Introduction: Biological soil crusts (BSCs) are distributed in arid and semiarid regions, and they function as important microhabitats for nitrogen fixation. The diazotroph community is critical for nitrogen fixation in BSCs and their subsoils. However, little is known about the key groups in different types of BSCs and subsoils in temperate semi-arid or arid deserts.Methods: Here, we sampled three types of BSCs and their subsoils from the Inner Mongolian plateau, investigated the distribution characteristics of the diazotroph community by high-throughput sequencing, predicted keystone species using the molecular ecological network analyses pipeline (MENAP), and verified their close relationship with the available nitrogen (AN) content.Results: The results showed that available nitrogen content in BSCs was higher than that in subsoils in three different types of BSCs, and there were differences among seasons and according to the mean annual precipitation. The abundance of diazotrophs was higher in Cyano-BSCs, while diversity had no significant difference among BSCs and subsoils. Cyanobacteria and Proteobacteria, Nostocaceae and Scytonemataceae, Skermanella, Scytonema, Azohydromonas, Nostoc and Trichormus were the dominant phyla, families, and genera, respectively. The dominant groups belong to Skermanella, Scytonema, and Nostoc formed the core diazotroph community in the three types of BSCs and subsoils, and each had a close relationship with AN.Discussion: These results indicate that diazotrophs in BSCs and subsoils had high diversity, and the core diazotroph communities have a close relationship with nitrogen fixation and that they may be the main contributor to nitrogen fixing in BSCs and subsoils in temperate deserts.

Biological soil crusts (BSCs) are critical ecological components in arid lands. Their formation and stability hinge on the assembly and interactive networks of cyanobacteria-led bacterial communities. Yet, how different functional cyanobacteria shape the underlying microbial structure and assembly rules is poorly understood. Here, we cultivated artificial algal crusts using two representative cyanobacteria: the nitrogen-fixing Leptolyngbya sp. and the non-nitrogen-fixing Microcoleus vaginatus (M. vaginatus CM01). A total of six treatments were established based on the presence or absence of spraying with in situ BSCs leachate: a control group without inoculation of algae or bacteria (soil, S); a treatment group sprayed only with bacterial suspension (soil + bacteria, SB); a treatment group sprayed only with M. vaginatus CM01 (soil + M. vaginatus CM01, SM); a treatment group co-inoculated with both BSCs leachate and M. vaginatus CM01 (soil + M. vaginatus CM01 + bacteria, SMB); a treatment group inoculated only with Leptolyngbya sp. CT01 (soil + Leptolyngbya sp. CT01, SL); and a treatment group co-inoculated with Leptolyngbya sp. CT01 and biocrust leachate (soil + Leptolyngbya sp. CT01 + bacteria, SLB). By integrating 16S rRNA gene sequencing, neutral community modeling (NCM), and structural equation modeling (SEM), we dissected differences in Cyano-BSCs development, bacterial community composition, co-occurrence networks, and assembly mechanisms. Inoculation with M. vaginatus CM01 (SM, SMB) superiorly promoted Cyano-BSCs development: the SM group achieved the highest coverage (23.33%), while the SMB group showed marked increases in organic matter (OM, 4.10 g·kg⁻¹) and chlorophyll a (Chla, 13.40 μg·g⁻¹), alongside a >5-fold rise in bacterial, cyanobacterial, and nitrogen-fixation gene abundances versus controls. The mechanism centers on extracellular polymeric substances (EPS) secreted by M. vaginatus, which homogenized the microenvironment, suppressed stochastic bacterial dispersal (NCM, SM: R² = 0.698), and enhanced deterministic selection. This process forged a highly cooperative network (89.74% positive links, average degree 34.71) that directionally enriched Cyanobacteria (relative abundance 40.40%). The Shannon index of Cyano-BSCs from the group (SMB) reached 7.72 ± 0.09, reflecting high microbial community diversity. SEM confirmed M. vaginatus directly regulated bacterial assembly (path coefficient = 0.59, p < 0.05) and indirectly improved the soil environment (path coefficient = 0.64, p < 0.05), establishing a “cyanobacteria-community-environment” feedback loop. Conversely, the Leptolyngbya sp. groups (SL, SLB), despite enriching nitrogen-fixing bacteria and fungi, exhibited low carbon fixation efficiency (notably 1.26 g·kg⁻¹ OM in SL) and lack of EPS; communities remained stochastic (NCM, SL: R² = 0.751) with no effective regulatory pathway—a pattern mirrored in S and SB groups. Our findings demonstrate that M. vaginatus acts as a core engineer of biological soil Cyano-BSCs formation via an “EPS-mediated habitat filtering—functional group enrichment—cooperative network assembly” cascade, enforcing deterministic community construction. Leptolyngbya sp., with limited niche-constructing ability, fails to exert comparable control. This work provides a targeted framework for the artificial restoration of Cyano-BSCs in arid zones.

