the proportion of reads of species in different groups.

FIG 6

Correlation heat map of the top 50 classes and soil properties of the communities of bacteria (A) and fungi (B). Environmental and class factors are represented by the x and y axes, respectively. The color range of different R values is shown in the right key. P values of <0.05 were considered significant and are indicated with an asterisk.

FIG 7

Locations of the research sites. (Left) Inner Mongolia map. (Right) Sampling site locations.