Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat

Abstract

Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

Introduction

Wheat (Triticum aestivum L.) is an important food crop that humans have been consuming for 5000 years¹. The quality and yield of wheat are affected by various factors². Dwarf bunt in wheat, which is caused by Tilletia controversa J.G. Kühn, spreads through seeds or soil³ and is a disease of quarantine significance in many countries⁴. This disease often harms winter wheat in areas covered by snow for long periods in winter. Wheat Dwarf bunt can lead to a reduction in wheat production, degrade flour quality and produce a rotten fish odour. Resistant varieties of wheat contribute considerably to controlling this disease⁵. The teliospores of T. controversa have strong resistance to stress and can survive for 10 years under favourable environments⁶.

Plant microbiota can help to maintain the health of plants and can provide important genetic variability, which is of strong significance for plant resistance to biotic and abiotic stress⁷. Plant entophytic bacteria are parasitic bacteria that are widely observed in the tissues of plants in nature⁸. These bacteria can exist in various parts of the plant, including the aboveground, belowground, and seed parts⁹, and they can promote plant growth by fixing nitrogen, producing plant hormones, and improving drought resistance^10,11,12; also, these bacteria can protect host plants from damage by inhibiting the growth of pathogenic bacteria^13,14,15. In a recent study on the response of wheat endophytes to stripe rust, it was observed that the abundance of endophytes in roots was higher than that in stems and leaves, and the abundances of endophytes in resistant and susceptible varieties was observed to vary considerably¹⁶.

Rhizosphere soil serves as a bridge between microbes and plant roots. This soil enables materials and energy to be exchanged between plants and microbes. The rhizosphere microbiota promotes plant growth and health by enhancing plant resistance to adverse conditions or improving plant nutrient absorption^17,18,19. The rhizosphere bacterial community in the soil can strongly reduce the morbidity and mortality in tobacco caused by mixed Fusarium-Alternaria disease²⁰. Thilagam and Hemalatha²¹ found that plant growth-promoting rhizobacterial (PGPR) actinobacterial isolates can effectively suppress chili anthracnose. At the same time, soil microbes can also increase the resistance of plants to some microbial stresses by enhancing plant drought resistance by intercepting hormones in plants²². The rhizosphere microbiota can also affect the nutritional status of plants. The symbiotic relationship between legumes and nitrogen-fixing rhizobia is a typical example of how soil microbiota helps plants absorb nitrogen²³. Some rhizosphere microbiota can promote iron and phosphorus absorption by plants through mineralization, dissolution, or the secretion of iron carriers^{19, 24}. Similarly, plants can also affect the structure and composition of the rhizosphere microbial community. Resistant and susceptible varieties exhibit differences between their rhizosphere microbial communities. In a study of the resistance and susceptibility of watermelon to Fusarium oxysporum f. sp. niveum, An et al.²⁵ observed that the populations of actinomycetes in the rhizosphere soil of resistant varieties are more abundant than those of susceptible varieties, but the fungal community exhibits the opposite property. Sun et al.^{http://drive5.com/uparse/), OTUs were clustered based on 97% similarity, and single sequences and chimaeras were removed during the clustering process. The RDP classifier (http://rdp.cme.msu.edu/) was utilized to classify and annotate each sequence. The Silva database (SSU123) was utilized to compare 16S rRNA sequences, and Unite (Release 6.0 http://unite.ut.ee/index.php) was utilized to compare the internal transcribed spacer region; the confidence threshold was 0.7. All raw paired-end Illumina sequence data have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive database (https://www.ncbi.nlm.nih.gov/sra) under BioProject no. PRJNA639912.}