Global food shortages and malnutrition necessitate innovative agricultural technologies to increase crop production and nutritional value while minimizing environmental impact. Traditional chemical fertilizers burden ecosystems, prompting a reconsideration of organic farming and resource recycling. Compost, a widely used soil conditioner, presents an opportunity, but its effects on crops remain uncertain due to variations in fermentation conditions and interactions with native soil microbiota. Previous research on thermophilic *Bacillaceae* in compost highlights their potential as plant growth-promoting bacteria (PGPB) with antifungal and denitrifying activities, demonstrating benefits in various animal and plant models. This study aims to comprehensively assess compost-soil-plant interactions using carrots as a model crop, employing multi-omics analysis and structural equation modeling to elucidate the mechanisms underlying compost's effects.

The introduction extensively cites literature highlighting global food security challenges, the environmental impacts of chemical fertilizers, the potential of organic farming, and the variable nature of compost quality. It reviews studies emphasizing the importance of amino acids in plant nutrition and the potential of *Bacillus* species as PGPB. Studies on the use of thermophilic *Bacillaceae*-fermented compost in improving the health and productivity of various animal and plant models are also presented, laying the groundwork for the current investigation.

The study employed a field experiment with two growing areas (1.8 m²/area) for carrots (Takii Seeds Phytorich Series, Kyo Kurenai). Carrots were grown and harvested twice, and various growth indices (stem and leaf weight, root weight, root diameter, root length, color, taste) were measured. Soil samples were collected, and metabolome and microbiome analyses were performed. Statistical analyses included correlation analyses, association analyses, structural equation modeling (SEM), causal mediation analysis (CMA), and BayesLINGAM. Compost-derived *Paenibacillus* strains were isolated, and their genomes were analyzed. *In vitro* soil models were used to assess nitrogen fixation and nitrous oxide generation. Appropriate statistical tests (Shapiro-Wilk, F test, Wilcoxon signed-rank test, X-squared test) were employed based on data distribution and variance. The data was processed and analyzed using R software, Prism software, and Microsoft Office.

Compost amendment significantly increased carrot yield and improved quality indices, including color and taste. Metabolome analysis revealed significant changes in leaf and root metabolites, particularly flavonoids and amino acids. Soil bacterial composition also shifted after compost application, with *Paenibacillus* showing an increasing trend. SEM analysis identified optimal models linking plant metabolites (amino acids, flavonoids, carotenoids) and antioxidant activity to compost exposure, and linking *Paenibacillus* and nitrogen compounds in the soil to compost. Isolated *Paenibacillus* strains from the compost possessed genes for nitrogen fixation, auxin production, phosphate solubilization, and siderophore reactions. *In vitro* tests confirmed the compost's capacity for nitrogen fixation and reduced nitrous oxide generation.

The findings address the research question by revealing the complex interactions between compost, soil microbiota, and plant metabolism. The SEM models provide a mechanistic understanding of how compost enhances carrot productivity and quality by influencing nitrogen metabolism, antioxidant activity, and nutrient uptake. The identification and characterization of compost-derived *Paenibacillus* strains with PGPB functions support the observed effects. The reduction in nitrous oxide generation highlights the compost's potential for mitigating greenhouse gas emissions. The results are relevant to the field by providing insights into sustainable organic farming practices and the development of effective, environmentally friendly biofertilizers.

This study provides a comprehensive understanding of the agroecological effects of thermophilic *Bacillaceae*-fermented compost. The integration of multi-omics data and SEM revealed a complex network of interactions influencing plant growth and soil health. The findings demonstrate the potential of this compost as a sustainable and efficient biofertilizer, promoting crop productivity while mitigating environmental impacts. Future research could explore the optimization of compost composition and application methods for various crops and soil types, investigate the long-term effects of compost on soil health, and further elucidate the mechanisms underlying the observed interactions.

The study focused on a single crop (carrots) and a specific type of compost. The generalizability of the findings to other crops and compost types should be investigated. While *Paenibacillus* strains were isolated and their genes analyzed, the specific roles of individual bacterial species and their interactions within the soil microbial community need further exploration. The *in vitro* experiments, while informative, may not fully capture the complexity of field conditions.