Molecular-biological data and omics tools have increasingly been used to characterize microorganisms responsible for the turnover of reactive compounds in the environment, such as reactive-nitrogen species in groundwater. While transcripts of functional genes and enzymes are used as measures of microbial activity, it is not yet clear how they are quantitatively related to actual turnover rates under variable environmental conditions. As an example application, we consider the interface between rivers and groundwater which has been identified as a key driver for the turnover of reactive-nitrogen compounds, that cause eutrophication of rivers and endanger drinking water production from groundwater. In the absence of measured data, we developed a reactive-transport model for denitrification that simultaneously predicts the distributions of functional-gene transcripts, enzymes, and reaction rates. Applying the model, we evaluate the response of transcripts and enzymes at the river-groundwater interface to stable and dynamic hydrogeochemical regimes. While functional-gene transcripts respond to short-term (diurnal) fluctuations of substrate availability and oxygen concentrations, enzyme concentrations are stable over such time scales. The presence of functional-gene transcripts and enzymes globally coincides with the zones of active denitrification. However, transcript and enzyme concentrations do not directly translate into denitrification rates in a quantitative way because of nonlinear effects and hysteresis caused by variable substrate availability and oxygen inhibition. Based on our simulations, we suggest that molecular-biological data should be combined with aqueous geochemical data, which can typically be obtained at higher spatial and temporal resolution, to parameterize and calibrate reactive-transport models.

中文翻译：

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河流-地下水界面的反硝化驱动转录和酶生产：来自反应运输模型的见解

分子生物学数据和组学工具越来越多地用于表征负责环境中活性化合物周转的微生物，例如地下水中的活性氮物种。虽然功能基因和酶的转录本被用作微生物活性的量度，但尚不清楚它们如何与可变环境条件下的实际周转率定量相关。作为一个示例应用，我们考虑河流和地下水之间的界面，该界面已被确定为活性氮化合物周转的关键驱动因素，导致河流富营养化并危及地下水的饮用水生产。在没有测量数据的情况下，我们开发了一种反硝化反应转运模型，该模型可以同时预测功能基因转录本、酶和反应速率的分布。应用该模型，我们评估了河流-地下水界面处的转录物和酶对稳定和动态的水文地球化学状态的响应。虽然功能基因转录物对底物可用性和氧浓度的短期（昼夜）波动作出反应，但酶浓度在这样的时间尺度上是稳定的。功能基因转录物和酶的存在与活跃的反硝化区域一致。然而，由于可变底物可用性和氧抑制引起的非线性效应和滞后，转录物和酶浓度不能以定量方式直接转化为反硝化速率。