Alin Song

Background: Engineering root microbiomes holds great promise to enhance plant health. Enhanced plant resistance via breeding or genetic modification can promote recruiting beneficial microbes, but is challenging to achieve. Results: Here we showed that calcium (Ca) addition caused significant changes in tomato physiology, resulting in enhanced immunity towards the pathogen Ralstonia solanacearum along with increased levels of salicylic acid (SA), sugar content, and defense enzyme activities in roots. High Ca levels significantly altered the root microbiomes, enriching sixteen bacterial genera, including Dyella japonica , Rhodanobacter glycinis , Paenibacillus polymyxa , and Pseudomonas aeruginosa , with the mostly enriched genus showing a 16.5-fold increase in the relative abundance compared to no Ca addition. Associated with the enhancement of these bacterial genera, tomato wilt incidence was reduced from 80 to 0%. The growth of these four bacterial strains was promoted to varying extent by the addition of SA, sucrose, trehalose, and Ca in vitro. All the four bacterial strains had antagonistic ability against R. solanacearum . A synthetic microbial community (SynCom) of these four strains significantly inhibited R. solanacearum growth in whole root exudates treated with Ca, and the combination of SynCom and Ca addition resulted in nearly eradication of the tomato bacterial wilt. Conclusions: Our findings revealed an effective and simple method for enriching beneficial microbiomes to protect plants against pathogens. Our results also suggested that combination of immunity boosters and beneficial microbes offers a novel strategy to combat soil-borne diseases.

Soil health reflects the sustained capacity of soil to function as a vital living ecosystem, ensuring support for all forms of life. The evaluation of soil health relies heavily on physicochemical indicators. However, it remains unclear whether and how microbial traits are related to soil health in soil with long-term organic manure amendment. This study aims to examine how detrimental and beneficial microbial traits change with soil health based on physicochemical indicators. This research measures the effects of 9-year manure supplementation on soil health using multiomics techniques. We found that, compared to 100% chemical fertilizers, the soil health index increased by 5.2%, 19.3%, and 72.6% with 25%, 50%, and 100% organic fertilizer amendments, respectively. Correspondingly, the abundance of beneficial microorganisms, including Actinomadura, Actinoplanes, Aeromicrobium, Agromyces, Azospira, Cryobacterium, Dactylosporangium, Devosia, Hyphomicrobium, Kribbella, and Lentzea, increased progressively, while the abundance of the pathogenic fungus Fusarium decreased with the organic manure application rate. In addition, the application of organic manure significantly increased the concentrations of soil metabolites, such as sugars (raffinose, trehalose, maltose, and maltotriose) and lithocholic acid, which promoted plant growth and soil aggregation. Moreover, the abundances of pathogens and beneficial microorganisms and the concentrations of beneficial soil metabolites were significantly correlated with the soil health index based on physicochemical indicators. We conclude that organic fertilizer can enhance soil health by promoting the increase in beneficial microorganisms while suppressing detrimental microorganisms, which can serve as potential indicators for assessing soil health. In agricultural production, substituting 25–50% of chemical fertilizers with organic fertilizers significantly helps improve soil health and promotes crop growth.

There are many kinds of soil amendments that consist of different materials. The soil amendment is usually of benefit to plant health. However, the effects of the soil amendments on plant disease have rarely been compared and the involved mechanisms are largely unknown. In the present study, we investigated the influences of five contrasting soil amendments (i.e., potassium silicate (PS), calcium silicate (CS), biochar (BC), calcium silicate humic acid (SCHA), and bio-organic fertilizer (BOF)) on tomato bacterial wilt. In addition, we dissected the mechanism with high-throughput sequencing. The results showed that BC, SCHA, and BOF significantly reduced the incidence and delayed the disease, while BOF significantly reduced the incidence of bacterial wilt disease in the whole tomato growing period. In the early stage of the disease, BC, SCHA, and BOF significantly reduced the soil pH compared to CK. However, the contents of soil NH₄⁺-N and NO₃⁻-N were significantly increased. Some beneficial bacteria genera (Burkholderia, Mortierella, and Trichoderma) had a certain correlation with the incidence. Burkholderia and Mortierella were negatively associated with morbidity, but Trichoderma was positively associated with morbidity. Particularly, the Spearman correlation and the least partial squares path analysis indicated that Trichoderma was significantly positively correlated with the disease incidence, the soil physicochemical properties, and the numbers of soil pathogens (NSP) were significantly positively correlated with the number of root pathogens (NRP) and the physicochemical properties of plants were negatively correlated with the disease incidence. Moreover, BOF had better inhibitory effect on the occurrence of tomato bacterial wilt. Our results have implications for the better integrated management of tomato bacterial wilt.

