Carbon dots (CDs), as a class of carbon-based nanomaterials have been confirmed to have great potential in promoting crop growth, but its molecular mechanism remains largely unknown. In this study, novel soluble humic acid- derived CDs (HA-CDs) was developed and it could promote soybean growth and symbiotic nitrogen fixation (SNF) within a certain concentration range, which significantly lowered than the precursor. Further biochemical and molecular-level analyses revealed that this growth- and SNF-promoting effects of HA-CDs was mainly due to improving the photosynthesis, regulating C/N metabolism and antioxidant enzyme activity of host, and enhancing rhizobial growth and its symbiotic ability with soybeans that depended on the genes rsh and rpoZ. This study provided significant advance in our understanding of the molecular mechanism of HA-CDs on legume growth and nitrogen fixation, as well as the potential application value of HA-CDs in agriculture system.

Yogurt, a fermented dairy food, has been increasingly recognized for its potential to modulate gut microbiota and promote host health. Accumulating evidence suggests that yogurt consumption influences gut microbial composition, diversity, and functional activity. In this narrative review, we synthesized the findings on yogurt-related effects on the gut microbiota, intestinal barrier, microbial metabolites, immune responses, and selected extra-intestinal outcomes. We distinguished traditional yogurt, probiotic yogurt, synbiotic yogurt, fortified yogurt, and non-dairy or regional yogurt-like fermented products, and then organized proposed mechanisms into a hierarchical framework that separated direct yogurt-derived inputs, including starter cultures, added probiotic strains, fermentation-derived compounds, and dairy matrix components, from resident microbiota-mediated secondary metabolites and host downstream responses. Importantly, limitations and controversies, such as variability in yogurt formulations, strain-specific effects, and inter-individual responses, were critically evaluated. Finally, we highlighted future research directions that emphasize standardized study designs, defined endpoints, long-term randomized controlled trials, and integrative multi-omics approaches to support the development of personalized dietary strategies. Together, this review provides a structured framework for understanding the complex interactions between yogurt, gut microbiota, and host physiology, while outlining key steps needed to translate evidence into actionable nutritional recommendations.

Low light (LL) is a major constraint on the productivity of intercropped legumes and dense planting crops, and also affects the root-associated microbial communities. However, how LL reshapes the root-microbe interactions and whether the root microbiota can mitigate LL-induced damage in legumes remain unclear. Here, a meta-analysis based on field observations revealed that negative effects predominated (>70%) in intercropped and dense planting legume systems, with the light intensity emerging as the primary determinant of yield variation. Using soybean as a model, we found that LL suppressed photosynthesis, biomass accumulation and nodulation, and these effects were further aggravated in sterile soil. Furthermore, soil-transplantation experiments showed that soils conditioned by LL-grown plants reduced subsequent plant biomass. Compared to normal light (NL), LL shifted rhizosphere microbial assembly toward a more deterministic process, reducing bacterial diversity and simplifying bacterial co-occurrence networks, with Rhizobiales and Burkholderiales being the significantly reduced taxa. Metabolomic analysis identified sucrose and pipecolic acid as LL-responsive metabolites that were strongly correlated with these taxa. Chemotaxis and growth assays demonstrated that sucrose functions as both a carbon source and a chemoattractant, whereas pipecolic acid acts as a chemoattractant. Reintroduction of representative isolates or simplified SynCom alleviated LL-induced growth inhibition by enhancing photosynthetic performance, modulating redox status, and reprogramming host transcriptional responses. Together, our findings provide evidence of a belowground regulatory mechanism linking root exudates, rhizosphere microbiota, and plant performance under LL, and highlight the potential of microbiome-based strategies to improve crop production in low-light environments.

Triacylglycerol (TAG), a universal energy reserve and biodiesel feedstock, accumulates under stress in microalgae. However, the regulatory mechanisms linking stress signals to TAG synthesis remain unclear. In this study, we identified ApGRX1724, a novel glutaredoxin 1 family member found in Auxenochlorella protothecoides, that could translocate to the nucleus and interact with the transcription factor ApbZIP4896, which regulating TAG synthesis by interacting with the synthetase ApPAP6812. Additionally, ApbZIP4896 modulated the levels of reactive oxygen species (ROS) and influenced TAG polyunsaturation. This shifted the carbon metabolism of microalgae from lipid production to growth by interacting with ApMyb_rel4269 and ApbZIP0838, ultimately enhancing the resistance of microalgae to cadmium (Cd). This study revealed a novel signaling pathway involving ApGRX1724 and ApbZIP4896 that positively mediates resistance to Cd-induced ROS stress and promotes TAG accumulation, providing valuable insights into how microalgae resist Cd toxicity.

