Stable Isotope Probing-metagenomics of river microbial populations degrading the aromatic pollutant para-nitrophenol (PNP)

降解芳香族污染物对硝基苯酚 (PNP) 的河流微生物种群的稳定同位素探测宏基因组学

• 批准号: NE/J014168/1
• 负责人: Hendrik Schaefer
• 金额: $ 6.47万
• 依托单位: University of Warwick
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ014168%2F1
• 关键词: Stable; Isotope; Probing; metagenomics; river

Para-nitrophenol (PNP) is an aromatic pollutant that is widely distributed in the environment. This is due to its utilisation as a dye and as a compound used in a wide range of organic syntheses, for instance of explosives and pesticides. As a result of its industrial use PNP causes environmental pollution of soils and water courses, at and near the site of manufacture but also during degradation of a range of pesticids in agricultural soil. While PNP is chemically stable, microorganisms can degrade it. Bacteria are responsible for bioremediation of the chemical in the environment, but the identity of the specific populations and metabolic pathways that contribute to PNP degradation are as yet uncharacterised. Knowledge of the identity of PNP degrading microorganisms is of major interest in order to further enhance the biodegradation of PNP, for instance in engineered systems such as water treatment works or in agricultural soils.PNP degradation of bacteria has been mostly studied using purified strains that are grown in the lab. The genes and their functions that confer PNP degradation capability have been identified in a number of bacteria, but whether these represent the most important pathways and bacteria that are the pivotal for PNP degradation in in natural environments is uncertain. This is mainly because the great majority of bacteria that live in the environment resist cultivation. Using specific techniques, one can identify such 'unculturable' populations. This is done by feeding natural populations of microbes with a version of the substrate that is chemically identical to the normal one but which is, literally, heavier. In our case, we will use PNP in which the carbon atoms have an atomic weight of 13, not the more conventional 12. When a microbe digests such a heavy molecule, the heavy carbon is incorporated into its molecules, including DNA. By purifying this heavy DNA from the light form and by looking for signature sequences in the genes, the microorganisms that used the PNP can be identified and the mechanisms by which they do so can be inferred from sequencing their genomic DNA.We will do these experiments using river water from the River Dene, in Warwickshire. We have already studied PNP degrading bacteria in this river and have been able to isolate particular strains that degraded PNP. We have also developed a number of genetic probes that target key genes of PNP degradation in a wide range of bacteria and analysed the diversity of these markers in the PNP degradation microcosms. These analyses have shown that there are a number of unculturable bacteria that contribute to PNP degradation in this river - very likely using enzymes that have not previously been shown to be involved in PNP degradation. This project would allow us to apply cutting-edge molecular tools to identify these populations and some of the candidate novel enzymes that may contribute to PNP degradation in addition to the ones already known. The results will be beneficial in that they will increase our understanding of an important microbial process that is responsible for the removal of toxic anthropogenic aromatic pollutants from the environment. Understanding the process of bioremediation better may lead to improvement of the efficacy of this environmental process, for instance in waste water treatment plants or agricultural soils where it is particularly important.

二硝基苯酚（PNP）是一种芳香族污染物，在环境中广泛分布。这是由于它用作染料的利用以及在各种有机合成中使用的化合物，例如炸药和农药。由于其工业用途，PNP在制造地点及其附近以及在农业土壤中的一系列农药降解期间，引起了土壤和水课程的环境污染。尽管PNP化学稳定，但微生物可以降解它。细菌负责对环境中化学物质的生物修复，但是有助于PNP降解的特定种群和代谢途径的身份尚未表达。了解PNP降解微生物的认识是为了进一步增强PNP的生物降解，例如在工程系统（例如水处理工作）或农业土壤中的生物降解。在实验室生长。在许多细菌中已经鉴定出了赋予PNP降解能力的基因及其功能，但是这些基因是否代表了自然环境中PNP降解的关键的最重要的途径和细菌。这主要是因为生活在环境中的绝大多数细菌都可以抵抗种植。使用特定的技术，可以识别这种“无法养设的”人群。这是通过将微生物的天然种群喂入具有化学在化学上与正常同等的底物的自然种群来完成的，但从字面上看，这是更重的。在我们的情况下，我们将使用PNP，其中碳原子的原子量为13，而不是更常规的12。当微生物消化这样的重分子时，将重碳掺入了其分子中，包括DNA。通过从光形式纯化这种重的DNA并通过寻找基因的签名序列，可以鉴定使用使用PNP的微生物，并且可以通过对其基因组DNA进行测序来推断它们的机制。我们将进行这些实验利用沃里克郡迪内河的河水。我们已经研究了这条河中PNP降解细菌的PNP，并且能够分离出降解PNP的特定菌株。我们还开发了许多遗传探针，这些遗传探针靶向PNP降解的关键基因在广泛的细菌中，并分析了PNP降解缩影中这些标记的多样性。这些分析表明，有许多不可培养的细菌在这条河中导致PNP降解 - 很可能使用以前尚未证明与PNP降解有关的酶。该项目将使我们能够应用尖端的分子工具来识别这些人群以及一些候选新型酶，除了已经知道的酶外，这些酶还可能导致PNP降解。结果将是有益的，因为它们将增加我们对重要的微生物过程的理解，该过程负责从环境中去除有毒人为芳香族污染物。更好地理解生物修复的过程可能会改善这种环境过程的功效，例如在废水处理厂或尤其重要的农业土壤中。

项目成果

Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol.

• DOI: 10.1016/j.chemosphere.2016.08.095
• 发表时间: 2016-12
• 期刊: Chemosphere
• 影响因子: 8.8
• 作者: A. Kowalczyk;O. Price;C. J. van der Gast;C. Finnegan;R. V. van Egmond;H. Schäfer;G. Bending