Piriformospora indica, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of P. indica to improve growth, yield, and disease resistance in wheat in the field. In the present study, P. indica successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with P. indica chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, P. indica colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the P. indica-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against Fusarium pseudograminearum (81.59 ± 1.32%), Bipolaris sorokiniana (82.19 ± 1.59%), and Rhizoctonia cerealis (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in P. indica-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following P. indica inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that P. indica colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, P. indica improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.

Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent organic pollutants composed of two or more fused benzene rings, posing serious threats to ecological environments and human health. Biodegradation is an efficient, economical, and sustainable approach for remediating PAHs pollution. In our previous work, we isolated and characterized a PAH-degrading bacterium, Burkholderia sp. FM-2. FM-2 demonstrated strong tolerance and efficient degradation capacity toward various PAHs, achieving 81.98% degradation of 2 mM phenanthrene within 3 days, and over 58% degradation of 2 mM fluorene, dibenzofuran, and dibenzothiophene under the same conditions. Through combined genomic and transcriptomic analyses, a putative PAH degradation gene cluster was identified in the FM-2 genome. Phylogenetic and domain architecture analyses were conducted on seven oxygenase genes within the cluster. Using AlphaFold 3, we predicted the three-dimensional structure of the downstream transport protein OmpW and proposed a potential transmembrane channel for PAHs uptake. To eliminate the phenanthrene degradation intermediate 1-hydroxy-2-naphthoic acid, a genetically engineered strain FM-2::nahG was constructed by heterologous expression of the salicylate hydroxylase gene (nahG). The modified strain completely abolished the accumulation of 1-hydroxy-2-naphthoic acid and achieved complete mineralization of phenanthrene. This study not only reveals the molecular basis of PAHs degradation in Burkholderia sp. FM-2 but also demonstrates the potential of metabolic engineering to enhance biodegradation ability, providing a promising microbial candidate for the bioremediation of PAH-polluted environments.

This study investigated the fluorene degradation ability and metabolic pathway of Burkholderia sp. FM-2. The FM-2 demonstrated a 72.16 % degradation rate of 300 mg/L fluorene over a period of three days. HPLC-MS analysis identified major metabolites including 9-fluorenol, 9-fluorenone, and phthalate. The impact of heavy metals on fluorene degradation was also assessed. FM-2 exhibited strong tolerance to heavy metals, with a minimum inhibitory concentration (MIC) of 1000 mg/L for Cd(II). The study found that the removal rate of 100 mg/L Cd(II) was 70.42 %, and it was observed that this concentration had a slightly enhancing effect on fluorene degradation. Proteomic analysis revealed that multicopper oxidases and proteins involved in metabolic pathways for instance glutathione metabolism, sulfur metabolism were up-regulated under Cd(II) stress, suggesting potential mechanisms for Cd(II) tolerance and co-metabolism. Moreover, the effect of biochar on FM-2 for the remediation of co-contamination with fluorene and Cd(II) was evaluated. After immobilizing FM-2 with modified biochar (BC-BW), the degradation efficiency of fluorene significantly increased from 72.58 % to 84.93 % and the removal efficiency of Cd(II) increased from 70.42 % to 84.50 %. In the contaminated soil remediation experiment, the removal rates of fluorene and Cd(II) by the immobilized bacteria were 72.59 % and 66.67 %, respectively. These findings demonstrate that modified biochar enhances the remediation efficiency of FM-2 in co-contaminated soils. This study provides theoretical support and practical guidance for the application of biochar-based immobilization techniques in microbial remediation of complex polluted environments.

