Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China.
Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
Mol Ecol. 2024 Sep;33(18):e17507. doi: 10.1111/mec.17507. Epub 2024 Aug 19.
Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.
反硝化作用是全球氮循环中的一个关键过程，其中两个功能等效的基因nirS 和 nirK 催化了关键反应，通常被用作标记基因。nirK 基因可以独立发挥作用，而 nirS 需要额外的基因来编码亚硝酸盐还原酶，并且比 nirK 对环境因素更敏感。然而，那些反硝化微生物群落的生态分化机制及其对环境胁迫的适应策略仍不清楚。在这里，我们对来自中国东湖的沉积物和生物反应器样本进行了宏基因组分析。我们发现，nirS 型反硝化群落的水平基因转移频率明显低于 nirK 型反硝化群落，并且 nirS 基因系统发育与分类学更一致，而 nirK 基因则不一致。对宏基因组组装基因组的代谢重建进一步表明，nirS 型反硝化群落具有强大的能量守恒代谢系统，使它们能够在环境胁迫下存活。然而，nirK 型反硝化群落似乎能够适应缺氧环境，具有利用各种碳和氮化合物的能力。因此，本研究为 nirS 和 nirK 型反硝化群落的生态分化机制以及全球氮循环和温室气体排放的调控提供了新的见解。
