Organic Fertilizer Application Mediates Tomato Defense Against Pseudomonas syringae pv. Tomato, Possibly by Reshaping the Soil Microbiome

Abstract

Bacterial speck caused by Pseudomonas syringae pv. tomato is a serious foliar disease on tomato. However, it is still unknown how organic fertilizers application mediates plant defense against foliar pathogens by altering the composition of the soil microbial community. We conducted a 2-cycle pot experiment involving chemical and organic fertilizers and tracked tomato foliar pathogen incidence. Using microbiome sequencing, we then compared the differences in bulk and rhizosphere microbial communities. The results showed that, compared with soils amended with chemical fertilizer, soils amended with organic fertilizer gradually and significantly presented a reduction in tomato foliar disease, and the bacterial richness and diversity significantly increased. Moreover, the bacterial and fungal compositions of the bulk soil and rhizosphere soil of the organic fertilizer and chemical fertilizer treatments were different from each other. More importantly, the abundance of some potentially beneficial bacteria, such as Luteolibacter, Glycomyces, Flavobacterium, and Flavihumibacter, increased in the organic fertilizer-amended soil, and these genera were significantly negatively correlated with the incidence of tomato foliar disease. These results suggest that organic fertilizers can alter the taxonomy of the soil microbiome and that some specific beneficial microbial communities may play an important role in reducing the infection of foliar pathogens by inducing plant resistance.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

“…Specifically, the present study revealed that substrate, rhizosphere, and fruit samples under an organic SCS have altered relative abundance of 20, 21, and 12 families (listed in Figure 2 e), respectively, with all of them members of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Importantly, the dysbiosis characterized by a remarkable change in the relative abundance of Enterobacteriaceae , Flavobacteriaceae , Hyphomicrobiaceae , Pseudomonadaceae Rhizobiaceae , Rhodobacteraceae , and Xanthomonadaceae in substrate, rhizosphere, and fruit samples from the organic production system has been documented by many other studies [ 19 , 69 , 96 , 98 , 99 , 100 ], suggesting that these bacterial families could represent a microbial target that could be used to improve tomato plant health, productivity, and quality.…”

“…Furthermore, we hypothesize that the dysbiosis observed in the organic SCS could be attributed to the organic source of nitrogen, phosphorus, and potassium used in the present study. Numerous studies have shown that the use of organic fertilizers increases the relative abundance of different bacterial groups in soil and soilless cultivation systems [ 19 , 100 , 141 , 142 , 143 , 144 ]. Additional studies are in progress to evaluate this hypothesis.…”

Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil

“…Bacteria, including species within the genera Arthrobacter and Bacillus , can solubilize phosphate or mitigate salinity stress ( Jiang et al, 2019 ; Tchakounté et al, 2020 ). The abundance of some potentially beneficial bacteria, such as Luteolibacter , Glycomyces , Flavobacterium , and Flavihumibacter , increases in organic fertilizer-amended soil ( Huang et al, 2022a ; Huang et al, 2022b ). The application of both types of biochar increases the nodule number by 52% under well-watered and drought conditions by improving the symbiotic performance of chickpeas with Mesorhizobium ciceri ( Egamberdieva et al, 2019 ).…”

“…Biochar can improve the performance of the rhizome of ginger and increase the activity of soil enzymes, thereby improving soil nutrient supply ( Jabborova et al, 2021b ). The effect of biochar on improving fruit quality is related to the improvement of acidic soil properties ( Wu et al, 2020 ; Huang et al, 2022a ; Huang et al, 2022b ). The impact of biochar on vegetable quality in weakly alkaline soil deserves attention.…”

Organic inputs with reduced chemical fertilizers improve yield, antioxidant components, and defense mechanisms in Tomato (var. Pusa Sheetal)

“…Treatment T3 resulted in the next best-fit for reducing the stress up to 4.0% and 3.2%, respectively, compared to the control. Thus, organic fertilizers significantly increase plant resistance, according to a study [36].…”