Natural biopolymer-degrading microbial communities drive carbon biogeochemical cycling. Within these communities, polymer degraders facilitate the growth of nondegraders by breaking down polymers through extracellular enzymes. However, the contributions of nondegraders to community dynamics, as well as the mechanisms that limit their access to degradation products, remain poorly understood. Here, we investigate EMSD5, a lignocellulose-degrading microbial community that efficiently converts corncob into isopropanol. We demonstrate that nondegraders, such as Escherichia coli, enable the growth of degraders (e.g., Lachnoclostridium sp. and Clostridium beijerinckii) by creating anaerobic conditions and supplying biotin. Within such expanded niches, lignocellulose degradation proceeds sequentially, and the availability of breakdown products to E. coli is constrained by two interlinked processes. Specifically, Lachnoclostridium sp. produces oligosaccharides that are largely inaccessible to E. coli. A subset of these oligosaccharides is utilized by C. beijerinckii to produce monosaccharides that support E. coli growth, while glycosidase secretion by C. beijerinckii is reduced under coculture conditions. Building on these findings, we designed a synthetic consortium by coculturing C. beijerinckii with an engineered E. coli strain that expresses xylanase genes from an unculturable Lachnoclostridium. This consortium achieved isopropanol production from hemicellulose without requiring anaerobic conditions. Our findings reveal the niche-expanding role of nondegraders and the processes that constrain their access to degradation products, offering insights into maintaining stable cooperation in biopolymer-degrading communities and designing efficient consortia for biopolymer conversion.

Enzyme immobilization technology holds significant value in biocatalysis. Carbohydrate-binding modules (CBMs), with their specific binding to natural polysaccharides, offer a highly promising immobilization method. In the present study, the binding ability with their natural substrates and heterologous expression levels of four CBMs using fluorescent protein tagging were studied, revealing that CBM2r presented the highest immobilization efficiency and expression level. Using the Design of Experiments (DOE), the immobilization conditions for mCherry-CBM2r were optimized, achieving a protein loading of 2.45 wt% on Avicel under optimal conditions: a solid-liquid ratio of 1:30, NaCl concentration of 108 mM, protein concentration of 6 mg/mL, and incubation time of 120 min. Subsequently, CBM2r gene was fused with chitosanase gene from Bacillus subtilis (BsCsn) and expressed in Escherichia coli for establishing a novel one-step immobilization of fusion enzymes mediated by CBM2r on microcrystalline cellulose. The immobilized CBM2r-BsCsn-Avicel was used for batch hydrolysis of high-concentration chitosan to produce chito-oligosaccharides, with the enzyme retaining 96 % substrate degradation efficiency over seven cycles and achieving a space-time yield of 232.8 kg/m3/h. This study provides a simple, cost-effective, environment friendly, and competitive biocatalytic immobilization strategy.

Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.

Microalgae are considered a promising candidate for cadmium biosorption material. However, the mechanisms behind their resistance to cadmium remain unclear. Here, we have uncovered that a lipid droplet (LD) protein caleosin of Auxenochlorella protothecoides regulates Cd tolerance in microalgae. The expression level of ApCaleosin significantly increases under Cd stress. ApCaleosin overexpression strain showed reduced sensitivity to cadmium, while the ApCaleosin knockdown resulted in increased sensitivity. Furthermore, ApCaleosin functions as a peroxygenase to alleviate oxidative stress through heteroexpression in Escherichia coli, which is a calcium-dependent process. Additionally, by supplementing ApCaleosin in yeast knockout strains, we discovered that ApCaleosin can promote an increase in LD numbers, thereby wrapping more cadmium ions and reducing cellular cadmium toxicity. These findings reveal the specific mechanism of microalgae's resistance to cadmium, offering new prospects for enhancing bioremediation efficiency.

