Fungal Diversity and Community Assembly in Saline–Alkaline Soils of the Yellow River Delta, China

The Yellow River Delta is a representative coastal saline–alkaline ecosystem in China, where high salinity and complex soil properties create a distinct habitat that significantly shapes microbial community structure and function. In this study, we analyzed 34 saline–alkaline soil samples from four regions within the delta. We characterized soil physicochemical properties (salt content, electrical conductivity, and pH) and systematically assessed fungal diversity, potential ecological functions, and their relationships with environmental variables using both internal transcribed spacer high-throughput sequencing and culture-based isolation. Sequencing generated 1,137,196 sequences that clustered into 13,574 operational taxonomic units (OTUs), with Good’s coverage values ranging from 0.96 to 1.00, indicating sufficient sequencing depth. The soils were generally alkaline and exhibited pronounced spatial heterogeneity in salinity and electrical conductivity. Sequencing analyses revealed Ascomycota and Basidiomycota as the dominant fungal phyla. Alpha diversity tended to decline with increasing salt content and electrical conductivity; however, substantial within-group variability indicated strong microenvironmental influences. Beta diversity analyses revealed distinct clustering patterns in community structure among regions based on PCoA ordinations. Redundancy analysis revealed that soil pH had the only significant unique contribution to fungal community variation. However, all three measured edaphic factors together explained only 17% of the total community variation. Functional inference using the FUNGuild database identified diverse fungal trophic modes and several plant-associated taxa in several samples. Culture-based approaches yielded 347 isolates representing 52 genera. Among the isolates, the vast majority (>95%) belonged to Ascomycota, with Basidiomycota represented by only a few isolates, which is consistent with the dominance of Ascomycota observed in the high-throughput sequencing data. Comparisons between sequencing and cultivation results demonstrated complementary diversity profiles and highlighted a substantial reservoir of nonculturable fungi in these soils. Overall, this study clarifies spatial patterns and key environmental drivers of fungal diversity in the Yellow River Delta and establishes a foundational culture collection for future ecological restoration efforts.