Contrasting ecological responses of abundant and rare bacterial and fungal subcommunities along an alpine marsh wetland degradation gradient.

Introduction: Abundant and rare microbial taxa may respond differently to wetland degradation, yet their relative contributions to community reorganization remain poorly resolved in alpine marsh wetlands. Methods: We investigated lightly (LD), moderately (MD), and severely degraded (SD) alpine marsh wetlands on the northern shore of Qinghai Lake using 15 soil metagenomes and nine soil physicochemical properties. Bacterial and fungal genera were classified as abundant, intermediate, rare, or low-prevalence taxa according to domain-specific prevalence and mean relative abundance. Sample-level richness and original abundance contributions, alpha and beta diversity, community composition, distribution breadth, candidate indicator genera, and environmental associations were compared across the degradation gradient. Results: Total detected bacterial richness declined from 346.2 genera per sample in LD to 287.0 in SD. The rare bacterial share of detected richness decreased from 45.3% to 40.4%, while its original abundance contribution decreased from 6.79% to 3.70%. Abundant fungi accounted for 97.1-98.5% of total fungal abundance. Rare bacterial richness declined monotonically with degradation, whereas Shannon diversity, Simpson diversity, and Pielou's evenness declined in abundant fungi. All four focal subcommunities differed significantly in composition among degradation levels, with the largest PERMANOVA effect observed for abundant fungi and the smallest for rare fungi. Rare fractions exhibited greater incidence-based beta diversity and narrower observed distributions than abundant fractions. Soil PC1 and PC2 were associated with 51.6%, 41.4%, and 55.1% of the variation in abundant bacterial, rare bacterial, and abundant fungal communities, respectively, but with only 0.6% of the variation in rare fungal communities. Discussion: Partitioning microbial communities into abundant and rare fractions revealed pronounced abundance- and domain-dependent reorganization along the wetland degradation gradient. Rare bacteria showed marked losses in richness and abundance contribution, whereas abundant fungi exhibited stronger declines in within-community diversity and greater environmental structuring. These contrasting responses were obscured in whole-community summaries, highlighting the value of explicitly separating abundant and rare taxa when evaluating microbial responses to alpine marsh wetland degradation.