The turnover of microbial biomass plays an important part in providing a significant source of carbon (C) to soil organic C. However, whether the decomposition of microbial necromass (non-living microbial biomass) in the soil varies at the individual taxa level remains largely unknown. To fill up these gaps, we compared the necromass decomposition of bacterial and archaeal taxa by separating live microbial biomass with ¹⁸O-stable isotope probing from dead microbial biomass in soil. Our results showed that most of the microbial necromass at the operational taxonomic unit level (88.51%), which mainly belong to Acidobacteria, Actinobacteria, Gemmatimonadetes, and Proteobacteria, decomposed significantly after 30 days. In addition, there were great variations in necromass decomposition within each phylum, such as the decomposition of operational taxonomic units in Proteobacteria that ranged from 51% (Beijerinckia) to 92% (Nitrosospira). More importantly, the necromass decomposition was not related to the chemical composition of the cell wall but might positively correlate with the guanine–cytosine content of DNA and negatively correlated with genome size. This study provided a new insight that the decomposition of microbial necromass in soil was divergent at the individual taxonomic level and could not be fully explained by previously proposed mechanisms.

Rice sheath blight, a fungal disease caused by Rhizoctonia solani, seriously threatens rice production. Some of the volatile organic compounds (VOCs) produced by microbes are inhibitory to the growth of the plant pathogen, and hence may have the potential as environmentally friendly antifungal substances. However, information on the inhibitory effect of VOCs released by rice rhizosphere bacteria on R. solani is scarce. In this study, bacteria from the rice rhizosphere capable of inhibiting the growth of R. solani via releasing VOCs were screened using a double Petri dish assay. Headspace solid phase microextraction and gas chromatography mass spectrometry (GC/MS) were used to identify and quantify the VOCs. The contributions of VOCs to the inhibition of the growth of R. solani were estimated by constructing a random forest model, and were verified using pure compounds. Nine strains (i.e., Pseudomonas sp. No. 3, Enterobacter sp. No. 26, Enterobacter sp. No. 34, Pseudomonas sp. No. 35, Ralstonia sp. No. 50, Bacillus sp. No. 62, Arthrobacter sp. No. 146, Brevibacillus sp. No. 2–18, and Paenisporosarcina sp. No. 2–60) showed various inhibition on R. solani growth via VOCs. The inhibitory effect ranged from 7.84% to 100%, with Ralstonia sp. No. 50 completely inhibiting the growth of R. solani. Five VOCs (i.e., benzoic acid ethyl ester, 3-methyl-butanoic acid, 2-ethyl-1-hexanol, 3-methyl-1-butanol, and 6-methyl-5-hepten-2-one) identified by random forest model were confirmed to be toxic to R. solani when applied as a pure chemical compound. In particular, benzoic acid ethyl ester, 3-methyl-butanoic acid, and 2-ethyl-1-hexanol were lethal to R. solani. In summary, the rice rhizosphere bacteria (Ralstonia sp. No. 50) and VOCs (benzoic acid ethyl ester, 3-methyl-butanoic acid, and 2-ethyl-1-hexanol) showed potential to be used as new resources for biological control of rice sheath blight.

Returning crop straw into soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for rice healthy growth. However, it remains elusive how straw return affects Si bioavailability, its uptake, and rice yield, owing to little knowledge about soil microbial communities responsible for straw degradation. Here, we investigated the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results showed that rice straw-return significantly increased soil bioavailable Si and rice yield to from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at the phylum level, Deltaproteobacteria and Holophagae at the class level were negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility via altering its transformation, resulting in the balance of various nutrient sources to drive biological silicon cycle in agroecosystem.

Bacterial community and soil enzymatic activity depend on soil and management conditions. Fertilization is an important approach to maintain and enhance enzyme activities and microbial community diversity. Although the effects of fertilizer application on soil microbial community and related parameters are explored, the effects on the soil microbiome associated with those of wheat plant organs, including those associated with roots and spikelets, are not well-known. Therefore, in this study, by using a sequencing approach, we assessed the effects of inorganic fertilizers, manure, and biochar on soil enzyme activities, bacterial community diversity and structure in the bulk soil, rhizosphere, roots, and spikelet of wheat (Triticumaestivum L.). For this, different treatment biochar (BC), manure (OM), low mineral fertilizer (HL), high mineral fertilizer (HF), and no fertilizer (FO) were used for the enzyme activities and bacterial community structure diversity tested. The result showed that organic amendment application increased total nitrogen, soil available phosphorus, and potassium compared to inorganic fertilizer and control, especially in the rhizosphere. Enzyme activities were generally higher in the rhizosphere than in the bulk soil and organic amendments increased activities of acid phosphatase (AcP), β-1,4-N-acetyl-glucosaminidase (NAG), and phenol oxydase (PhOx). Compared with soil and rhizosphere, bacterial diversity was lower in wheat roots and evenlower in the spikelet. From the bulk soil, rhizosphere to roots, the fertilization regimes maintained bacterial diversity, while organic amendment increased bacterial diversity in the spikelet. Fertilization regimes significantly influenced the relative abundances of 74 genera across 12 phyla in the four compartments. Interestingly, the relative abundance of Proteobacteria (Citrobacter, Pantoea, Pseudomonas, and unclassified Enterobacteriaceae) in the spikelet was decreased by increasing inorganic fertilizer and further by manure and biochar, whereas those of Actinobacteria (Microbacterium and an unclassified Microbacteriaceae) and Bacteroidetes (Hymenobacter and Chitinophagaceae) were increased. The results suggest that potential bacterial functions of both roots and above-ground parts of wheat would be changed by different organic amendment regimes (manure and biochar).