Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
复制标题
海洋生态系统的生物修复：生态模型与通量平衡分析相结合的计算研究
作者：
Marianna Taffi;Nicola Paoletti;C. Angione;S. Pucciarelli;M. Marini;P. Lio’
为受污染的生态系统寻找有效的生物修复方法的压力导致了对微生物物种和代谢降解途径的大规模鉴定。然而，对海洋食物网生物补救的研究和减少物种生物累积的综合战略的定义却没有给予多少关注。我们提出了一个新的计算框架，在生态系统水平上分析生物修复的多尺度效应，耦合食物网生物积累模型和降解细菌的代谢模型的基础上。合成生物学和生态网络分析技术的结合允许指定任意的污染物去除方案和基于天然或合成微生物菌株的战略评估。在这项研究中，我们推导出一个生物富集模型的多氯联苯（PCBs）在亚得里亚海的食物网，我们扩展了代谢重建的恶臭假单胞菌KT 2440（iJN746）与有氧途径的PCBs降解。我们评估不同的生物修复方案在减少物种中的多氯联苯浓度的有效性，我们研究的物种中心性指数，以衡量其重要性，通过喂养环节的污染物扩散。亚得里亚海的案例研究的分析表明，我们的框架可以代表一个实用的工具，在设计有效的修复策略，同时提供见解的生态作用的微生物群落内的食物网。
The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains. In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs) in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746) with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links. The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs.
什么是通量平衡分析？
影响因子：
46.9
作者：
通讯作者：
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