Microbial community structure and functional potential of tropical lithic habitats in northern Thailand

Rock (lithic) habitats are macroscopically inhospitable, characterized by oligotrophic conditions and exposure to environmental extremes across diverse climate regions. However, at the microscale, lithic substrates provide sheltered niches, such as pores, cracks, and fissures, that buffer external stressors and enable microbial persistence. While lithic microbial communities have been extensively studied in extreme climates, those in tropical regions remain underexplored. This study investigated epilithic communities on sandstone, as well as both epilithic and endolithic communities associated with limestone in northern Thailand. Bulk soil samples in the immediate vicinity of the lithic substrates were examined to compare microbial community differences between lithic and soil environments. Actinobacteria, Cyanobacteria, and Proteobacteria dominated in bacterial communities across lithic habitats and substrates, while Acidobacteria were more prevalent in soil communities. Lithic fungal communities were predominantly composed of lichen-forming fungi, including Dothideomycetes, Eurotiomycetes, and Lecanoromycetes. Differential abundance analysis revealed that photosynthetic bacteria, radio-resistant bacteria, and rock-inhabiting fungi (RIF) were predominant in the lithic communities. Metabolic functions related to oxygenic photoautotrophy were significantly enriched, corresponding with the high abundance of photosynthetic cyanobacteria. These cyanobacteria contribute to carbon fixation through photosynthesis and to nitrogen fixation, thereby enhancing nutrient availability for microbes that depend on organic carbon. Furthermore, functional predictions suggest that MND1, IS-44, mle1-7, Ellin6067, and SC-I-84 potentially contribute to ammonia oxidation and nitrate generation, while Nitrospira supports nitrification and Rhodoplanes facilitates denitrification. The presence of phosphate-solubilizing and siderophore-producing bacteria suggests active nutrient mobilization, supporting microbial community resilience and contributing to nutrient cycling and ecosystem functioning within lithic habitats. These findings suggest that lithic ecosystems in tropical regions represent ecologically unique niches that harbor microorganisms capable of facilitating nutrient cycling, thereby supporting their colonization. Moreover, this study highlights the untapped biodiversity of microbes in the tropical regions of northern Thailand.