Comparative Shotgun Metagenomics of Microbial Communities Associated with Two Geothermal Systems in Kazakhstan

Geothermal-associated microbial communities remain poorly characterized in Central Asia. Here, shotgun metagenomics was used to compare microbial communities associated with thermally influenced substrates from the Chundzha and Rakhman geothermal systems in Kazakhstan. Six metagenomes representing three spatial replicates per site yielded approximately 6.5–7.3 Gb of clean sequence data per sample. Species-level richness showed a directional trend toward higher values in Chundzha, whereas Shannon diversity was similar between sites. Genus-level Bray–Curtis ordination showed apparent site-associated separation, with sampling site explaining 87.3% of the variation, although the effect was not statistically significant (PERMANOVA, R2 = 0.873, p = 0.10). Chundzha showed greater relative representation of several halophilic and halotolerant taxa, whereas Rakhman showed greater representation of soil-associated lineages. Broad COG and KEGG functional profiles were largely shared between sites. Several hydrogenase-, nitrogenase-, and RuBisCO-associated genes showed higher relative representation in Rakhman, whereas selected fermentation- and photosynthesis-associated functions were relatively higher in Chundzha; however, none of the targeted KO comparisons remained significant after FDR correction. These results indicate candidate taxonomic and functional patterns that should be regarded as exploratory because of the limited replication. The dataset provides a baseline for future genome-resolved and metatranscriptomic studies of geothermal-associated microbial communities in Kazakhstan.