Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities

IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yuzhen Ming, Mamun Abdullah Al, Dandan Zhang, Wengen Zhu, Huanping Liu, Lanlan Cai, Xiaoli Yu, Kun Wu, Mingyang Niu, Qinglu Zeng, Zhili He, Qingyun Yan
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Abstract

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.

洞察 nirS 型和 nirK 型反硝化群落的进化和生态适应策略。
反硝化作用是全球氮循环中的一个关键过程,其中两个功能相当的基因 nirS 和 nirK 催化了这一关键反应,通常被用作标记基因。nirK 基因可以独立发挥作用,而 nirS 则需要额外的基因来编码亚硝酸还原酶,并且对环境因素比 nirK 更敏感。然而,这些反硝化微生物群落的生态分化机制及其对环境压力的适应策略仍不清楚。在此,我们对中国东湖的沉积物和生物反应器样本进行了元基因组分析。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,而且 nirS 基因的系统发育与分类学的一致性高于 nirK 基因。元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,使其能够在环境压力下生存。然而,nirK 型反硝化群落似乎能适应氧气有限的环境,具有利用各种碳氮化合物的能力。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。
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来源期刊
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
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