Various surfactants have been applied for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated environments, but their roles in bioremediation remain controversial. This study focused on rhamnolipid (a typical surfactant) and Burkholderia sp. FM-2 (a high-efficiency phenanthrene-degrading bacterium), investigating its effects on phenanthrene solubilization and biodegradation by analyzing cell surface characteristics and gene expression differences. Results showed that low concentrations of rhamnolipid (20–120 mg/L) promoted phenanthrene degradation, while high concentration (400 mg/L) exerted an inhibitory effect. At 20–56 mg/L, rhamnolipid altered the bacterial surface morphology and functional groups, facilitated lipopolysaccharide release, enhanced cell surface hydrophobicity, and increased zeta potential. When the rhamnolipid concentration was 20 mg/L, the phenanthrene degradation rates of cytoplasmic enzymes, periplasmic enzymes, and extracellular enzymes produced by the bacterium reached over 98% after 15 days of enzyme system culture, demonstrating its role in promoting enzyme production and activity. Transcriptomic analysis revealed that 56 mg/L (1 CMC) rhamnolipid enhanced degradation through multi-pathway regulation of gene expression: upregulating the gene encoding protocatechuate 3,4-dioxygenase to strengthen benzene ring cleavage; increasing the expression of genes related to ABC transporters and protein transport to promote phenanthrene transmembrane transport; and activating genes involved in metabolic processes such as pyruvate metabolism and the tricarboxylic acid (TCA) cycle to enhance central carbon metabolic flux. This regulatory mode optimizes energy supply and redox balance, and indirectly improves phenanthrene bioavailability by modulating membrane structure and function.

In this study, Bacillus amyloliquefaciens SQ-2, previously isolated from a commercial watercress paste, was investigated for its potential in promoting rice growth in Pb/Al-contaminated acidic soil, especially when used in conjunction with corn straw biochar. Firstly, the physiological properties of rice were enhanced, with the activities of catalase and superoxide dismutase increasing by 162.5% and 162.9%, respectively. Additionally, the total phenolic and chlorophyll contents of rice increased by 17.6% and 83.7%, respectively. Secondly, the nutrient content of the rice rhizosphere soil was improved. In particular, nitrate nitrogen, available potassium, and sucrase were enhanced by 9.4%, 45.9%, and 466.8%, respectively. Moreover, SQ-2–biochar was demonstrated to have a notable capacity for removing Pb²⁺ and Al³⁺. The mineralization of Pb²⁺ and Al³⁺ was achieved through the use of SQ-2–biochar, as revealed by SEM-EDS, XRD, XPS, and FT-IR analyses, with the main precipitates being Pb₃(PO₄)₂ and AlPO₄. Functional groups such as C-O-C, C=O, N-H, P-O, and -O-H on the microbial surface were found to be involved in the biosorption process of Pb²⁺ and Al³⁺. In summary, SQ-2–biochar can effectively mineralize Pb²⁺ and Al³⁺, enhance the physiological properties of rice, and improve soil nutrients, thereby augmenting the antioxidant capacity, photosynthesis, and stress resistance of rice and ultimately promoting rice growth.

CRISPR-associated Cas9 endonuclease (CRISPR/Cas9) systems are widely used to introduce precise mutations, such as knocking in/out at targeted genomic sites. Herein, we successfully disrupted the transcription of multiple genes in Bacillus pumilus LG3145 using a series of unspecific guide RNAs (gRNAs) and UgRNA:Cas9 system-assisted cre-box editing. The bases used as gRNAs shared 30–70% similarity with a consensus sequence, a cis-acting element (cre-box) mediating carbon catabolite repression (CCR) of many genes in Bacillus. This triggers trans-crRNA:Cas9 complex wobble cleavage up/downstream of cre sites in the promoters of multiple genes (up to 7), as confirmed by Sanger sequencing and next-generation sequencing (NGS). LG3145 displayed an obvious CCR release phenotype, including numerous secondary metabolites released into the culture broth, ∼ 1.67 g/L white flocculent protein, pigment overflow causing orange-coloured broth (absorbance = 309 nm), polysaccharide capsules appearing outside cells, improved sugar tolerance, and a two-fold increase in cell density. We assessed the relationship between carbon catabolite pathways and phenotype changes caused by unspecific UgRNA-directed cre site wobble editing. We propose a novel strategy for editing consensus targets at operator sequences that mediates transcriptional regulation in bacteria.