Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease

Abstract

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane–peanut intercropping systems

“…A NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA) and 2% agarose gel electrophoresis were used to assess the quantity and quality of DNA. The primer pairs 515F/907R (5′-GTGCCAGCMGCCGCGG-3′/5′-CCGTCAATTCMTTTRAGTTT-3′) (Xu et al, 2021b ) and ITS 1F/ITS 2R (5′-CTTGGTCATTTAGAGGAAGTAA-3′/5′-GCTGCGTTCTTCATCGATGC-3′) (Zhou et al, 2023 ) were used to amplify the bacterial 16S rRNA gene and fungal ITS gene, respectively. Polymerase chain reaction (PCR) was performed in a thermal cycler (ABI GeneAmp 9700) with a volume of 20 μl containing 4 μl of FastPfu Buffer (5 × ), 0.2 μl of BSA, 0.8 μl of forward primer (5 μM), 0.8 μl of reverse primer (5 μM), 2 μl of dNTPs (2.5 mM), 10 ng of DNA template, 0.4 μl of FastPfu Polymerase, and 11.8 μl of ddH 2 O.…”

“…Microbial beta diversity was conducted by the non-metric multidimensional scaling (NMDS) analysis based on the Bray–Curtis dissimilarity matrix using the “vegan” package and the first component (NMDS1) was used for the latter analysis (Bahram et al, 2018 ; Domeignoz-Horta et al, 2020 ). An analysis of similarities (ANOSIM) was used to evaluate the significant differences in soils (rhizosphere and bulk soil) and cropping systems (monoculture and intercropping) presented in NMDS (Ju et al, 2023 ; Zhou et al, 2023 ). The abundant and rare taxa were grouped by the relative abundance approach with the threshold of 1% at the phylum level, which was widely discussed in previous studies (Xu et al, 2021a ; Zhang G. Z. et al, 2022 ; Liu et al, 2023 ; Wang et al, 2024 ).…”

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community

“…Endophytes isolated from the plant tissues enhance the plant's ability to resist invasion by pathogens [ 27 , 28 ]. The utilization of these beneficial bacteria to construct SynComs is a promising strategy against soilborne pathogens and plant diseases, which can aid in promoting plant health [ 29 ]. Given this, this study explored cotton seed endophytes with a particular focus on their potential in combating V. dahliae by constructing synthetic seed endophytic microbial communities to address the defense against cotton Verticillium wilt in future cotton production.…”

Differential Responses of Bacterial Communities in Rhizosphere and Bulk Soils of Cotton to Long-Term Amelioration Practices Based on Freezing Saline Water Irrigation and Plastic Mulching in a Coastal Saline Soil

“…Amplification sequencing is the most widely used method for quickly revealing the composition of microbiota [47]. The development of high-throughput sequencing has given us a better understanding of the responses of soil microbiome to different crop planting patterns [48], fertilizer applications [49], tillage practices [50] and crop types [51] in agroecosystems. In addition, these factors provided us with an in-depth understanding of the coastal saline soil microorganisms under different conditions.…”