Yakushima, a Japanese island, features large and old Japanese cedars (Cryptomeria japonica D. Don), some over a thousand years old. Within their crowns, humus derived from plant litter, referred to as canopy soil, is deposited on large limbs. This canopy soil serves as a fundamental substrate for epiphytic plants, contributing to the formation of a unique arboreal ecosystem. However, the factors that allow epiphytes to inhabit in canopy soils are not well understood. This study focused on the nutrient conditions where these epiphytic plants grow in the canopy. We investigated (i) inorganic nitrogen content, a crucial nutrient source for plants and (ii) microbial communities in canopy soils compared to ground soils.

The study was conducted on four Japanese cedars in Yakushima, known for hosting 22 species of woody plants consisting of 1143 individuals in 2013. One canopy soil sample was collected at all spots where epiphytic plants grow, within the height range 13.2–30.2 m, while three ground soil samples were collected beneath each tree in 2021. Soil samples were collected from 0 cm to 5 cm depth at all spots and from 5 cm to 10 cm depth at several deeper spots. Ammonium and nitrate nitrogen contents were determined using absorbance spectrophotometry following KCl extraction. Soil DNA was extracted and amplicons of fungal ITS and bacterial 16S rRNA were sequenced, the most widely sequenced DNA region in molecular ecology of fungi and bacteria. Soil physicochemical properties that could affect these microbial communities were determined for each soil sample, including pH, volumetric water content, total organic carbon content, and truog phosphate content.

The results showed that (i) ammonium and nitrate nitrogen content per soil volume were lower in the canopy compared to the ground soils, and (ii) the microbial community structures differed between the ground and canopy soils (perMANOVA, P < 0.01), correlating with environmental factors. The canopy soils were dominated by microbes that prefer acidic conditions and active carbohydrate metabolism and lower nitrogen metabolism compared to the ground soils, based on the predictive gene abundances of genes coding for enzyme. The canopy of large and old Japanese cedars in Yakushima exhibited a potentially nutrient-poor environment for plants compared to the ground. However, essential levels of plant-available nitrogen for canopy plants are produced by the unique microbial community in the canopy environment, which may contribute to the different canopy epiphyte habitats relative to the ground.