Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
J Microbiol Methods. 2022 Nov;202:106595. doi: 10.1016/j.mimet.2022.106595. Epub 2022 Oct 5.
This study examined soil, sediment and groundwater microbial communities for a set of key functional genes important for contaminant biodegradation. This involved PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) predictions based on 16S rRNA gene amplicon datasets from three separate studies with different inocula and incubation conditions, as follows: aerobic soils, oxygen-limited microcosms containing sediments and groundwater, as well as methanogenic microcosms with different inocula. PICRUSt2 predicts functional profiles of microbial communities based on marker gene (16S rRNA gene) data. The relative abundances of genera previously associated with the biodegradation of chlorinated solvents/metabolites and/or 1,4-dioxane were also determined. Predicted values for each functional gene varied between the three datasets. In all, values were high for propane monooxygenase and low for soluble methane monooxygenase. Common phylotypes associated with propane monooxygenase in two of the three datasets included Mycobacterium, Rhodococcus and Pseudonocardia. Toluene monooxygenase predicted values were greater in the oxygen-limited microcosms compared to the other two datasets. The methanogenic microcosms exhibited the highest predicted values for particulate methane/ammonia monooxygenase. The most common genera detected, previously reported as chlorinated solvents/metabolites and/or 1,4-dioxane degraders, included Pseudomonas, Sphingomonas, Rhodococcus and Rhodanobacter. Eighteen of the queried genera were not detected. As expected, more potential anaerobic degrading genera were found in the oxygen-limited and methanogenic microcosms compared to the aerobic soils. The results provide key insights as to which genes and genera may be important for biodegradation over a range of inocula and redox conditions.
本研究检测了土壤、沉积物和地下水微生物群落中一组重要的污染物生物降解关键功能基因。这涉及基于三个不同接种和孵育条件的独立研究的 16S rRNA 基因扩增子数据集的 PICRUSt2（基于未观察状态重建的群落系统发育分析）预测，如下所示：有氧土壤、含沉积物和地下水的氧限制微宇宙，以及具有不同接种物的产甲烷微宇宙。PICRUSt2 根据标记基因（16S rRNA 基因）数据预测微生物群落的功能谱。还确定了先前与氯化溶剂/代谢物和/或 1,4-二恶烷生物降解相关的属的相对丰度。三个数据集之间每个功能基因的预测值都有所不同。总的来说，丙烷单加氧酶的预测值较高，而可溶性甲烷单加氧酶的预测值较低。与三个数据集中的两个数据集的丙烷单加氧酶相关的常见类群包括分枝杆菌、红球菌和假诺卡氏菌。与其他两个数据集相比，氧限制微宇宙中预测的甲苯单加氧酶值较高。产甲烷微宇宙表现出最高的颗粒状甲烷/氨单加氧酶预测值。检测到的最常见的属，先前报道为氯化溶剂/代谢物和/或 1,4-二恶烷降解菌，包括假单胞菌、鞘氨醇单胞菌、红球菌和罗得氏杆菌。查询的 18 个属未被检测到。正如预期的那样，与有氧土壤相比，在氧限制和产甲烷微宇宙中发现了更多潜在的厌氧降解属。这些结果为在一系列接种物和氧化还原条件下哪些基因和属可能对生物降解很重要提供了关键见解。
