ImageGP is an extensively utilized, open‐access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, ImageGP 2 (available at https://www.bic.ac.cn/BIC), introduces a redesigned interface leveraging cutting‐edge web technologies to enhance functionality and user interaction. Key enhancements include the following: (i) Addition of modules for data format transformation, facilitating operations such as matrix merging, subsetting, and transformation between long and wide formats. (ii) Streamlined workflows with features like preparameter selection data validation and grouping of parameters with similar attributes. (iii) Expanded repertoire of visualization functions and analysis tools, including Weighted Gene Co‐Expression Network Analysis, differential gene expression analysis, and FASTA sequence processing. (iv) Personalized user space for uploading large data sets, tracking analysis history, and sharing reproducible analysis data, scripts, and results. (v) Enhanced user support through a simplified error debugging feature accessible with a single click. (vi) Introduction of an R package, ImageGP, enabling local data visualization and analysis. These updates position ImageGP 2 as a versatile tool serving both wet‐lab and dry‐lab researchers with expanded capabilities.

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.

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.