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

Abstract

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

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

“…Other studies have shown that host selection pressure increased sequentially from soils to epiphytes to endophytes, reducing bacterial diversity and network complexity ( 62 ), resulting in differentiation of the structure and function of microbial communities between the endospheric layer and rhizospheric soil. Other studies have documented the hierarchical enrichment of the bacterial community from the rhizosphere to the rhizoplane to the endosphere in soybean ( 63 ). In addition, it has been reported that some PGPR epiphytes tend to form biofilms within an extracellular matrix, the roots provide a favorable attachment environment, and root-secreted organic acids can recruit beneficial soil bacteria ( 64 ), which may contribute to the augmented effects of these PGPR in the endospheric layer of soybean.…”

Root phenotypes as modulators of microbial microhabitats

“…In this scenario, it is possible that smaller pores act as isolated habitat patches, which can influence competitive interactions and strengthen patterns of coexistence among microbial taxa (Lowery and Ursell, 2019). This is corroborated by the fact that finer roots have been shown to contain more diverse microbial communities when compared to higher-order roots (Saleem et al, 2016;Pervaiz et al, 2020;King et al, 2021;Luo et al, 2021). Moreover, some microbial taxa have also been shown be more abundant in specific root orders (Wang et al, 2017), possibly due to their ability to compete in distinct habitat patch sizes with characteristic biotic and abiotic conditions.…”

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

“…However, ZZ6 displayed a more pronounced response to drought compared to ZZ1, which aligns with previous findings ( 23 ). The interaction between the Chao1 index of ZZ6 and root traits under drought stress highlights the influence of environmental changes and host plants on rhizosphere bacteria ( 47 , 48 ). Prolonged drought conditions cause changes in the rhizosphere-associated bacterial community structure in combinations selected to adapt to abiotic stresses, improve plant root phenotypes, and thereby increase stress resistance to promote plant health and drought tolerance ( 47 , 49 ).…”

“…Prolonged drought conditions cause changes in the rhizosphere-associated bacterial community structure in combinations selected to adapt to abiotic stresses, improve plant root phenotypes, and thereby increase stress resistance to promote plant health and drought tolerance ( 47 , 49 ). Additionally, soil properties can impact root traits by influencing nutrient and water availability, leading to variations in bacterial communities associated with the root system ( 48 ). β-Diversity analysis revealed distinct rhizosphere bacterial community compositions for ZZ1 and ZZ6 under different drought levels.…”

“…The Mantel tests showed that ZZ6 was more closely related to environmental factors than ZZ1, particularly root area, root diameter, and soil urease. This suggests that changes in the root system and rhizosphere soil environment impact bacterial community diversity ( 48 , 51 ). Plant roots obtain more water and nutrients under drought conditions by changing root phenotypes, such as root area and root diameter, to increase plant survival, whereas microorganisms favor root water and nutrients, and the root system provides a carbon source for growth ( 52 – 54 ).…”