Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from coastal saline-alkali soil in the Yellow River Delta was identified as Glutamicibacter endophyticus J2-5-19. The strain was capable of growing in media with up to 13% NaCl and producing proteases, siderophores, and the plant hormone IAA. Under 4‰ salt stress, inoculation with strain J2-5-19 significantly increased the wheat seed germination rate from 37.5% to 95%, enhanced the dry weight of maize seedlings by 41.92%, and notably improved the development of maize root systems. Moreover, this work presented the first whole-genome of Glutamicibacter endophyticus, revealing that G. endophyticus J2-5-19 resisted salt stress by expelling sodium ions and taking up potassium ions through Na⁺/H⁺ antiporters and potassium uptake proteins, while also accumulating compatible solutes such as betaine, proline, and trehalose. Additionally, the genome contained multiple key plant growth-promoting genes, including those involved in IAA biosynthesis, siderophore production, and GABA synthesis. The findings provide a theoretical foundation and microbial resources for the development of specialized microbial inoculants for saline-alkali soils.

Synthetic microbial communities (SynComs) have been shown to be an ecofriendly alternative for promoting plant growth. However, the mechanisms by which SynCom inoculants drive plant growth promotion in rhizosphere soil are still not fully explored. Herein, we designed a three-strain consortium based on the biocompatibility among strains and indole-3-acetic acid (IAA) production. The consortium containing Bacillus safensis 5-49, Bacillus stratosphericus 5-54, and Bacillus halotolerans 6-30 possessed a synergistic effect on IAA production and biofilm formation. Genetic analysis suggested that IAA was synthesized through tryptophan-dependent pathways in the strains. The consortium outperformed the plant growth-promoting effect observed with single strains, showing an increase in walnut (Juglans regia) seedling dry weight by 92.3% over the non-inoculated plants after 60 days of cultivation. This effect was underpinned by the synergistic interactions of the consortium, which was evidenced by the significantly increased relative abundance of Bacillus and tryptophan metabolism-associated genes in the rhizosphere of consortium-inoculated plants. Meanwhile, the consortium increased the relative abundance of indigenous Pseudomonas in rhizosphere soil, providing a synergistic effect on improving soil enzyme activities and thus available nutrients. The available N, P, and K contents in the consortium-inoculated plant rhizosphere were 3.77–28.4% higher than those in non-inoculated samples. This work provided an efficient bacterial consortium and proposed the mode of action by which this consortium improved plant growth and soil fertility.

Calcareous soils are typically deficient in essential nutrients such as iron, phosphorus, and potassium, which frequently results in nutrient deficiency in fruit trees. Bacillus licheniformis LCDD6 markedly enhanced Malus hupehensis seedling growth and plant iron nutrition in calcareous soil. This study aimed to elucidate the mechanism underlying these beneficial effects of strain LCDD6 under iron deficiency. Transcriptomic analysis revealed that iron deficiency induced metabolic reprogramming in strain LCDD6, characterized by a significant upregulation of genes involved in the biosynthesis of the siderophore bacillibactin and plant growth hormone indoleacetic acid (IAA). Consistently, metabolomic profiling identified bacillibactin and IAA as the dominant metabolites produced under iron-deficient conditions. A 60-day pot experiment further demonstrated that the cell-free fermentation broth of strain LCDD6 significantly enhanced plant growth and rhizosphere soil enzyme activities. The crude bacillibactin extract derived from the fermentation exerted the strongest effects on plant growth and iron accumulation, whereas IAA preferentially stimulated root development and promoted plant phosphorus accumulation. Additionally, different metabolites exerted distinct and selective effects on the rhizosphere microbial community, with fungi showing stronger and more metabolite-specific responses than bacteria. The crude bacillibactin extract enriched fungal taxa, particularly Coprinellus, which showed strong positive correlations with plant growth traits and iron accumulation, while Stachybotrys, enriched under IAA treatment, was positively correlated with plant phosphorus content. Overall, strain LCDD6 promotes plant growth under iron-deficient conditions through the coordinated action of multiple metabolites, with bacillibactin as the primary contributor and IAA providing complementary effects. These findings offer mechanistic insight and a scientific basis for developing Bacillus-based biofertilizers to improve nutrient acquisition in calcareous soils.

Bacteria play an important role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs), especially the more recalcitrant high-molecular-weight compounds like pyrene. In this study, we isolated and characterized a novel pyrene-degrading bacterium, Glutamicibacter soli ENR6, from petroleum-contaminated soil. Strain ENR6 was able to utilize various PAHs as sole carbon sources and degrade 88.8% of 50 mg L ⁻¹ pyrene and 76.8% of 100 mg L ⁻¹ pyrene within 15 days. During pyrene degradation, eight metabolites were detected, with 2,2′-diphenic acid emerging as the predominant intermediate. By day 7, 40.6% of the degraded pyrene had accumulated in the form of 2,2′-diphenic acid, which was subsequently metabolized via the phthalate pathway. To our knowledge, this is the first report identifying 2,2′-diphenic acid as an intermediate in pyrene degradation. Integrated genomic and transcriptomic analyses revealed four gene clusters (clusters I–IV) involved in pyrene degradation in strain ENR6. Reverse transcription-quantitative PCR (RT-qPCR) analysis demonstrated that these clusters were specifically induced by pyrene and its intermediates, with genes chr_3400-chr_3404 in cluster I strongly associated with 2,2′-diphenic acid degradation. Based on these findings, we propose a distinct 2,2′-diphenic acid-centered pathway for pyrene degradation in strain ENR6. This study not only broadens the bacterial repertoire available for PAH bioremediation but also provides new insights into the metabolic diversity of PAH-degrading microorganisms. IMPORTANCE: Polycyclic aromatic hydrocarbons (PAHs) are widespread, highly toxic, and persistent environmental pollutants. Microbial biodegradation offers a sustainable approach for PAH remediation, yet the metabolic mechanisms remain incompletely understood. In this study, we isolated and characterized a novel pyrene-degrading bacterium, Glutamicibacter soli ENR6, thereby expanding the bacterial repertoire available for PAH bioremediation. The identification of 2,2′-diphenic acid as a key intermediate reveals a previously unrecognized pathway of pyrene degradation, in which the subsequent catabolism of 2,2′-diphenic acid is mediated by a newly identified ring-hydroxylating dioxygenase. This pathway provides an alternative metabolic entry point into the broadly conserved phthalate pathway when the classical 1-hydroxy-2-naphthoic acid-centered pathway is inhibited. The distinct 2,2′-diphenic acid-mediated pyrene degradation pathway elucidated in strain ENR6 highlights metabolic diversity among PAH-degrading microorganisms and provides a mechanistic foundation for applying this strain in the bioremediation of PAH-contaminated sites.