Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
mBio. 2019 Aug 13;10(4):e01470-19. doi: 10.1128/mBio.01470-19.
Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H- and CO-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.
生命存在于大陆深生境充满水的基岩裂缝中，其受到能量和营养可用性的广泛限制。尽管这些群落仍然存在，但缺乏对深层含水层中活跃种群和代谢过程进行比较的有力研究。本研究分析了三个贫营养的芬兰-瑞典斯堪的纳维亚盾状地下水，其中两个是“现代海洋”水，它们从波罗的海补充有机碳，并且可能不到 20 年（低于海平面 171.3 和 415.4 米），而一个极度贫营养的“彻底混合”水（低于海平面 448.8 米）的年龄未知，由非常古老的咸水和海水组成。细胞要么使用快速固定 RNA 的采样装置捕获，要么在固定之前通过过滤流动的地下水延长时间进行捕获。对两种方法的宏转录组比较表明，各自水样的转录谱在统计学上相似，并且将它们作为生物重复进行分析。对小亚基（SSU）rRNA 的研究证实了来自所有三个生命领域的活跃种群，其中存在许多潜在的新的未分类种群。群落之间具有统计学支持的差异包括在低于海平面 171.3 米的现代海洋水中的异养硫酸盐还原菌，其有机碳含量高于主要为自养的 H 和 CO 喂养的彻底混合水中的种群。虽然现代海洋水具有产甲烷作用的特征，但共生种群主要存在于彻底混合水中。该研究首次对通过有机碳或“地质气体”差异补给的地下水的活跃微生物群落的差异进行了统计评估。尽管深生境与光合作用驱动的地表之间存在距离和时间的双重隔离，但它仍然是地球碳和能量循环的重要驱动因素。然而，由于难以进入和细胞数量少，强大的统计组学研究尚未进行，这限制了可以得出的结论。本研究为两种不同采样系统的使用提供了基准，并证明它们提供了统计学上相似的 RNA 转录谱，重要的是验证了几个先前发表的研究。所产生的数据用于识别活跃微生物群落成员和代谢过程中具有统计学意义的差异。结果突出了现代海洋水中的对比分类群和生长策略，这些差异受到波罗的海海水最近渗透的影响，而与氢和二氧化碳供应的、极度贫营养的、彻底混合的水相比则不同。
