Metabolic pathways profiling of aerobiomes in the Earth’s lower atmosphere

Abstract The study explores the vertical stratification of microbial diversity and metabolic potential in Earth’s lower atmosphere. Using 16S rRNA sequencing data spanning the planetary boundary layer to the lower stratosphere, we conducted taxonomic profiling and metabolic pathways predictions. The aim was to elucidate microbial community dynamics and their ecological roles under diverse atmospheric conditions. Methods: 51 Publicly available datasets with 3584 samples were retrieved from repositories such as Sequencing Read Archive and European Nucleotide Archive, filtered for studies employing 16S rRNA sequencing. Quality control was performed using FastQC and Trimmomatic, followed by taxonomic classification with Qiime2 and the Silva132 database. Functional pathway predictions were derived using PICRUSt2, and statistical analyses included Kruskal-Wallis tests for diversity comparisons and Mann-Whitney U tests for pathway activity. Results: Microbial diversity decreased with altitude, with the Surface Layer exhibiting the highest Shannon diversity and the significantly decreased in Low Stratosphere. Taxonomic composition shifted along the elevation gradient, with Actinobacteria and Alphaproteobacteria predominant at lower altitudes. In contrast, Bacilli and Gammaproteobacteria became more dominant at higher elevations, though they maintained a notable presence at lower sites as well. Functional analysis revealed altitude-specific adaptations, including significant upregulation of CO 2 fixation pathways in the Free Troposphere Transition Layer and secondary metabolite biosynthesis in the lower stratosphere. Discussion: These findings reveal distinct microbial metabolic profiles across atmospheric layers with varying conditions such as oxygen levels, UV radiation, and nutrient availability. While these differences may represent adaptive strategies, they could also reflect source environment characteristics or selective transport processes. The conserved metabolic pathways across altitude layers suggest functional resilience despite taxonomic divergence. These results have implications for astrobiology, providing analogs for microbial life in extraterrestrial environments like Mars or Europa. In summary, this study advances our understanding of aerobiomes’ ecological roles and their potential as models for life detection in extreme environments, bridging atmospheric microbiology with astrobiological exploration.