The extreme environmental conditions of a plateau seriously threaten human health. The relationship between gut microbiota and human health at high altitudes has been extensively investigated. However, no universal gut microbiota biomarkers have been identified in the plateau population, limiting research into gut microbiota and high-altitude adaptation. 668 16s rRNA samples were analyzed using meta-analysis to reduce batch effects and uncover microbiota biomarkers in the plateau population. Furthermore, the robustness of these biomarkers was validated. Mendelian randomization (MR) results indicated that Tibetan gut microbiota may mediate a reduced erythropoietic response. Functional analysis and qPCR revealed that butyrate may be a functional metabolite in high-altitude adaptation. A high-altitude rat model showed that butyrate reduced intestinal damage caused by high altitudes. According to cell experiments, butyrate may downregulate hypoxia-inducible factor-1α (HIF-1α) expression and blunt cellular responses to hypoxic stress. Our research found universally applicable biomarkers and investigated their potential roles in promoting human health at high altitudes.

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

Background As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. Results WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. Conclusion All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, S phingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

Efficient saccharification of lignocellulose to fermentable sugars is crucial for bioconversion, yet the process is often hindered by insufficient β-glucosidase, β-xylosidase, and α-L-arabinofuranosidase activities in enzyme cocktails from Trichoderma reesei. This study addresses this gap by identifying BX1, a multifunctional enzyme from the underexplored fungus Trichoderma harzianum EM0925, which demonstrates a triad of activities targeting hemicellulose-derived oligosaccharides preferentially. We used structural analysis, molecular docking, and mutation studies to elucidate the roles of specific residues (Asp389, Glu589, Gln185, Cys390, Tyr354, and Tyr526) in BX1's multifunctionality. The enzyme showed synergistic effects with cellulase and xylanase, leading to a 90.23% increase in fermentable sugar yields at 2% (w/v) solid substrate loads and a 22.14% improvement at 15% (w/v) loads when added to Celluclast 1.5L. These findings highlight BX1's potential to enhance lignocellulosic bioconversion efficiency and reduce associated costs, paving the way for more cost-effective saccharification processes and future enzyme engineering advancements.

Symbiotic nitrogen fixation (SNF) is a crucial process for nitrogen geochemical cycling and plant-microbe interactions. Water-soluble humic acid (WSHM), an active component of soil humus, has been shown to promote SNF in the legume-rhizobial symbiosis, but its molecular mechanism remains largely unknown. To reveal the SNF-promoting mechanism, we conducted transcriptomic analysis on soybean treated with WSHM. Our findings revealed that up- and downregulated differentially expressed genes (DEGs) were mainly involved in plant cell-wall/membrane formation and plant defence/immunity in the early stage, while the late stage was marked by the flavonoid synthesis and ethylene biosynthetic process. Further study on representative DEGs showed that WSHM could inhibit GmBAK1d-mediated immunity and BR signalling, thereby promoting rhizobial colonisation, infection, and nodulation, while not favoring pathogenic bacteria colonisation on the host plant. Additionally, we also found that the ethylene pathway is necessary for promoting the soybean nodulation by WSHM. This study not only provides a significant advance in our understanding of the molecular mechanism of WSHM in promoting SNF, but also provides evidence of the beneficial interactions among the biostimulator, host plant, and soil microbes, which have not been previously reported.

Xylanolytic enzymes, with both endo-xylanase and arabinoxylan arabinofuranohydrolase (AXH) activities, are attractive for the economically feasible conversion of recalcitrant arabinoxylan. However, their characterization and utilization of these enzymes in biotechnological applications have been limited. Here, we characterize a novel bifunctional enzyme, rAbf43A, cloned from a bacterial consortium that exhibits AXH and endo-xylanase activities. Hydrolytic pattern analyses revealed that the AXH activity belongs to AXHd3 because it attacked only the C(O)-3-linked arabinofuranosyl residues of double-substituted xylopyranosyl units of arabinoxylan and arabinoxylan-derived oligosaccharides, which are usually resistant to hydrolysis. The enzyme rAbf43A also liberated a series of xylo-oligosaccharides (XOSs) from beechwood xylan, xylohexaose and xylopentaose, indicating that rAbf43A exhibited endo-xylanase activity. Homology modelling based on AlphaFold2 and site-directed mutagenesis identified three non-catalytic residues (H161, A270 and L505) located in the substrate-binding pocket essential for its dual-functionality, while the mutation of A117 located in the -1 subsite to the proline residue only affected its endo-xylanase activity. Additionally, rAbf43A showed significant synergistic action with the bifunctional xylanase/feruloyl esterase rXyn10A/Fae1A from the same bacterial consortium on insoluble wheat arabinoxylan and de-starched wheat bran degradation. When rXyn10A/Fae1A was added to the rAbf43A pre-hydrolyzed reactions, the amount of released reducing sugars, xylose and ferulic acid increased by 9.43% and 25.16%, 189.37% and 93.54%, 31.39% and 32.30%, respectively, in comparison with the sum of hydrolysis products released by each enzyme alone. The unique characteristics of rAbf43A position it as a promising candidate not only for designing high-performance enzyme cocktails but also for investigating the structure-function relationship of GH43 multifunctional enzymes.

