Understanding the Impact of Cultivar, Seed Origin, and Substrate on Bacterial Diversity of the Sugar Beet Rhizosphere and Suppression of Soil-Borne Pathogens

Abstract

The rhizosphere microbiome is crucial for plant health, especially for preventing roots from being infected by soil-borne pathogens. Microbiota-mediated pathogen response in the soil-root interface may hold the key for microbiome-based control strategies of phytopathogens. We studied the pathosystem sugar beet-late sugar beet root rot caused by Rhizoctonia solani in an integrative design of combining in vitro and in vivo (greenhouse and field) trials. We used five different cultivars originating from two propagation sites (France, Italy) with different degrees of susceptibility towards R. solani (two susceptible, one moderately tolerant and two cultivars with partial resistance). Analyzing bacterial communities in seeds and roots grown under different conditions by 16S rRNA amplicon sequencing, we found site-, cultivar-, and microhabitat-specific amplicon sequences variants (ASV) as well as a seed core microbiome shared between all sugar beet cultivars (121 ASVs representing 80%-91% relative abundance). In general, cultivar-specific differences in the bacterial communities were more pronounced in seeds than in roots. Seeds of Rhizoctonia-tolerant cultivars contain a higher relative abundance of the genera Paenibacillus, Kosakonia, and Enterobacter, while Gaiellales, Rhizobiales, and Kosakonia were enhanced in responsive rhizospheres. These results indicate a correlation between bacterial seed endophytes and Rhizoctonia-tolerant cultivars. Root communities are mainly substrate-derived but also comprise taxa exclusively derived from seeds. Interestingly, the signature of Pseudomonas poae Re*1-1-14, a well-studied sugar-beet specific biocontrol agent, was frequently found and in higher relative abundances in Rhizoctonia-tolerant than in susceptible cultivars. For microbiome management, we introduced microbial inoculants (consortia) and microbiome transplants (vermicompost) in greenhouse and field trials; both can modulate the rhizosphere and mediate tolerance towards late sugar beet root rot. Both, seeds and soil, provide specific beneficial bacteria for rhizosphere assembly and microbiota

The treasure inside barley seeds: microbial diversity and plant beneficial bacteria

“…Although an influence of the soil on the establishment of the endophytic seed microbiome was reported before [ 70 ], it seems that the genotype represents higher impact on the seed microbiome. Previous studies reported similar results for the rice seed microbiome and the sugar beet seed microbiome showing that the genotype had a higher influence on the seed microbiome than the geographic location [ 71 , 72 ].…”

Microbiome Modulation—Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

“…Surprisingly, breeding was shown to cause similar, long-term microbiome shifts as well ( Pérez-Jaramillo et al, 2018 ). In the last centuries, plant breeding was directed to high yields and to resistance toward pathogens; high yield cultivars enriched plant growth promoting microorganisms ( Pérez-Jaramillo et al, 2018 ), while resistant cultivars enrich microorganisms antagonistic toward pathogens ( Adam et al, 2018 ; Mendes et al, 2019 ; Wolfgang et al, 2020 ). For example, Rhizoctonia -tolerant cultivars of sugar beet, mainly mediated by the Fort Collins Resistance (USDA), resulted in an enrichment of bioactive Pseudomonas strains in the rhizosphere.…”

“…For example, Rhizoctonia -tolerant cultivars of sugar beet, mainly mediated by the Fort Collins Resistance (USDA), resulted in an enrichment of bioactive Pseudomonas strains in the rhizosphere. Strains of Pseudomonas are also able to induce the same resistance under experimental settings ( Wolfgang et al, 2020 ). Only recently two independent studies have shown that microorganisms can shape their host phenotypes by evoking resistance traits that are undistinguishable from innate plant immunity: in sugar beets two members of the native endorhiza microbiota ( Chitinophaga and Flavobacterium) were shown to confer resistance to the host plant against Rhizoctonia solani ( Carrión et al, 2019 ) and in rice a seed-endophytic Sphingomonas melonis strain was shown to confer disease resistance against Burkholderia plantarii that causes seedling blight ( Matsumoto et al, 2021 ).…”

Red Beetroot’s NMR-Based Metabolomics: Phytochemical Profile Related to Development Time and Production Year

“…The observed beneficial effects of RBs are relatable to their phytochemical profile, that in turn depends on agronomic and pedoclimatic conditions [19][20][21][22]. Indeed, an high biochemical variability, related to cultivar specificity and geographical origin, has been shown in previous studies [23][24][25], but yet the variability of the RB chemical composition, induced by harvest time and seasonality, has not been deeply investigated. Therefore, the scarce knowledge of a defined metabolic profile of red beetroot could barely help the producer to address its use in terms of a top-quality food for health care.…”