Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated Naval Sites
Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated Naval Sites
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两个受污染海军基地地下水和沉积物中异生物质生物降解的预测功能基因
DOI：
10.1007/s00253-021-11756-3
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发表时间：
2022
影响因子：
5
通讯作者：
Cupples, Alison M.
中科院分区：
文献类型：
--
作者：
Vera, Andrea;Paes Wilson, Fernanda;Cupples, Alison M.
本研究的目的是预测与有机污染物的生物降解相关的基因，并检查从两个污染场地的样品中的微生物群落结构。该方法涉及一种预测生物信息学工具（PICRUSt 2），靶向来自12个KEGG异生物质生物降解途径（苯甲酸酯、氯代烷烃和氯代烯烃、氯代环己烷和氯苯、甲苯、二甲苯、硝基甲苯、乙苯、苯乙烯、二恶英、萘、多环芳烃和细胞色素P450对异生物质的代谢）的基因。此外，确定了与每个途径中早期的功能基因相关的预测的转录因子类型。系统发育分析表明，在沉积物中的地下水样品相比，更大的多样性。沉积物/微宇宙中最丰富的属包括假单胞菌属、Methylotenera属、红球菌属、寡养单胞菌属和Brevundimonas属，地下水/微宇宙中最丰富的属包括假单胞菌属、贪铜菌属、固氮螺菌属、红球菌属和未分类的伯克霍尔德菌科。来自所有12个KEGG途径的基因被预测发生。七条通路包含的基因少于25个。预测的基因最低的外源物质代谢细胞色素P450和苯甲酸酯的生物降解和最高的生物降解。值得注意的趋势包括第一个三硝基甲苯和2，4-二硝基甲苯降解基因的出现。此外，预测了从甲苯到苯甲酰-CoA的完整路径。预测了22个二恶英途径基因，包括第一步中的基因。以下几种类型与最多的通路相关：未分类伯克霍尔德氏菌科，伯克霍尔德氏菌属-Caballeronia-副伯克霍尔德氏菌属，假单胞菌属，红球菌属，未分类β-变形菌，这项工作说明了PICRUSt 2预测生物降解潜力的价值，并表明一个亚类的微生物类型可能对有机污染物或其代谢物的分解很重要。鸟枪测序的成本替代方案。预测了编码异生物质降解的基因和基因型。一个亚类的ESTA类型与许多途径。
The goals of this study were to predict the genes associated with the biodegradation of organic contaminants and to examine microbial community structure in samples from two contaminated sites. The approach involved a predictive bioinformatics tool (PICRUSt2) targeting genes from twelve KEGG xenobiotic biodegradation pathways (benzoate, chloroalkane and chloroalkene, chlorocyclohexane and chlorobenzene, toluene, xylene, nitrotoluene, ethylbenzene, styrene, dioxin, naphthalene, polycyclic aromatic hydrocarbons, and metabolism of xenobiotics by cytochrome P450). Further, the predicted phylotypes associated with functional genes early in each pathway were determined. Phylogenetic analysis indicated a greater diversity in the sediment compared to the groundwater samples. The most abundant genera for sediments/microcosms includedPseudomonas,Methylotenera,Rhodococcus,Stenotrophomonas, andBrevundimonas, and the most abundant for the groundwater/microcosms includedPseudomonas,Cupriavidus,Azospira,Rhodococcus, and unclassifiedBurkholderiaceae. Genes from all twelve of the KEGG pathways were predicted to occur. Seven pathways contained less than twenty-five genes. The predicted genes were lowest for xenobiotics metabolism by cytochrome P450 and ethylbenzene biodegradation and highest for benzoate biodegradation. Notable trends include the occurrence of the first genes for trinitrotoluene and 2,4-dinitrotoluene degradation. Also, the complete path from toluene to benzoyl-CoA was predicted. Twenty-two of the dioxin pathway genes were predicted, including genes within the first steps. The following phylotypes were associated with the greatest number of pathways: unclassifiedBurkholderiaceae,Burkholderia-Caballeronia-Paraburkholderia,Pseudomonas,Rhodococcus, unclassifiedBetaproteobacteria, andPolaromonas.This work illustrates the value of PICRUSt2 for predicting biodegradation potential and suggests that a subset of phylotypes could be important for the breakdown of organic contaminants or their metabolites.Key points• The approach is a low-cost alternative to shotgun sequencing.• The genes and phylotypes encoding for xenobiotic degradation were predicted.• A subset of phylotypes were associated with many pathways.