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Long-term ecosystem development involves changes in plant community composition and diversity associated with pedogenesis and nutrient availability, but comparable changes in soil microbial communities remain poorly understood. In particular, it is unclear whether the diversity of plants and microbes respond to similar abiotic drivers, or become decoupled as resources change over long time-scales. We characterized communities of archaea, bacteria and fungi in soils along a 2-million-year chronosequence of coastal dunes in a biodiversity hot spot in Western Australia. The chronosequence involves marked changes in soil pH and nutrient availability that drive major shifts in plant community composition and diversity as soils age. Patterns of alpha-diversity for microbial groups differed along the chronosequence. Bacterial alpha-diversity was greatest in intermediate-aged soils; archaeal diversity was greater in young alkaline or intermediate-aged soils, while fungal alpha-diversity-like plant diversity-was greatest in old, strongly weathered soils where phosphorus is the limiting nutrient. Changes in microbial community composition along the chronosequence were explained primarily by the long-term decline in soil pH, with a smaller influence of the relative abundance of plant nutrient-acquisition strategies. However, changes between the prokaryote and fungal communities, and between fungal and plant communities, became increasingly decoupled along the chronosequence, demonstrating that the coordination of change in biological communities by abiotic drivers becomes weaker during long-term ecosystem development. Several bacterial taxa, including DA101 (Verrucomicrobia), "Candidatus Solibacter" (Acidobacteria) and Gaiella (Actinobacteria), were particularly abundant on the oldest dunes, indicating that they are adapted to acquire phosphorus from extremely infertile soils. However, we cannot disentangle the influence of phosphorus from the long-term decline in soil pH along the chronosequence. Synthesis. These results provide evidence for contrasting patterns of plant and microbial community composition and alpha-diversity in response to acidification and nutrient depletion during long-term pedogenesis.