Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.
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DOI：
10.1038/ismej.2012.82
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发表时间：
2013-01
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芳香污染环境中的微生物代谢具有重要的生态学意义，对这一过程的全面了解仍然是一个相关的目标。为了了解生物多样性和芳香介导的遗传和代谢重排的作用，我们在受（Nbs）或不(N)生物刺激的人为影响和多芳烃（PAH）污染的土壤中进行了“OMIC”研究，这些土壤分别使用硝酸铵钙、NH4NO3和KH2PO4以及商业表面活性剂Iveysol，以及来自两种土壤的两个富萘群落（分别为CN2和CN1）。利用宏基因组方法，在N、Nbs、CN1和CN2群落中分别鉴定出52、53、14和12种不同的物种（根据我们工作中相当于分类学物种的操作系统发生单位（OPU））。在实验条件下，95个不同的物种中有10个和3293个同源基团（COGs）蛋白家族中有238个被明显刺激，而只有2个物种和1465个COGs符合所有中胚层的共同设置。结果表明，利用潜在的支持生长的芳烃具有明显的生物降解能力，这导致生物刺激群落非常适合萘的利用，而非刺激群落表现出比先前预测的更大的代谢窗口。在比较蛋白质表达谱和宏基因组数据集的基础上，假设成员之间的相互作用。本文讨论并首次使用整理数据库来重建复杂微生物群落的“假定”降解网络。
Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted ‘OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH4NO3 and KH2PO4 and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct ‘presumptive' degradation networks for complex microbial communities.
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