Manjarrez-Rascón Dannia Merari, Muñoz-Ramirez Zilia Yanira, Carrillo-Campos Javier, Ortiz-Aguirre Ismael, González-Escobedo Román
Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico Francisco R. Almada km 1, Chihuahua, 31453, Mexico.
Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua, 31125, Mexico.
World J Microbiol Biotechnol. 2025 Sep 15;41(9):326. doi: 10.1007/s11274-025-04540-2.
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.
洞穴是贫营养、光照匮乏的生态系统，其中栖息着高度专业化且多样的微生物群落，这些群落在生物地球化学循环和生态稳定性中发挥着关键作用。在本研究中，我们首次全面描述了墨西哥北部奇瓦瓦州“Nombre de Dios洞穴”内的细菌群落。我们使用PacBio HiFi技术对全长16S rRNA基因进行测序，分析了五个洞穴腔室中的细菌多样性。共鉴定出36个细菌门，包括822个属，其中拟杆菌门、假单胞菌门和芽孢杆菌门最为占主导地位。在属水平上，JC017、葡萄球菌属、聚球藻属和肠杆菌属是最丰富的分类群。α多样性分析显示，香农多样性和均匀度存在显著差异，这表明特定腔室的局部因素可能会影响细菌丰富度和群落平衡。同样，β多样性分析表明，不同腔室之间存在明显的组成差异，特别是在棕榈树腔室和浴室腔室，后者明显与游客通道隔离。这种空间变化突出了环境异质性和人类活动对微生物群落结构的影响。微生物群落包括一些具有重要生态意义的属，如以固氮、胞外多糖产生和生物膜形成而闻名的聚球藻属和结节丝菌属。还检测到了与临床相关的属，包括大肠杆菌属、克雷伯菌属、葡萄球菌属和肠球菌属，这表明可能通过人为活动引入了外来微生物。这些发现强调了洞穴微生物群落的生态和公共卫生意义，并为脆弱岩溶环境中的微生物监测和保护策略提供了有价值的见解。
