1Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan.
2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565 Japan.
Commun Biol. 2019 May 13;2:179. doi: 10.1038/s42003-019-0418-2. eCollection 2019.
Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.
尽管宏基因组学研究已经揭示了众多生物圈中的微生物多样性，但由于生态系统的复杂性，理解单个微生物的功能仍然很困难。为了解决这个问题，我们采用了一种非依赖于宏基因组、基于从头组装的宏转录组学方法来研究复杂的微生物群落——活性污泥，它已经被用于污水处理超过一个世纪。尽管两个生物反应器在相同的条件下运行，但它们的性能却因未知原因而有所不同。在高性能和低性能反应器中的宏转录组谱表明，反硝化菌有助于重油的厌氧降解；然而，在基因表达方面并没有发现明显的差异。相反，只有在高性能反应器中，基于基因表达的硝化作用活动才会显著增加，为反硝化菌提供呼吸底物。少数相对丰度<0.25%的硝化菌控制着反应器对重油的降解性能，揭示了复杂微生物群落中碳氮代谢的意外联系。
