Spatial and seasonal variations of active micro-eukaryotic community structure in heavy metal-contaminated soils

Heavy metal contamination of soil poses a significant hazard to the environment. However, numerous eukaryotic microbes can sustain themselves and thrive in such polluted soils, playing a pivotal role in transforming heavy metal contaminants into more stable and less toxic forms. This study employed an amplicon-based metatranscriptomic approach to investigate the active micro-eukaryotic community structure in heavy metal-contaminated soils across two locations in India, KJ (Jajmau) and UZ (Zawar Mines), during two different seasons (spring and autumn). The diversity assessment targeted the V4 hypervariable region of the 18S rRNA gene, amplified from reverse-transcribed RNA. The supergroup Opisthokonta was found to be dominant across all soil samples, constituting a significant proportion of the eukaryotic community. The microbial communities exhibited clear seasonal variation. In UZ, the genera Aplanochytrium and Colpoda dominated in spring, whereas Hypocreales prevailed in autumn. In KJ, Chlorella, Acari, and Colpoda dominated in spring, while Acari remained dominant in autumn. Regardless of seasonal or spatial fluctuations, 44 genera were found to be common across all samples. Alpha and beta diversity measures, along with hierarchical clustering, network analysis, heatmap visualization, and Principal Component Analysis (PCA), provided strong support for the variations in biodiversity and community organization across the datasets. The ecological significance of these findings lies in demonstrating how micro-eukaryotic communities reorganize spatially and seasonally to maintain resilience in contaminated soils. Such adaptive associations highlight their potential role in natural attenuation and provide a foundation for developing targeted bioremediation strategies by leveraging stress-adapted micro-eukaryotes.

The online version contains supplementary material available at 10.1007/s13205-025-04605-x.