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The effects of companion planting on soil antibiotic resistance genes (ARGs) and associated microbial composition have remained largely unclear until now. In this study, we assessed the changes in the soil microbiome and ARGs frequencies for tomato growing soils that were companion planted with basil (TB) or cilantro (TC) using a metagenome approach. The abundance of the phytopathogen Ralstonia solanacearum was significantly lower in the TC or TB treatments compared to the tomato monoculture soils (TT). A significant enrichment of Pseudomonas and Aquabacterium and a depletion of Nocardioides and Streptomyces were observed in the TC treatment. Interestingly, both TC and TB companion planting reduced the absolute abundance and the number of subtypes of ARGs. The TC soil showed the lowest numbers of unique ARG subtypes, especially the ARGs resistant to vancomycin and rifamycin, as well as those associated with multidrug resistance. Furthermore, network analysis further revealed that Nocardioides and Streptomyces were potential hosts of ARGs, whereas Flavobacterium negatively correlated with mdtG, suggesting a suppressive effect in reducing ARGs. Together, our results suggest that the companion planting of tomatoes with basil or cilantro can reduce the risk of ARG accumulation, making it a feasible farming management tool to promote soil and plant health in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Trichoderma is a widely recognized plant-growth-promoting fungus that has been extensively utilized in various agricultural applications. However, research on the economic production of Trichoderma spores and their effects on tea cuttings must be further advanced. In this study, T. guizhouense NJAU 4742 (NJAU 4742) emerged as a growth-promoting strain for tea cuttings, and the spore-production conditions of NJAU 4742 attained through solid-state fermentation (SSF) using tea residues were optimized. In a pot experiment, nursery substrates containing different concentrations of NJAU 4742 spores were tested for their influence on tea cutting growth and the rhizosphere fungal community. The optimal conditions for spore yield were determined as a 7:3 (w/w) ratio of tea residue to rice bran, a material thickness of 3 cm, an inoculum concentration of 15% (v/w), and an incubation time of 4 days, resulting in a spore count of 1.8 × 109 CFU/g. Applying NJAU 4742 spore products significantly increased the biomass of tea cuttings and influenced the fungal community composition. Moreover, higher concentrations of NJAU 4742 spores yielded better growth performance, and applying nursery substrate with 1.0 × 107 CFU/mL spores was the most economically viable option. Notably, among the top ten fungal genera with the highest relative abundance, Trichoderma showed a positive correlation with the fresh weight of tea cuttings, while the others exhibited a negative correlation. Overall, utilizing tea residue for SSF to produce NJAU 4742 was a feasible approach, and the application of NJAU 4742 spores enhanced the growth of tea cuttings by increasing the relative abundance of Trichoderma. [ABSTRACT FROM AUTHOR]

The photosynthetic rate increases under high-N supply, resulting in a large CO2 transport conductance in mesophyll cells. It is less known that water movement is affected by nitrogen supply in leaves. This study investigated whether the expression of aquaporin and water transport were affected by low-N (0.7 mM) and high-N (7 mM) concentrations in the hydroponic culture of four rice varieties: (1) Shanyou 63 (SY63), a hybrid variant of the indica species; (2) Yangdao 6 (YD6), a variant of indica species; (3) Zhendao 11 (ZD11), a hybrid variant of japonica species; and (4) Jiuyou 418 (JY418), another hybrid of the japonica species. Both the photosynthetic and transpiration rate were increased by the high-N supply in the four varieties. The expressions of aquaporins, plasma membrane intrinsic proteins (PIPs), and tonoplast membrane intrinsic protein (TIP) were higher in high-N than low-N leaves, except in SY63. Leaf hydraulic conductance (Kleaf) was lower in high-N than low-N leaves in SY63, while Kleaf increased under high-N supply in the YD6 variant. Negative correlations were observed between the expression of aquaporin and the transpiration rate in different varieties. Moreover, there was a significant negative correlation between transpiration rate and intercellular air space. In conclusion, the change in expression of aquaporins could affect Kleaf and transpiration. A feedback effect of transpiration would regulate aquaporin expression. The present results imply a coordination of gas exchange with leaf hydraulic conductance. [ABSTRACT FROM AUTHOR]

Aquaporins (AQPs) are integral membrane proteins facilitating the transport of water and some small neutral molecules across cell membranes. In past years, much effort has been made to reveal the location of AQPs as well as their function in water transport, photosynthetic processes, and stress responses in higher plants. In the present review, we paid attention to the character of AQPs in determining carbon and nitrogen status. The role of AQPs during photosynthesis is characterized as its function in transporting water and CO2 across the membrane of chloroplast and thylakoid; recalculated results from published studies showed that over-expression of AQPs contributed to 25% and 50% increases in stomatal conductance (gs) and mesophyll conductance (gm), respectively. The nitrogen status in plants is regulated by AQPs through their effect on water flow as well as urea and NH4 + uptake, and the potential role of AQPs in alleviating ammonium toxicity is discussed. At the same time, root and/or shoot AQP expression is quite dependent on both N supply amounts and forms. Future research directions concerning the function of AQPs in regulating plant carbon and nitrogen status as well as C/N balance are also highlighted. [ABSTRACT FROM AUTHOR]

