Biological soil crusts (BSCs) play a fundamental role in desert ecosystems by stabilizing soil, cycling nutrients, and retaining moisture. However, the assembly processes governing bacterial communities within BSCs remain largely unknown. This study aimed to reveal the spatiotemporal variations in the bacterial community diversity, co-occurrence patterns, and ecological assembly processes of BSCs and their underlying soils across different desert and seasonal conditions. We systematically analyzed the spatial differences in the bacterial diversity, co-occurrence networks, and community assembly processes of BSCs and their underlying soils using samples collected at various soil depths from different BSC types in different deserts. We discovered that BSC type and soil depth were the primary factors driving bacterial community assembly, while seasonal effects were weaker and more indirect, and mainly regulated community dynamics through changes in resource availability and environmental conditions. The underlying soils of moss- and lichen-BSCs exhibited higher bacterial diversity and richness than those of algae BSCs. In contrast, cyano-BSCs exhibited a lower diversity, but Cyanobacteria demonstrated the highest photosynthetic function. Among the different deserts, the community assembly of samples from the eastern Inner Mongolia deserts was largely influenced by environmental selection, whereas stochastic processes were more prominent in the central and western desert regions. A β-nearest taxon index (βNTI) analysis indicated that stochastic processes were dominant in surface BSC samples, while environmental selection played a stronger role in deeper layers. A co-occurrence network analysis revealed that surface BSC samples had a high degree of network connectivity, with those from moss- and lichen-BSCs being particularly high, and they also exhibited high modularity and local clustering that promoted the functional stability of the microbial communities. This study revealed the integrated effects of soil depth, BSC type, desert type, and resource availability on microbial community assembly in desert ecosystems. These findings provide a theoretical basis for the microbial management of BSCs and scientific insights to support restoration strategies in desert ecosystems.

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.