In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce β-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.

Antibiotics present in the natural environment would induce the generation of antibiotic-resistant bacteria (ARB), causing great environmental risks. The effects of antibiotic resistance genes (ARGs) and antibiotics on bacterial transport/deposition in porous media yet are unclear. By using E. coli without ARGs as antibiotic-susceptible bacteria (ASB) and their corresponding isogenic mutants with ARGs in plasmids as ARB, the effects of ARGs and antibiotics on bacterial transport in porous media were examined under different conditions (1-4 m/d flow rates and 5-100 mM NaCl solutions). The transport behaviors of ARB were comparable with those of ASB under antibiotic-free conditions, indicating that ARGs present within cells had negligible influence on bacterial transport in antibiotic-free solutions. Interestingly, antibiotics (5-1000 μg/L gentamicin) present in solutions increased the transport of both ARB and ASB with more significant enhancement for ASB. This changed bacterial transport induced by antibiotics held true in solution with humic acid, in river water and groundwater samples. Antibiotics enhanced the transport of ARB and ASB in porous media via different mechanisms (ARB: competition of deposition sites; ASB: enhanced motility and chemotaxis effects). Clearly, since ASB are likely to escape sites containing antibiotics, these locations are more likely to accumulate ARB and their environmental risks would increase.

As the third pole of the world and Asia's water tower, the Tibetan Plateau experiences daily release of pharmaceutical and personal care products (PPCPs) due to increasing human activity. This study aimed to explore the potential relationship between the concentration and composition of PPCPs and human activity, by assessing the occurrence of PPCPs in areas of typical human activity on the Qinghai-Tibet Plateau and evaluating their ecological risk. The results indicate that 28 out of 30 substances were detected in concentrations ranging from less than 1 ng/L to hundreds of ng/L, with the average concentration of most PPCPs in the Tibet Autonomous Region being higher than that in Qinghai Province. Among the detected substances, CAF, NOR, CTC, CIP, TCN, OTC, AZN, and DOX accounted for over 90% of the total concentration. The emission sources of PPCPs were identified by analyzing the correlation coefficients of soil and water samples, with excess PPCPs used by livestock breeding discharged directly into soil and then into surface water through leaching or runoff. By comparing the concentration and composition of PPCPs with those in other regions, this study found that CIP, ENR, LOM, NOR, CTC, DOX, OTC, and TCN were the most commonly used PPCPs in the Qinghai-Tibet Plateau. To assess the ecological risk of PPCPs, organisms at different trophic levels, including algae, crustaceans, fish, and insects, were selected. The prediction of the no effect concentration of each PPCP showed that NOR, CTC, TCN, CAF, and CBZ may have deleterious effects on water biota. This study can assist in identifying the emission characteristics of PPCPs from different types and intensities of human activities, as well as their occurrence and fate during the natural decay of aquatic systems.

Development of a whole-cell catalysis system for an efficient conversion of glutamate to 5-aminolevulinic acid.

Abstract The economical production of 5‐aminolevulinic acid (ALA) has recently received increasing attention for its extensive use in agriculture. In this study, a strain of Bacillus cereus PT1 could initially produce ALA at a titre of 251.72 mg/L by using a hydrolysate mixture of low‐cost cassava residue and fish waste. The integration of endogenous hemA encoding glutamyl‐tRNA reductase led to a 39.30% increase in ALA production. Moreover, improving cell permeability by deletion of the LytR‐CpsA‐Psr (LCP) family gene tagU led to a further increase of 59.73% in ALA production. Finally, the engineered strain B. cereus PT1‐hemA‐ΔtagU produced 2.62 g/L of ALA from the previously mentioned hydrolysate mixture in a 7‐L bioreactor. In a pot experiment, foliar spray of the ALA produced by B. cereus PT1‐hemA‐ΔtagU from the hydrolysates increased salt tolerance of cucumber by improving chlorophyll content and catalase activity, while decreasing malondialdehyde content. Overall, this study demonstrated an economic way to produce ALA using a microbial platform and evidenced the potential of ALA in agricultural application.