Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China.
Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
Environ Microbiol. 2022 Jan;24(1):390-403. doi: 10.1111/1462-2920.15882. Epub 2021 Dec 28.
Marine intertidal sediments fluctuate in redox conditions and nutrient availability, and they are also known as an important sink of nitrogen mainly through denitrification, yet how denitrifying bacteria adapt to this dynamic habitat remains largely untapped. Here, we investigated novel intertidal benthic ecotypes of the model pelagic marine bacterium Ruegeria pomeroyi DSS-3 with a population genomic approach. While differing by only 1.3% at the 16S rRNA gene level, members of the intertidal benthic ecotypes are complete denitrifiers whereas the pelagic ecotype representative (DSS-3) is a partial denitrifier lacking a nitrate reductase. The intertidal benthic ecotypes are further differentiated by using non-homologous nitrate reductases and a different set of genes that allow alleviating oxidative stress and acquiring organic substrates. In the presence of nitrate, the two ecotypes showed contrasting growth patterns under initial oxygen concentrations at 1 vol% versus 7 vol% and supplemented with different carbon sources abundant in intertidal sediments. Collectively, this combination of evidence indicates that there are cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria. This knowledge will in turn help understand how these benthic environments operate to effectively remove nitrogen.
海洋潮间带沉积物的氧化还原条件和养分可用性会发生波动，它们也是氮的一个重要汇，主要通过反硝化作用实现，但硝化细菌如何适应这种动态生境在很大程度上仍未被开发。在这里，我们采用种群基因组学的方法研究了模型海洋浮游细菌 Ruegeria pomeroyi DSS-3 的新型潮间带底栖生态型。尽管在 16S rRNA 基因水平上只存在 1.3%的差异，但潮间带底栖生态型的成员是完全的反硝化细菌，而浮游生态型代表（DSS-3）是缺乏硝酸还原酶的部分反硝化细菌。通过使用非同源硝酸盐还原酶和一组不同的基因，潮间带底栖生态型进一步分化，这些基因可以缓解氧化应激并获取有机底物。在硝酸盐存在的情况下，两种生态型在初始氧气浓度为 1%与 7%以及补充潮间带沉积物中丰富的不同碳源的情况下表现出截然不同的生长模式。总的来说，这些证据表明，沿海潮间带沉积物中存在隐藏的小生境，支持硝化细菌的分歧进化。这一知识反过来将有助于了解这些底栖环境如何有效地去除氮。
