Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. U. 1, 2100, Gödöllő, Hungary.
Group for Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Universitäts Str. 5, 45141, Essen, Germany.
Environ Sci Pollut Res Int. 2023 Mar;30(15):44518-44535. doi: 10.1007/s11356-022-24975-6. Epub 2023 Jan 24.
Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l. The results indicated that most probably diclofenac biodegrading cultures consisted of members of genera Ferrovibrio, Hydrocarboniphaga, Zavarzinia, and Sphingopyxis, while in ibuprofen biodegradation Nocardioides and Starkeya, and in carbamazepine biodegradation Nocardioides, Pseudonocardia, and Sphingopyxis might be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. Except Starkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation. Stenotrophomonas humi DIC_5 and Rhizobium daejeonense IBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.
双氯芬酸、布洛芬和卡马西平是水生生态系统中检测到的最广泛和最令人关注的三种药物残留。本研究的目的是从细菌生物膜中鉴定可能参与其降解的细菌。在含有药物化合物作为唯一碳源和能源的无机盐溶液中设置选择性富集培养物，并使用鸟枪法宏基因组测序监测种群动态。使用基因组解析宏基因组学重建细菌基因组。获得了 30 个细菌分离株，在物种水平上进行了鉴定，并在 1.5mg/L 的初始浓度下测试了药物的生物降解性。结果表明，双氯芬酸生物降解培养物可能由 Ferrovibrio、Hydrocarboniphaga、Zavarzinia 和 Sphingopyxis 属的成员组成，而在布洛芬生物降解中 Nocardioides 和 Starkeya，在卡马西平生物降解中 Nocardioides、Pseudonocardia 和 Sphingopyxis 可能参与。在富集过程中，与初始状态相比，这些属的相对丰度百分比增加了三个数量级。除了 Starkeya 之外，这些细菌的基因组都被重建和注释。注释基因组的代谢分析表明，这些细菌携带有与药物生物降解相关的基因。 Stenotrophomonas humi DIC_5 和 Rhizobium daejeonense IBU_18 分离株在存在葡萄糖（3g/L）或 R2A 肉汤的情况下，在测试中消除了双氯芬酸和布洛芬。两种化合物的浓度都降低了 90%以上。
