Root-knot nematode (Meloidogyne incognita) is a globally destructive plant-parasitic nematode that severely impedes the sustainable production of horticultural crops. Metabolic reprogramming in plant roots represents the host response to M. incognita infection that can also be exploited by the nematode to facilitate its parasitism. In this study, untargeted metabolomics was employed to analyze metabolic changes in cucumber roots following nematode inoculation, with the goal of identifying differentially accumulated metabolites that may influence M. incognita behavior. Metabolomic analysis revealed that M. incognita significantly altered the cucumber root metabolome, triggering an accumulation of lipids and organic acids and enriching biotic stress-related pathways such as alkaloid biosynthesis and linoleic acid metabolism. Among differentially accumulated metabolites, myristic acid and hexadecanal were selected for further study due to their potential roles in nematode inhibition. In vitro assays demonstrated that both metabolites suppressed egg hatching and reduced infectivity of M. incognita, while pot experiments indicated a correlation between their application and reduced root gall formation. Chemotaxis assays further revealed that both metabolites exerted repellent effects on the chemotactic migration of M. incognita J2 and suppressed the transcriptional expression of two motility-and feeding-related neuropeptides, Mi-flp-1 and Mi-flp-18. In conclusion, this study demonstrates the significant potential of differentially accumulated metabolites induced by M. incognita infection for nematode disease control, achieved by interfering with nematode chemotaxis and subsequent infection. This work also provides deeper insights into the metabolomic mechanisms underlying the cucumber-M. incognita interaction.

The microbial community plays a vital role in root–environment interactions, which affect plant performance under biotic stress. Rust disease significantly affects plant growth, which may also affect rhizosphere microbial community. However, there is a scarcity of studies investigating the microbial community of rhizosphere under rust disease stress. Iris lactea is a widely utilized plant in gardening and landscaping due to its versatility and ornamental value, but it is often susceptible to rust disease in landscape settings. In this study, we compared the bacterial communities between bulk soil (non-cultivated control), rhizosphere soil of healthy Iris lactea plants, and rhizosphere soil of Iris lactea plants infected with rust disease (rhizosphere-R). Results revealed significant alterations in the abundance and composition of bacterial communities associated with rust disease infection. Specifically, the rhizosphere-R samples exhibited a decreased Shannon index at 1.9% compared to bulk soil and the relative abundance of Proteobacteria was increased at 31.65%. Moreover, distinct changes in β-diversity were shown between bulk soil and rhizosphere samples. Notably, potentially pathogenic bacteria increased in abundance under rust disease stress, while beneficial bacterial taxa decreased. Overall, our results show that rust disease affects the rhizosphere microbial community, which emphasizes the ecological implications of plant–microbe interactions under biotic stress and implications for developing targeted rhizobacterial-based biocontrol strategies.

Root-knot nematodes induce the formation of feeding sites within the host roots and the relocation of auxin into galls results in abnormal lateral root growth. Here, we analyzed the changes in cucumber root architecture under Meloidogyne incognita stress and the distribution of auxin in these morphological and molecular root changes. The number of root tips significantly decreased, and regression analysis showed a positive relationship between the size of root galls and the numbers of nematodes in galls compared with the lateral roots on galls, emphasizing the effect of nematode parasitism on root development. Data generated via a promoter-reporter system using the transgenic hairy root system first characterized the auxin distribution during nematode parasitism in cucumber. Using DR5:GUS staining of root galls, we further detected the expression of CsPIN1 and CsAUX1, which regulate polar auxin transport. The results showed that both CsPIN1 and CsAUX1 were induced in galls, and the relative expression of the two genes significantly increased at 21 DAI. The TIBA treatment, which can disrupt polar auxin transport inhibited the numbers of cucumber root tips and total length following increasing concentration gradients. Moreover, the numbers of galls were significantly affected by TIBA treatment, which showed the vital role of auxin during nematode parasitism. Our findings suggest that the transportation of auxin plays an important role during gall formation and induces cucumber lateral root development within nematode feeding sites.

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable and eco-friendly strategy to enhance crop productivity and support integrated agricultural systems. Among these, members of the genus Bacillus are highly valued for their resilience and multifaceted beneficial traits. The growth-promoting effects of Bacillus sp. L11 on S. lycopersicum seedlings were investigated in soil and artificial peat-based substrates. Rhizosphere microbial diversity was subsequently analyzed to investigate the interaction between L11 and the indigenous microbiota. We evaluated plant growth parameters, root growth parameters, and rhizosphere bacterial community dynamics using 16S rRNA high-throughput sequencing. Overall, L11 inoculation was associated with significantly improved growth indices of S. lycopersicum seedlings in both cultivation systems. Notably, the phosphate-buffered saline (PBS)-resuspended L11 markedly increased shoot fresh weight and plant height, and enhanced root-associated parameters such as total root length and root surface area. While L11 did not significantly alter alpha diversity, principal coordinates analysis (PCoA) revealed that its presence was associated with substantial restructuring of the rhizosphere bacterial community. Inoculation specifically enriched beneficial genera, including Chitinophaga, Devosia, and Pseudomonas. Correlation analyses showed that these microbial shifts were positively associated with the enhancement of seedling biomass and development. In conclusion, these findings suggest that Bacillus sp. L11 may promote S. lycopersicum growth through direct stimulation and by reshaping the rhizosphere microbiome, positioning it as a promising microbial inoculant for sustainable vegetable production.

Lignin is an abundant and renewable aromatic polymer, but its structural heterogeneity hinders its efficient bioconversion. Unlike previous reviews that focused on isolated topics such as single enzymes, pathway engineering, or specific bioproducts, this paper comprehensively reviews the latest advances in the structural characteristics, microbial degradation mechanisms, and bioconversion of lignin. Particular emphasis is placed on the catalytic mechanisms of key lignin-degrading enzymes, including laccase, lignin peroxidase (LiP), and manganese peroxidase (MnP), as well as the applications of fungi, bacteria, and synthetic microbial consortia in lignin bioconversion. Metabolic pathways that channel heterogeneous lignin-derived aromatics into central carbon metabolism through sequential catalytic reactions are also covered. Furthermore, we evaluate the emerging applications of artificial intelligence and machine learning in enzyme design and bioprocess control. Finally, techno-economic and life-cycle considerations are integrated to guide large-scale deployment. This review provides in-depth insights into the cross-scale translation from laboratory biocatalysis to industrial biorefineries.