<p>Biological soil crusts (BSCs) play essential roles in arid ecosystems by stabilizing soil and regulating hydrological processes. BSC microbial communities comprise a small number of abundant taxa and a large pool of rare taxa, which differ in their transcriptional capacities. However, the respective contributions of abundant and rare taxa to alkali‑metal homeostasis, a process crucial for maintaining cellular osmotic balance and metabolic activity, remain poorly understood. Here, we integrated metatranscriptomic sequencing with chemical fractionation analysis of Na⁺ and K⁺ to compare transcriptional patterns and influencing factors between rare and abundant microbial taxa in moss‑dominated (MD) and lichen‑dominated (LD) crusts. Our results indicated that abundant bacteria expressed the Na⁺/H⁺ antiporter <i>nhaA</i> and the <i>trk/ktr</i> K⁺ uptake protein, particularly in MD crusts. In contrast, rare taxa expressed diverse genes, including Na⁺/H⁺ antiporter <i>nhaB</i>, <i>nhaC</i>, and <i>nhaD</i>, K⁺-stimulated Na⁺-pyrophosphatase <i>nsaA</i>, and <i>kup</i> K⁺ uptake. Abundant fungi dominated expression of the NHE‑type Na⁺/H⁺ antiporter <i>nha1</i>, while rare fungi expressed a variety of genes. Analysis of the integrated co-occurrence network indicated that abundant bacterial and fungal taxa displayed greater node degree and connectivity relative to rare taxa, and were dominant in both microbial co-occurrence links and the expression of key Na⁺/K⁺ uptake and transport genes. The expression of these genes was more strongly correlated with bioavailable Na and K fractions, particularly carbonate- and oxide-bound forms, than with soil pH or electrical conductivity. These findings indicate that bioavailable Na and K contents induce distinct transcriptional responses in abundant and rare taxa, thereby regulating key alkali-metal homeostasis within BSC microbial communities.</p>