Driven by increasingly severe drought stress associated with global warming, this study investigated a synthetic microbial community, SynCom-SASW01, with strong stress tolerance and plant growth-promoting potential, and systematically elucidated its mechanisms for enhancing drought resistance in wheat (Triticum aestivum L.). Dual-site field trials demonstrated that SynCom-SASW01 significantly alleviated drought-induced growth suppression, increasing grain yields by 10.42% and 8.52% at the Hohhot and Hulunbuir sites, respectively. This improvement was primarily associated with increased effective tiller number and enhanced root vigor. Physiologically, inoculation promoted root proline and glutathione accumulation and enhanced antioxidant enzyme activities, including superoxide dismutase, thereby reducing malondialdehyde levels. Environmental analyses showed that the consortium established rhizosphere “micro-reservoirs” through exopolysaccharide secretion, improving soil relative water content and the availability of alkali-hydrolyzable nitrogen and phosphorus. High-throughput sequencing revealed that SynCom-SASW01 reshaped the endosphere microbiome through early colonization priority effects, selectively enriching beneficial taxa such as Pseudomonas. Functional prediction indicated upregulated branched-chain amino acid biosynthesis, promoting osmotic adjustment and redox homeostasis. These findings provide a microbiome-based strategy for stabilizing wheat productivity in arid regions.

Continuous cropping obstacles (CCOs) seriously constrain tomato yield and quality in facility agriculture, primarily due to rhizosphere microbial imbalance. Indigenous synthetic microbial communities (SynCom) offer superior colonization and stability compared to single strains. This study aimed at constructing a simplified SynCom from indigenous rhizobacteria in Northwest China to alleviate tomato CCOs. A total of 155 rhizobacterial strains (29 genera) were isolated. Sixteen strains with significant growth-promoting effects were selected through seedling assays. Based on the carbon source niche overlap index (NOI > 70%) with Ralstonia solanacearum QL-Rs1115, eight candidate strains were retained. Using the broken-stick model, 29 simplified SynComs were constructed. SynCom28, composed of six functionally complementary strains (Azospirillum brasilense, Massilia niabensis, Enterobacter hormaechei, Chryseobacterium sp., Priestia megaterium and Pseudomonas brassicacearum), showed the best performance. Pot experiments revealed that SynCom28 reduced the bacterial wilt disease index to 32.41, with a biocontrol efficacy of 41.72%. Greenhouse trials under continuous cropping demonstrated that SynCom28 significantly increased seedling Dickson quality index (DQI), stem diameter and biomass. Fruit yield increased by 12.98–15.30% across the 2nd to 4th cropping cycles (p < 0.05). Fruit quality parameters were also enhanced, with soluble sugar, lycopene, and vitamin C contents increasing by 47.22–65.07%, 33.07–81.71% and 80.56–166.67%, respectively. In conclusion, the indigenous simplified SynCom28 effectively alleviates tomato CCOs, enhancing growth, yield, and quality while suppressing bacterial wilt, providing a promising strategy for sustainable facility agriculture.