Synthetic microbial communities (SynComs) are a promising tool for making full use of the beneficial functions imparted by whole bacterial consortia. However, the complexity of reconstructed SynComs often limits their application in sustainable agriculture. Furthermore, inter-strain interactions are often neglected during SynCom construction. Here, we propose a strategy for constructing a simplified and functional SynCom (sfSynCom) by using elite helper strains that significantly improve the beneficial functions of the core symbiotic strain, here Bradyrhizobium elkanii BXYD3, to sustain the growth of soybean (Glycine max). We first identified helper strains that significantly promote nodulation and nitrogen fixation in soybean mediated by BXYD3. Two of these helper strains assigned to the Pantoea taxon produce acyl homoserine lactones, which significantly enhanced the colonization and infection of soybean by BXYD3. Finally, we constructed a sfSynCom from these core and helper strains. This sfSynCom based on the core-helper strategy was more effective at promoting nodulation than inoculation with BXYD3 alone and achieved effects comparable to those of a complex elite SynCom previously constructed on the basis of potential beneficial functions between microbes and plants alone. Our results suggest that considering interactions between strains as well as those between strains and the host plant might allow construction of sfSynComs.

Soil salinity is a worldwide problem threatening crop yields. Some plant growth-promoting rhizobacteria (PGPR) could survive in high salt environment and assist plant adaptation to stress. Nevertheless, the genomic and metabolic features, as well as the regulatory mechanisms promoting salt tolerance in plants by these bacteria remain largely unknown. In the current work, a novel halotolerant PGPR strain, namely, Bacillus sp. strain RA can enhance tomato tolerance to salt stress. Comparative genomic analysis of strain RA with its closely related species indicated a high level of evolutionary plasticity exhibited by strain-specific genes and evolutionary constraints driven by purifying selection, which facilitated its genomic adaptation to salt-affected soils. The transcriptome further showed that strain RA could tolerate salt stress by balancing energy metabolism via the reprogramming of biosynthetic pathways. Plants exude a plethora of metabolites that can strongly influence plant fitness. The accumulation of myo-inositol in leaves under salt stress was observed, leading to the promotion of plant growth triggered by Bacillus sp. strain RA. Importantly, myo-inositol serves as a selective force in the assembly of the phyllosphere microbiome and the recruitment of plant-beneficial species. It promotes destabilizing properties in phyllosphere bacterial co-occurrence networks, but not in fungal networks. Furthermore, interdomain interactions between bacteria and fungi were strengthened by myo-inositol in response to salt stress. This work highlights the genetic adaptation of RA to salt-affected soils and its ability to impact phyllosphere microorganisms through the adjustment of myo-inositol metabolites, thereby imparting enduring resistance against salt stress in tomato.

Investigations into the nitrogen-fixing symbiosis between legumes and rhizobia can yield innovative strategies for sustainable agriculture. Legume species of the Inverted Repeat-Lacking Clade (IRLC) and the Dalbergioids, can utilize nodule cysteine-rich (NCR) peptides, a diverse family of peptides characterized by four or six highly conserved cysteine residues, to communicate with their microbial symbionts. These peptides, many of which exhibit antimicrobial properties, induce profound differentiation of bacteroids (semi-autonomous forms of bacteria) within nodule cells. This terminal differentiation endows the bacteroids with the ability to fix nitrogen, at the expense of their reproductive capacity. Notably, a significant number of NCR peptides is expressed in the nodule fixation zone, where the bacteroids have already reached terminal differentiation. Recent discoveries, through forward genetics approaches, have revealed that the functions of NCR peptides extend beyond antimicrobial effects and the promotion of differentiation. They also play a critical role in sustaining the viability of terminally differentiated bacteroids within nodule cells. These findings underscore the multifaceted functions of NCR peptides and highlight the importance of these peptides in mediating communications between host cells and the terminally differentiated bacteroids.

Hydrogen sulfide (H₂S), a well-established gaseous signaling molecule, can effectively enhance plant tolerance to various environmental stresses. However, there is still a lack of suitable methods to release H₂S in agricultural production, and the mechanism by which H₂S improves stress resistance remains poorly understood. Here, we show the novel role of sodium butyrate (NaB) in producing H₂S consistently in rice rhizosphere soil and the epigenetic mechanism of H₂S to enhance rice drought tolerance. We found that NaB increased sulfate-reducing bacteria (SRB) abundance in the rhizosphere soil, resulting in higher expression of sulfite reductase (SiR), and consequently increased H₂S production. Mechanistic investigation showed that H₂S enhanced the level of H4K5ac in promoter regions of drought-tolerant genes, facilitating their expression by repressing the histone deacetylase (HDAC) gene OsHDA710. Loss-of-function mutants of OsHDA710 exhibited enhanced drought tolerance compared to wild-type (WT) plants, while OsHDA710 overexpression plants showed drought hypersensitivity. Moreover, we demonstrated that OsHDA710 could bind directly to promoters of drought-tolerance genes by recognizing the TGACC motif. Our findings illustrate an efficient way to produce H₂S and a novel mechanism for H₂S in improving the drought resistance of plants.