Ulbrich Joseph, Jobe Nathaniel E, Jones Daniel S, Kieft Thomas L
Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA.
OpenEye Scientific, 9 Bisbee Court, Suite D, Santa Fe, NM, 97508, USA.
Microb Ecol. 2024 Dec 26;87(1):163. doi: 10.1007/s00248-024-02479-9.
Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.
病毒是地球上数量最为丰富的生物实体，它们在环境和生物圈中发挥着关键作用，能够调节微生物种群并促进养分循环。环境病毒在海洋中受到的研究最多，但目前病毒研究已扩展到其他环境。在此，对卡尔斯巴德洞穴国家公园的四个洞穴水池中的病毒群落进行了特征分析，以检验以下假设：（i）洞穴水池中的病毒丰度比原核细胞丰度高十倍；（ii）洞穴水池包含新的病毒序列；（iii）洞穴已开发区域水池中的病毒群落与同一洞穴未开发区域水池中的病毒群落不同。通过直接落射荧光显微镜计数确定病毒与微生物丰度之间的关系。构建病毒宏基因组以检查水池间的病毒多样性、识别新病毒并表征辅助代谢基因（AMG）。通过16S rRNA基因扩增子测序对细菌群落进行特征分析。落射荧光显微镜显示，所有位点的类病毒颗粒（VLP）与微生物的比例约为22:1。游客流量较大的水池中的病毒群落彼此之间比与游客较少的水池中的病毒群落更为相似，不过令人惊讶的是，病毒并未遵循与反映水池地球化学特征的细菌群落相同的模式。使用iPHoP从病毒序列预测的细菌宿主与16S rRNA基因数据集中稀有和丰富的属及科均有重叠。基因共享网络分析显示，与参考病毒数据库以及其他水生环境相比，病毒多样性较高。AMG的存在表明四个水池之间的代谢潜力存在差异。总体而言，卡尔斯巴德洞穴中存在新病毒，同一系统内的水池之间具有丰富的多样性，这表明洞穴可能是未被探索的病毒组的重要储存库。
