Understanding the sugar beet holobiont for sustainable agriculture

Abstract

The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.

Keywords: Beta vulgaris; Rhizoctonia; biocontrol; biofertilization; microbiome; phylosymbiosis; soil-borne pathogens.

Figure 1

Simplified temporal (Left) and spatial (Right) holobiont model of sugar beet taproot. The arrow width indicates the relative importance of vertically and horizontally assembled endophytes (Top Left). A: Root exudation and/or endophyte release leads to an increase in measured diversity in taproot-associated rhizosphere communities (Zachow et al., ; Cardinale et al., ; Wolfgang et al., 2020). CFU number in the peel can exceed the CFU number in the rhizosphere (Okazaki et al., 2014). B: Relative sugar content increases toward the center, higher in proximity to vascular bundles. Sucrose further decreases with increasing distance to the secondary cambia (Milford, ; Hoffmann and Kenter, 2018). C: Diversity decreases toward the center, while the relative abundance of copiotrophic bacteria increases (Lilley et al., ; Okazaki et al., 2014). D: Microbial abundance is highest in the root elongation zone near the root tip, with a high relative abundance of exudate responders, e.g., Variovorax and Pseudomonas (Jacobs et al., ; Lübeck et al., ; Shi et al., 2009a). E: The sugar content of beet tissue is highest in lower taproot (Milford, 2006).

Figure 2

Microbiome-based defense mechanism toward Rhizoctonia solani in sugar beet. *Root exudate-mediated enrichment of rhizosphere-associated microbes. ⁺The deposition of initial seed endophytes from taproot toward the rhizosphere is not proven in sugar beet so far.

Figure 3

Summary of microbiome-based targets to increase sugar beet farming sustainability. BCA, Biological control agents; PGP, plant growth promoter; SPA, stress protecting agents. For a description see Section 3.3.