Understanding the sugar beet holobiont for sustainable agriculture.

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.

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

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-mediated pathogen tolerance. This can be translated into microbiome management strategies for plant and ecosystem health.

Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant.

10.1601/nm.2592 strain RM1-1-4 is a rhizosphere colonizer of oilseed rape. A previous study has shown that this motile, Gram-negative, non-sporulating bacterium is an effective stress protecting and biocontrol agent, which protects their hosts against abiotic and biotic stresses. Here, we announce and describe the complete genome sequence of P. corrugata RM1-1-4 consisting of a single 6.1 Mb circular chromosome that encodes 5189 protein coding genes and 85 RNA-only encoding genes. Genome analysis revealed genes predicting functions such as detoxifying mechanisms, stress inhibitors, exoproteases, lipoproteins or volatile components as well as rhizobactin siderophores and spermidine. Further analysis of its genome will help to identify traits promising for stress protection, biocontrol and plant growth promotion properties.

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima-ancestor of all beet crops-and modern sugar beets.

The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.

Assessing the effects of three potential chemical repellents to prevent bird damage to corn seeds and seedlings.

BACKGROUND: Bird damage to seeds and seedlings of maize (Zea mays) and other crops is widespread, especially in organic farming, because no adequate seed protection is available. In this study, the effect of seed treatments with three substances likely to affect bird feeding behaviour (anthraquinone, pulegone and methyl anthranilate) was tested. Their repellent effect was tested in food and seedling choice (treated versus untreated) experiments with feral pigeons (Columba livia f. domestica) in aviaries. Most efficient variants were additionally tested in the field, where wild birds had unlimited access. RESULTS: In aviaries, untreated seeds were clearly preferred over treated seeds by pigeons. The highest feeding deterrence effect occurred with the treatment variants pulegone 1.4 mL kg(-1) and methyl anthranilate 0.085 mL kg(-1). In contrast, there was no repellent effect if seedlings were offered to the pigeons in aviaries. The same applies to the number of maize seeds and seedlings grown from treated and untreated seeds, which were damaged in the field mainly by pheasants (Phasianus colchicus). CONCLUSION: The study shows that the chemicals failed to repel feeding by birds in Germany. Further studies should concentrate on alternative, systemic effective substances possibly based on plant secondary metabolites to yield a bird repellent usable in organic farming.

Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14, a Disease-Suppressive Bacterium.

The endophytic bacterium Pseudomonas poae RE*1-1-14 shows broad antagonistic activity and is applied to seeds as a biocontrol agent to suppress late root rot in the sugar beet. The completely sequenced 5.5-Mb genome reveals genes that putatively contribute to this antagonistic activity and the intimate plant-microbe interaction.

Strain-specific colonization pattern of Rhizoctonia antagonists in the root system of sugar beet.

To develop effective biocontrol strategies, basic knowledge of plant growth promotion (PGP) and root colonization by antagonists is essential. The survival and colonization patterns of five different biocontrol agents against Rhizoctonia solani AG2-2IIIB in the rhizosphere of greenhouse-grown sugar beet plants were analysed in single and combined treatments. The study included bacteria (Pseudomonas fluorescens L13-6-12, Pseudomonas trivialis RE(*) 1-1-14, Serratia plymuthica 3Re4-18) as well as fungi (Trichoderma gamsii AT1-2-4, Trichoderma velutinum G1/8). Microscopic analysis by confocal laser scanning microscopy revealed different colonization patterns for each DsRed2/green fluorescent protein-labelled strain. Bacteria and T. velutinum G1/8 colonized the root surface and the endorhiza in single and co-culture, while for T. gamsii AT1-2-4, only the transfer of spores was observed. Whereas Pseudomonas strains formed large microcolonies consisting of hundreds of cells, S. plymuthica was arranged in small endophytic clusters or clouds around the entire root system. In co-culture, each strain showed its typical pattern and occupied specific niches on the root, without clear evidence of morphological interactions. PGP was only observed for four strains with rhizosphere competence and not for T. gamsii AT1-2-4. The results provide useful information on which combination of strains to test in larger biocontrol experiments directed to applications.

Sugar beet-associated bacterial and fungal communities show a high indigenous antagonistic potential against plant pathogens.

The aim of this study was to analyze microbial communities in/on sugar beet with special focus on antagonists toward plant pathogens. For this purpose, the composition of microorganisms isolated from the rhizosphere, phyllosphere, endorhiza, and endosphere of field-grown sugar beet plants was analyzed by a multiphasic approach at three different plant development stages at six locations in Europe. The analysis of microbial communities by Single Strand Conformation Polymorphism (SSCP) of 16S/18S rRNA clearly revealed the existence of discrete microenvironment- and site-specific patterns. A total of 1952 bacterial and 1344 fungal isolates screened by dual testing for antagonism toward the pathogens Aphanomyces cochlioides, Phoma betae, Pythium ultimum, and Rhizoctonia solani resulted in 885 bacterial (=45%) and 437 fungal (=33%) antagonists. In general, the indigenous antagonistic potential was very high and influenced by (a) the location, (b) the plant developmental stage, and (3) the microenvironment. Furthermore, we showed for the first time that the antagonistic potential was highly specific for each target pathogen. The majority of antagonistic microorganisms suppressed only one pathogen (bacteria: 664 = 75%; fungi: 256 = 59%), whereas the minority showed a broad host range (bacteria: 4 = 0.5%; fungi: 7 = 1.6%). The bacterial communities harbored the highest antagonistic potential against P. ultimum, whereas the fungal communities contained more antagonists against A. cochlioides and R. solani. In contrast to their high proportion, only a low diversity of antagonists at genotypic and species level was found. Novel antagonistic species, e.g., Subtercola pratensis or Microbacterium testaceum were found in the internal part of the sugar beet body.