Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA.
Appl Environ Microbiol. 2011 Jul;77(13):4597-602. doi: 10.1128/AEM.00114-11. Epub 2011 May 6.
Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.
在采用分子诊断生物修复群落作为指导生物修复策略发展的常规实践之前，需要简单且廉价的方法来评估地下微生物的代谢状态和生物修复活性。定量基因转录本可以诊断生物修复过程中微生物生理学的重要方面，但技术上具有挑战性，并且不能说明翻译后修饰对蛋白质丰度的影响。另一种策略是直接定量可能对生理状态具有诊断意义的关键蛋白质的丰度。为了评估该策略，开发了一种基于抗体的定量方法来研究地下 Geobacter 群落。柠檬酸合酶的丰度与 Geobacter bemidjiensis 在恒化培养物中的代谢速率相对应。在铀污染地下水的原位生物修复过程中，随着向地下水中添加乙酸盐，Geobacter 柠檬酸合酶的数量增加，当乙酸盐添加剂停止时，其数量减少。固氮蛋白 NifD 的丰度随着地下水中铵的可用性降低而增加，当铵浓度增加时，其丰度降低。在石油污染的含水层中，参与 Geobacter 种厌氧降解单芳香族化合物的 BamB 酶亚基的丰度在预期 Geobacter 在芳烃降解中发挥重要作用的区域增加。这些结果表明，基于抗体的关键代谢蛋白检测方法（应该很容易适应标准化试剂盒）可能是诊断负责生物修复的微生物群落代谢状态的可行方法，有助于合理设计生物修复策略。
