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 CO2 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.

Ethanolamine (Etn) contained in milk is the base constituent of phosphatidylethanolamine and is required for the proliferation of intestinal epithelial cells and bacteria, which is important for maintenance of the gut microbiome and intestinal development. The present study investigated the effect of Etn on intestinal function and microbiome using 21-d-old Sprague–Dawley rats treated with 0, 250, 500 and 1000 μm Etn in drinking water for 2 weeks immediately after weaning. Growth performance, intestinal morphology, antioxidant capacity and mucosal immunity, as well as gut microbiota community composition, were evaluated. Metagenomic prediction and metabolic phenotype analysis based on 16S RNA sequencing were also carried out to assess changes in metabolic functions. We found that weaned rats administered 500 μm Etn enhanced mucosal antioxidant capacity, as evidenced by higher superoxide dismutase and glutathione peroxidase levels in the jejunum (P<0·05) compared with those in the control group. Predominant microbes including Bacteroidetes, Proteobacteria, Elusimicrobia and Tenericutes were altered by different levels of Etn compared with the control group. An Etn concentration of 500 µm shifted colonic microbial metabolic functions that are in favour of lipid- and sugar-related metabolism and biosynthesis. Etn also altered the metabolic phenotypes such as anaerobic microbial counts, and oxidative stress tolerance at over 250 µm. This is the first report for a role of Etn in modifying gut microbiota and intestinal functions. Our findings highlighted the important role of Etn in shaping gut microbial community and promotes intestinal functions, which may provide a better insight of breast-feeding to infant’s gut health.

The Bacillus stearothermophilus ribosomal protein S15 binds to a phylogenetically conserved three-way junction formed by the intersection of helices 20, 21, and 22 of eubacterial 16S ribosomal RNA, inducing a large conformational change in the RNA. Like many RNA structures, this three-way junction can also be folded by the addition of polyvalent cations such as magnesium, as demonstrated by comparing the mobilities of the wild-type and mutant junctions in the absence and presence of polyvalent cations in nondenaturing polyacrylamide gels. Using a modification interference assay, critical nucleotides for folding have been identified as the phylogenetically conserved nucleotides in the three-way junction. NMR spectroscopy of the junction reveals that the conformations induced by the addition of magnesium or S15 are extremely similar. Thus, the folding of the junction is determined entirely by RNA elements within the phylogenetically conserved junction core, and the role of Mg2+ and S15 is to stabilize this intrinsically unstable structure. The organization of the junction by Mg2+ significantly enhances the bimolecular association rate (kon) of S15 binding, suggesting that S15 binds specifically to the folded form of the three-way junction via a tertiary structure capture mechanism.