Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data.
Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data.
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DOI：
10.3389/fmicb.2015.01270
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发表时间：
2015
影响因子：
5.2
通讯作者：
Ferrer M
中科院分区：
文献类型：
--
作者：
Bargiela R;Gertler C;Magagnini M;Mapelli F;Chen J;Daffonchio D;Golyshin PN;Ferrer M
使用不同氮源的生物刺激通常被认为是防治海洋环境中漏油的一种选择策略。这种环境通常会耗尽氮，因此限制了微生物对富含碳的石油成分的平衡利用。分析应用生物刺激剂的分解代谢后果是基本的，但很少被考虑到。在这里，我们使用长期受到原油污染的意大利安科纳港海洋沉积物中的沉积物，经天然肥料、尿酸(UA)或铵(AMM)修正，研究了浓缩微宇宙中的这种变化。我们应用基于网络的AromaDeg资源，使用Illumina HiSeq元序列(UA：27,893个开放阅读框架；AMM：32,180个)作为查询，以确定潜在的分解代谢差异。共有45个(UA)和65个(AMM)编码关键分解代谢酶的基因序列与AromaDeg匹配，它们参与了芳香族降解反应。降解2-氯苯甲酸酯、吲哚-3-乙酸酯、联苯、龙胆酸盐、喹啉和菲等芳香族化合物的基因组特征在这两个微观世界中都是共同的。而对地衣酚、布洛芬、苯丙酸酯、高原儿茶酸盐和苯(在尿酸中)和对氨基苯磺酸盐(在AMM中)、二苯并呋喃和邻苯二甲酸酯(在AMM中)的降解则被选择性地富集。进行了实验验证，并观察到与预测很好地吻合。这表明这些生物刺激剂对石油组分或芳烃污染物分解代谢的初始微生物群落的基因组含量的作用存在一定的差异。在这两个案例中，新出现的微生物群落在系统发育上高度相似，并且由非常相同的蛋白细菌家族组成。然而，对分类任务的检查进一步揭示了生物水平上不同的分解代谢途径组织，这应该被考虑到在设计海上溢油缓解策略时。
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.