Light is perceived by photoreceptors in fungi and further integrated into the stress-activated MAPK HOG pathway, and thereby potentially activates the expression of genes for stress responses. This indicates that the precise control of light conditions can likely improve the conidial yield and stress resistance to guarantee the low cost and long shelf life of Trichoderma-based biocontrol agents and biofertilizers. In this study, effects of wavelengths and intensities of light on conidial yield and stress tolerance to osmotic, oxidative and pH stresses in Trichoderma guizhouense were investigated. We found that 2 μmol photons/(m2 × s) of blue light increased the conidial yield more than 1000 folds as compared to dark condition and simultaneously enhanced conidial stress resistance. The enhanced conidial stress resistance is probably due to the upregulated stress-related genes in blue light, which is under the control of the blue light receptor BLR1 and the MAP kinase HOG1. [ABSTRACT FROM AUTHOR]

Background: MicroRNA plays an important role in multifarious biological processes by regulating their corresponding target genes. However, the biological function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) remain poorly understood. Methods: In this study, combined with deep sequencing and bioinformatics analysis, milRNAs and their targets from Trichoderma guizhouence NJAU 4742 were isolated and identified under solid-state fermentation (SSF) by using rice straw as the sole carbon source at 28 °C and 37 °C, respectively. Results: A critical milRNA, TGA1_S04_31828 (Tr-milRNA1), was highly expressed under heat stress (37 °C) and adaptively regulated lignocellulase secretion. Overexpression of Tr-milRNA1 (OE-Tr-milRNA1) did not affect vegetative growth, but significantly increased lignocellulose utilization under heat stress. Based on the bioinformatics analysis and qPCR validation, a target of Tr-milRNA1 was identified as Trvip36, a lectin-type cargo receptor. The expression of Tr-milRNA1 and Trvip36 showed a divergent trend under SSF when the temperature was increased from 28 °C to 37 °C. In addition, the expression of Trvip36 was suppressed significantly in Tr-milRNA1 overexpression strain (OE-Tr-milRNA1). Compared with the wild type, deletion of Trvip36 (ΔTrvip36) significantly improved the secretion of lignocellulases by reducing the retention of lignocellulases in the ER under heat stress. Conclusions: Tr-milRNA1 from NJAU 4742 improved lignocellulose utilization under heat stress by regulating the expression of the corresponding target gene Trvip36. These findings might open avenues for exploring the mechanism of lignocellulase secretion in filamentous fungi. [ABSTRACT FROM AUTHOR]

Chemotaxis, the ability of motile bacteria to direct their movement in gradients of attractants and repellents, plays an important role during the rhizosphere colonization by rhizobacteria. The rhizosphere is a unique niche for plant–microbe interactions. Root exudates are highly complex mixtures of chemoeffectors composed of hundreds of different compounds. Chemotaxis towards root exudates initiates rhizobacteria recruitment and the establishment of bacteria–root interactions. Over the last years, important progress has been made in the identification of root exudate components that play key roles in the colonization process, as well as in the identification of the cognate chemoreceptors. In the first part of this review, we summarized the roles of representative chemoeffectors that induce chemotaxis in typical rhizobacteria and discussed the structure and function of rhizobacterial chemoreceptors. In the second part we reviewed findings on how rhizobacterial chemotaxis and other root–microbe interactions promote the establishment of beneficial rhizobacteria-plant interactions leading to plant growth promotion and protection of plant health. In the last part we identified the existing gaps in the knowledge and discussed future research efforts that are necessary to close them. [ABSTRACT FROM AUTHOR]

The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus' evolution was directed by the environment and HGT events. [ABSTRACT FROM AUTHOR]

Closing yield (YG) and nitrogen use efficiency (NUE) gaps amongst smallholder farmers are critical to ensuring food security and environmental sustainability. Here we report a comprehensive analysis of a data set derived from farm-surveys and previously published studies in a typical high N input area of China. Using scenario analysis, farmers from both sources were divided into four rice production levels to assess the YG and NUE of smallholder farmers. Farm surveys showed that rice yield and partial factor productivity of applied N (PFPN) averaged 8273 kg ha−1 and 23.1 kg kg−1 at regional-scale, with a potential increase of 21–43% and 33–52%, respectively. A wide variation in yield and PFPN across different types of farmer was observed. Optimized N management significantly narrowed YGs by 3.7% and PFPN gap by 63.5% on average based on the published literature. Multiple factors, including excessive N rates, small rice planting area (0.33 ha), the aging (51 years old) and low education level (6 years of education) of the major labor force, can partly explain causes of yield and NUE gaps. These findings provide farm-based evidence that centralized management, good agronomy plus advances in knowledge and technologies are essential for future agricultural development. [ABSTRACT FROM AUTHOR]