Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural Universitygrid.27871.3b, Nanjing, China.
Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
Appl Environ Microbiol. 2021 Oct 28;87(22):e0156221. doi: 10.1128/AEM.01562-21. Epub 2021 Sep 15.
-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in -dichlorprop degradation. However, the compositions of the microbial consortia involved in -dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for -dichlorprop degradation in a -dichlorprop-degrading enrichment. OTU340 ( sp.) and OTU348 ( sp.) were significantly enriched in the -[C]dichlorprop-labeled heavy DNA fractions. A -dichlorprop degrader, sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between -dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes and , involved in the initial degradation of the ()- and ()-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to species, indicating that species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as , , Pseudomonas, and were presumed to synergistically cooperate with the key degraders for enhanced degradation of -dichlorprop. Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide -dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of -dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders , , Pseudomonas, and synergistically cooperated with the key degraders / for enhanced degradation of -dichlorprop. Our study provides new insights into the synergistic degradation of -dichlorprop at the community level and implies the existence of novel degrading genes for -dichlorprop in nature.
-Dichlorprop，一种常用的苯氧羧酸类除草剂，经常在环境中被检测到，对环境安全和人类健康构成威胁。微生物群落被认为在 -dichlorprop 降解中起着关键作用。然而，参与 -dichlorprop 降解的微生物群落的组成在很大程度上仍然未知。在这项研究中，DNA 稳定同位素探针 (SIP) 和宏基因组分析相结合，揭示了在 -dichlorprop 降解富集物中负责 -dichlorprop 降解的关键微生物群落。OTU340（sp.）和 OTU348（sp.）在 -[C]dichlorprop 标记的重 DNA 部分中明显富集。通过传统的富集方法从富集物中分离出一种 -dichlorprop 降解菌， sp. 菌株 L3，但在宏基因组分析指导下，还额外补充了抗生素环丙沙星，该抗生素与 -dichlorprop 降解菌和抗生素抗性基因之间的关联有关。通过重 DNA 的功能谱分析，最初降解（）-和（）-dichlorprop 对映体的基因 和 ，主要在分类上被分配到 种，表明 种可能含有新的 -dichlorprop 降解基因。此外，假定分类多样化的细菌属，如 、 、Pseudomonas 和 ，与关键降解菌 协同合作，增强对 -dichlorprop 的降解。 了解参与苯氧羧酸类除草剂 -dichlorprop 降解的关键微生物群落对于设计用于增强受除草剂污染场地生物修复的协同菌群至关重要。然而，微生物群落的组成以及在 -dichlorprop 生物降解过程中群落成员之间的相互作用尚不清楚。在这项研究中，DNA-SIP 和宏基因组分析相结合，揭示了代谢物 2,4-二氯苯酚降解菌 、 、Pseudomonas 和 与关键降解菌 / 协同合作，增强对 -dichlorprop 的降解。我们的研究为社区水平上 -dichlorprop 的协同降解提供了新的见解，并暗示自然界中存在用于 -dichlorprop 的新型降解基因。
