Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms
Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms
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DOI：
10.1016/j.mimet.2021.106401
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发表时间：
2022-02-01
影响因子：
2.2
通讯作者：
Thelusmond, Jean-Rene
中科院分区：
文献类型：
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作者：
Cupples, Alison M.;Thelusmond, Jean-Rene
共代谢氧化涉及通常通过单加氧酶或双加氧酶对化学物质的氧化，并且可以是三氯乙烯（TCE）或1，4-二氧六环等环境污染物的去除过程。关于这些基因及其相关微生物在环境样品中的出现的信息有可能提高我们对污染物去除的理解。总体目标是1）确定编码单加氧酶（来自甲烷氧化菌、氨氧化细菌和甲苯/苯酚氧化菌）和其他关键酶的基因存在于土壤微宇宙中，2）确定哪些酶类型与这些基因相关。该方法涉及称为PICRUSt 2的预测工具和来自先前两个土壤微宇宙研究的16 S rRNA基因扩增子数据集。检查了KEGG数据库中的以下靶点：pmo/amo、mmo、dmp/pox/tomA、tmo/tbu/tou、bssABC（和下游基因）、tod、xylM、xylA、gst、dhaA、catE、dbfA 1、dbfA 2和苯酚2-单加氧酶。大量系统型与pmo/amo相关，而mmo仅与五个相关。几种类型的pmo/amo和mmo相关。对mmoX预测的最主要的微生物是分枝杆菌（也对pmo/amo预测）。大量的p53型与来自dmp/pox/tomA KEGG组的所有六个基因相关。预测的tmo/tbu/tou KEGG组的分类学关联更为有限。在这两个数据集中，Gestrin是苄基琥珀酸合酶的关键酶类型。由todC 1C 2BA编码的双加氧酶介导的甲苯降解途径在很大程度上不存在，编码二甲苯单加氧酶的基因（xylM，xylA）也是如此。所有其他研究的基因都被预测存在，并与许多微生物相关。总体而言，分析预测，与编码pMMO/AMO（pmo/amo）和苯酚单加氧酶/T2 MO（dmp/poxA/tomA）的基因相比，编码sMMO（mmo）、T3 MO/T3 MO/ToMO（tmo/tbu/tou）和苄基琥珀酸合酶（bssABC）的基因存在于有限数量的cDNA类型中。这些研究结果表明，在土壤中通过pMMO/AMO或苯酚单加氧酶/T2 MO的污染物去除可能是常见的，因为这些酶的发生与大量的酶类型。
Cometabolic oxidation involves the oxidation of chemicals often by monooxygenases or dioxygenases and can be a removal process for environmental contaminants such as trichloroethene (TCE) or 1,4-dioxane. Information on the occurrence of these genes and their associated microorganisms in environmental samples has the potential to enhance our understanding of contaminant removal. The overall aims were to 1) ascertain which genes encoding for monooxygenases (from methanotrophs, ammonia oxidizing bacteria and toluene/phenol oxidizers) and other key enzymes are present in soil microcosms and 2) determine which phylotypes are associated with those genes.The approach involved a predictive tool called PICRUSt2 and 16S rRNA gene amplicon datasets from two previous soil microcosm studies. The following targets from the KEGG database were examined: pmo/amo, mmo, dmp/pox/tomA, tmo/tbu/tou, bssABC (and downstream genes), tod, xylM, xylA, gst, dhaA, catE, dbfA1, dbfA2 and phenol 2-monooxygenase.A large number of phylotypes were associated with pmo/amo, while mmo was linked to only five. Several phylotypes were associated with both pmo/amo and mmo. The most dominant microorganism predicted for mmoX was Mycobacterium (also predicted for pmo/amo). A large number of phylotypes were associated with all six genes from the dmp/pox/tomA KEGG group. The taxonomic associations predicted for the tmo/tbu/tou KEGG group were more limited. In both datasets, Geobacter was a key phylotype for benzylsuccinate synthase. The dioxygenase-mediated toluene degradation pathway encoded by todC1C2BA was largely absent, as were the genes (xylM, xylA) encoding for xylene monooxygenase. All other genes investigated were predicted to be present and were associated with a number of microorganisms. Overall, the analysis predicted the genes encoding for sMMO (mmo), T3MO/T3MO/ToMO (tmo/tbu/tou) and benzylsuccinate synthase (bssABC) are present for a limited number of phylotypes compared to those encoding for pMMO/AMO (pmo/amo) and phenol monooxygenase/T2MO (dmp/poxA/tomA). These findings suggest in soils contaminant removal via pMMO/AMO or phenol monooxygenase/T2MO may be common because of the occurrence of these enzymes with a large number of phylotypes.