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
{"title":"洞察 nirS 型和 nirK 型反硝化群落的进化和生态适应策略。","authors":"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","doi":"10.1111/mec.17507","DOIUrl":null,"url":null,"abstract":"<p>Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, <i>nirS</i> and <i>nirK</i>, catalyse the critical reaction and are usually used as marker genes. The <i>nirK</i> gene can function independently, whereas <i>nirS</i> requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than <i>nirK</i>. 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 <i>nirS</i>-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of <i>nirK</i>-type denitrifying communities, and <i>nirS</i> gene phylogeny was more congruent with taxonomy than that of <i>nirK</i> gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that <i>nirS</i>-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, <i>nirK</i>-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 <i>nirS</i> and <i>nirK</i>-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5000,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities\",\"authors\":\"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\",\"doi\":\"10.1111/mec.17507\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, <i>nirS</i> and <i>nirK</i>, catalyse the critical reaction and are usually used as marker genes. The <i>nirK</i> gene can function independently, whereas <i>nirS</i> requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than <i>nirK</i>. 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 <i>nirS</i>-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of <i>nirK</i>-type denitrifying communities, and <i>nirS</i> gene phylogeny was more congruent with taxonomy than that of <i>nirK</i> gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that <i>nirS</i>-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, <i>nirK</i>-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 <i>nirS</i> and <i>nirK</i>-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.</p>\",\"PeriodicalId\":210,\"journal\":{\"name\":\"Molecular Ecology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.5000,\"publicationDate\":\"2024-08-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Ecology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/mec.17507\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Ecology","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/mec.17507","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities
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.
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