Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.
Appl Microbiol Biotechnol. 2022 Jan;106(2):835-853. doi: 10.1007/s00253-021-11756-3. Epub 2022 Jan 11.
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 included Pseudomonas, Methylotenera, Rhodococcus, Stenotrophomonas, and Brevundimonas, and the most abundant for the groundwater/microcosms included Pseudomonas, Cupriavidus, Azospira, Rhodococcus, and unclassified Burkholderiaceae. 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: unclassified Burkholderiaceae, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Rhodococcus, unclassified Betaproteobacteria, and Polaromonas. 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.
本研究的目的是预测与有机污染物生物降解相关的基因，并研究两个污染地点样本中的微生物群落结构。该方法涉及一种针对 12 种 KEGG 异生物降解途径（苯甲酸、氯烷烃和氯烯烃、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 代谢异生物）的基因的预测生物信息学工具（PICRUSt2）。此外，还确定了与每个途径早期功能基因相关的预测类群。系统发育分析表明，沉积物中的多样性高于地下水样本。沉积物/微宇宙中最丰富的属包括假单胞菌、甲基营养菌、红球菌、寡养单胞菌和 Brevundimonas，而地下水/微宇宙中最丰富的属包括假单胞菌、铜绿假单胞菌、节旋菌、红球菌和未分类的伯克霍尔德氏菌科。预测到所有 12 种 KEGG 途径都存在基因。有 7 种途径的基因少于 25 个。预测基因最低的是细胞色素 P450 代谢异生物和乙苯生物降解，最高的是苯甲酸生物降解。值得注意的趋势包括出现了三硝基甲苯和 2,4-二硝基甲苯降解的第一个基因。此外，还预测了从甲苯到苯甲酰辅酶 A 的完整途径。预测了 22 种二恶英途径基因，包括前几个步骤的基因。与最多途径相关的类群包括：未分类的伯克霍尔德氏菌科、伯克霍尔德氏菌-卡巴列罗尼亚-副伯克霍尔德氏菌、假单胞菌、红球菌、未分类的β变形菌和极性单胞菌。这项工作说明了 PICRUSt2 预测生物降解潜力的价值，并表明一小部分类群可能对有机污染物或其代谢物的分解很重要。要点：• 该方法是一种比 shotgun 测序成本更低的替代方法。• 预测了编码异生物降解的基因和类群。• 与许多途径相关的一小部分类群。
