Subsurface environments host most of the fresh water on Earth as well as diverse microorganisms that may constitute a significant part of the biosphere. However, the dynamics and spatial distribution of subsurface microorganisms and their response to hydrological processes are poorly understood. Here we used chemical and metagenomic analyses of groundwater in a fractured rock aquifer in western France to determine the role of fractures in the formation of deep microbial hotspots in the subsurface. The majority of fractures, sampled in a 130-m-deep borehole, were anoxic, but a fracture carrying oxic groundwater was detected at 54-m depth, associated with a fivefold increase in the abundance of iron-oxidizing bacteria. We developed a mechanistic model of fluid flow and mixing in fractures and found that such microbial hotspots are sustained by the mixing of fluids with contrasting redox chemistries at intersections of fractures. The model predicts that metre-scale changes in near-surface water table levels cause intermittent oxygen delivery through deep fractures, which can extend the depth of the habitable zone for iron-oxidizing bacteria hundreds of metres into the subsurface. Given that fractures are ubiquitous at multiple scales in the subsurface, such deep microbial hotspots may substantially influence microbial communities and their effect on Earth’s biogeochemical cycles.

地下环境拥有地球上大部分淡水以及可能构成生物圈重要组成部分的各种微生物。然而，人们对地下微生物的动力学和空间分布及其对水文过程的反应知之甚少。在这里，我们使用了法国西部破裂岩石含水层中地下水的化学和宏基因组分析，以确定裂缝在地下深层微生物热点形成中的作用。在 130 米深的钻孔中取样的大多数裂缝是缺氧的，但在 54 米深度处检测到带有含氧地下水的裂缝，这与铁氧化细菌的丰度增加了五倍有关。我们开发了流体在裂缝中流动和混合的机械模型，发现这种微生物热点是通过在裂缝交叉处混合具有对比氧化还原化学物质的流体来维持的。该模型预测，近地表地下水位的米级变化会导致通过深层裂缝间歇性地输送氧气，这可以将铁氧化细菌的可居住区的深度扩展到地下数百米。鉴于裂缝在地下的多个尺度上无处不在，这种深层微生物热点可能会极大地影响微生物群落及其对地球生物地球化学循环的影响。该模型预测，近地表地下水位的米级变化会导致通过深层裂缝间歇性地输送氧气，这可以将铁氧化细菌的可居住区的深度扩展到地下数百米。鉴于裂缝在地下的多个尺度上无处不在，这种深层微生物热点可能会极大地影响微生物群落及其对地球生物地球化学循环的影响。该模型预测，近地表地下水位的米级变化会导致通过深层裂缝间歇性地输送氧气，这可以将铁氧化细菌的可居住区的深度扩展到地下数百米。鉴于裂缝在地下的多个尺度上无处不在，这种深层微生物热点可能会极大地影响微生物群落及其对地球生物地球化学循环的影响。