Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

Adaptation of rhizosphere bacterial communities of drought-resistant sugarcane varieties under different degrees of drought stress

Sugarcane is highly sensitive to changes in moisture, and increased drought severely restricts its growth and productivity. Recent studies have shown that plant growth-promoting microorganisms are essential to reduce the adverse effects of environmental stresses, especially drought. However, our knowledge about the dynamics of rhizosphere microbial community structure in sugarcane under varying degrees of drought stress is limited. We analyzed the effects of different degrees of drought stress on the rhizosphere microbial communities of Zhongzhe 1(ZZ1) and Zhongzhe 6(ZZ6) with differences in drought resistance, by combining soil enzyme activity, nutrient content, and physiological and morphological characteristics of sugarcane roots. The results showed that rhizosphere bacterial community began to change at a field capacity of 50%, enriching the sugarcane rhizosphere with drought-resistant bacteria. The core strains of ZZ1 and ZZ6 rhizosphere enrichment were mainly Streptomycetales, Sphingomonadales, and Rhizobiales. However, compared to ZZ1, the changes in rhizosphere bacterial abundance in ZZ6 were primarily associated with the abundance of Streptomycetales as drought levels increased. Rhizobiales and Streptomycetales, enriched in the rhizosphere of ZZ6 under drought, were positively correlated with root tip number and total root length (TRL), increasing the distribution area of roots and, thus, improving water and nutrient uptake by the roots thereby enhancing the resistance of sugarcane to drought stress. This research enhances our understanding of the composition of the rhizosphere microbial community in sugarcane under different levels of drought stress and its interaction with the roots, thereby providing valuable insights for enhancing drought resistance in sugarcane. IMPORTANCE Drought stress is expected to further increase in intensity, frequency, and duration, causing substantial losses in sugarcane yields. Here, we exposed sugarcane to varying degrees of drought treatment during growth and quantified the eventual composition of the resulting sugarcane rhizosphere bacterial community groups. We found that sugarcane rhizosphere under mild drought began to recruit specific bacterial communities to resist drought stress and used the interactions of root tip number, total root length, and drought-resistant strains to improve sugarcane survival under drought. This research provides a theoretical basis for the rhizosphere microbiome to help sugarcane improve its resistance under different levels of drought stress.

Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil

Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea, A. tertiaricarbonis, and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.

Root phenotypes as modulators of microbial microhabitats

Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.