Watahiki Saori, Kimura Nobutada, Yamazoe Atsushi, Miura Takamasa, Sekiguchi Yuji, Noda Naohiro, Matsukura Satoko, Kasai Daisuke, Takahata Yoh, Nojiri Hideaki, Fukuda Masao
Life Sciences and Bioengineering, Graduate School of Life and Environmental Science, University of Tsukuba.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
J Gen Appl Microbiol. 2019 Dec 19;65(5):225-233. doi: 10.2323/jgam.2018.10.003. Epub 2019 Mar 8.
Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.
生物修复可能会影响生物修复场地周围的生态系统。然而，对于在最初注入降解菌后微生物群落结构如何随时间变化，人们知之甚少。在本研究中，我们使用宏基因组学和宏转录组学方法评估了生物强化的生态影响，以去除由约氏红球菌RHA1菌株作为需氧化合物降解剂的三氯乙烯/顺式二氯乙烯（TCE/cDCE）。宏基因组分析表明，在注入点，属于红球菌属的生物体数量，包括RHA1菌株，从第0天占总微生物群落的0.1%增加到76.6%。随后，RHA1菌株和其他TCE/cDCE降解细菌的数量随时间逐渐减少，而厌氧脱氯剂地杆菌属和脱卤球菌属的数量在后期增加。宏转录组分析显示，在注入RHA1后，RHA1菌株中芳香族化合物降解基因（bphA1 - A4）的表达很高。从这些结果中，我们得出结论，直到第1天，TCE/cDCE的关键脱氯剂主要是需氧细菌，如RHA1，之后在注入井第6天后，关键脱氯剂转变为厌氧细菌，如地杆菌属和脱卤球菌属。基于α多样性，在注入RHA1菌株后，微生物群落的丰富度水平增加，并且在处理后的19天内微生物群落组成未恢复到原始组成。这些结果为评估生物修复场地中RHA1的生态影响和生物强化过程提供了见解。
