Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, 04318 Leipzig, Germany.
ISME J. 2012 Dec;6(12):2291-301. doi: 10.1038/ismej.2012.68. Epub 2012 Jul 12.
Benzene is a major contaminant in various environments, but the mechanisms behind its biodegradation under strictly anoxic conditions are not yet entirely clear. Here we analyzed a benzene-degrading, sulfate-reducing enrichment culture originating from a benzene-contaminated aquifer by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). The time-resolved, quantitative analysis of carbon fluxes within the community supplied with either (13)C-labeled benzene or (13)C-labeled carbonate yielded different functional groups of organisms, with their peptides showing specific time dependencies of (13)C relative isotope abundance indicating different carbon utilization. Through a detailed analysis of the mass spectrometric (MS) data, it was possible to quantify the utilization of the initial carbon source and the metabolic intermediates. The functional groups were affiliated to Clostridiales, Deltaproteobacteria and Bacteroidetes/Chlorobi. The Clostridiales-related organisms were involved in benzene degradation, putatively by fermentation, and additionally used significant amounts of carbonate as a carbon source. The other groups of organisms were found to perform diverse functions, with Deltaproteobacteria degrading fermentation products and Bacteroidetes/Chlorobi being putative scavengers feeding on dead cells. A functional classification of identified proteins supported this allocation and gave further insights into the metabolic pathways and the interactions between the community members. This example shows how protein-SIP can be applied to obtain temporal and phylogenetic information about functional interdependencies within microbial communities.
苯是各种环境中的主要污染物，但在严格缺氧条件下其生物降解的机制尚不完全清楚。在这里，我们通过基于宏基因组的功能宏蛋白质组学方法，使用基于蛋白质的稳定同位素探测（protein-SIP），对来自受污染含水层的苯降解硫酸盐还原富集培养物进行了分析。对用（13）C 标记的苯或（13）C 标记的碳酸盐供应的群落内碳通量进行的时间分辨、定量分析，得到了不同的生物种群，其肽显示出（13）C 相对同位素丰度的特定时间依赖性，表明了不同的碳利用。通过对质谱（MS）数据的详细分析，有可能定量利用初始碳源和代谢中间产物。功能群与梭菌目、Delta 变形菌门和拟杆菌门/Chlorobi 有关。与梭菌目相关的生物参与苯的降解，可能通过发酵进行，并且还大量使用碳酸盐作为碳源。其他生物种群被发现具有多种功能，Delta 变形菌门降解发酵产物，拟杆菌门/Chlorobi 是可能以死细胞为食的清道夫。鉴定出的蛋白质的功能分类支持这种分配，并进一步深入了解代谢途径和群落成员之间的相互作用。这个例子展示了如何应用 protein-SIP 来获得微生物群落中功能相互依存关系的时间和系统发育信息。
