Spatial variation and composition of bacterial communities in a cave system from Northern Mexico

Caves are oligotrophic, light-deprived ecosystems that host highly specialized and diverse microbial communities playing critical roles in biogeochemical cycling and ecological stability. In this study, we present the first comprehensive characterization of bacterial communities within the Nombre de Dios Caves in Chihuahua, northern Mexico. Using full-length 16S rRNA gene sequencing with PacBio HiFi technology, we analyzed bacterial diversity across five cave chambers. A total of 36 bacterial phyla, including 822 genera, were identified, with Bacteroidota, Pseudomonadota, and Bacillota being the most dominant. At the genus level, JC017, Staphylococcus, Crocosphaera, and Enterobacter were among the most abundant taxa. Alpha diversity analyses revealed significant differences in Shannon diversity and evenness, suggesting that local chamber-specific factors may influence bacterial richness and community balance. Similarly, beta diversity analyses showed clear compositional differences between chambers, particularly in the palm tree and bathroom chambers, the latter being notably isolated from tourist access. This spatial variation highlights the influence of environmental heterogeneity and human presence on microbial community structure. The microbial assemblages included ecologically important genera such as Crocosphaera and Nodosilinea, known for nitrogen fixation, exopolysaccharide production, and biofilm development. Clinically relevant genera, including Escherichia, Klebsiella, Staphylococcus, and Enterococcus, were also detected, suggesting the possible introduction of allochthonous microbes through anthropogenic activity. These findings underscore the ecological and public health significance of cave microbiomes and offer valuable insights for microbial monitoring and conservation strategies in fragile karst environments.