Zhihua Bao, Jing Cui, Jumei Liu, Meng Zhang, Linxia Chen, Weiwei Cao, Ke Yu, Lixin Wang, Zhongjun Jia, Ji Zhao
{"title":"通过转录组分析揭示葭根组织中固氮作用与甲烷氧化作用之间的耦合关系","authors":"Zhihua Bao, Jing Cui, Jumei Liu, Meng Zhang, Linxia Chen, Weiwei Cao, Ke Yu, Lixin Wang, Zhongjun Jia, Ji Zhao","doi":"10.1007/s00374-024-01869-y","DOIUrl":null,"url":null,"abstract":"<p>The root-associated type II methanotrophs significantly contribute to CH<sub>4</sub> oxidation-dependent N<sub>2</sub> fixation. However, it is unclear whether type I methanotrophs are involved in CH<sub>4</sub> oxidation and N<sub>2</sub> fixation, especially in natural wetlands. So far, limited attention has given to root-associated active microorganisms. Here, metatranscriptomic analysis of root-associated microbes has been proposed to reveal the aerobic methanotrophs contributing to CH<sub>4</sub> and nitrogen cycles in the roots of <i>Phragmites australis</i> grown in a natural wetland. Results showed Methylocystaceae (type II methanotrophs) and Methylococcaceae (type I methanotrophs) as major taxa (relative abundance, 14%) at transcription level. However, based on 16S rRNA gene sequencing, contribution of these taxa was < 1% at DNA level. Genes encoding methane monooxygenase (enzyme responsible for the first step of CH<sub>4</sub> oxidation) were detected in <i>Methylomonas</i> (<i>pmoCBA</i>) and <i>Methylosinus</i> (<i>mmoXYZCB</i>). Furthermore, genes related to methanol dehydrogenase, formaldehyde dehydrogenase, and formate dehydrogenase were also detected in <i>Methyosinus</i> and <i>Methylomonas</i>, while <i>mcrA</i> gene was observed in <i>Methanospirillum</i> and <i>Methanofollis</i>. Moreover, nitrogenase structural genes, such as <i>nifHDK,</i> were found in <i>Methylosinus</i> (Methylocystaceae) and <i>Methylomonas</i> (Methylococcaceae). Minor nitrogenase genes were detected in <i>Cyanothece</i>, <i>Lyngbya</i>, <i>Pelobacter</i> and <i>Smithella</i> of Cyanobacteriaceae family. In addition, N<sub>2</sub> fixing activity of <i>P. australis</i> was determined by analyzing the natural abundance of δ<sup>15</sup>N from June to August. The N<sub>2</sub> fixing activity of <i>P. australis</i> increased in presence of CH<sub>4</sub> in root system under <sup>15</sup>N-N<sub>2</sub> feeding. Metatranscriptomic analysis revealed that not only type II methanotrophs, but also type I methanotrophs oxidize CH<sub>4</sub> and fix N<sub>2</sub>.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"11 1","pages":""},"PeriodicalIF":5.1000,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Metatranscriptomic analysis to reveal the coupling between nitrogen fixation and CH4 oxidation in root tissues of Phragmites australis\",\"authors\":\"Zhihua Bao, Jing Cui, Jumei Liu, Meng Zhang, Linxia Chen, Weiwei Cao, Ke Yu, Lixin Wang, Zhongjun Jia, Ji Zhao\",\"doi\":\"10.1007/s00374-024-01869-y\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The root-associated type II methanotrophs significantly contribute to CH<sub>4</sub> oxidation-dependent N<sub>2</sub> fixation. However, it is unclear whether type I methanotrophs are involved in CH<sub>4</sub> oxidation and N<sub>2</sub> fixation, especially in natural wetlands. So far, limited attention has given to root-associated active microorganisms. Here, metatranscriptomic analysis of root-associated microbes has been proposed to reveal the aerobic methanotrophs contributing to CH<sub>4</sub> and nitrogen cycles in the roots of <i>Phragmites australis</i> grown in a natural wetland. Results showed Methylocystaceae (type II methanotrophs) and Methylococcaceae (type I methanotrophs) as major taxa (relative abundance, 14%) at transcription level. However, based on 16S rRNA gene sequencing, contribution of these taxa was < 1% at DNA level. Genes encoding methane monooxygenase (enzyme responsible for the first step of CH<sub>4</sub> oxidation) were detected in <i>Methylomonas</i> (<i>pmoCBA</i>) and <i>Methylosinus</i> (<i>mmoXYZCB</i>). Furthermore, genes related to methanol dehydrogenase, formaldehyde dehydrogenase, and formate dehydrogenase were also detected in <i>Methyosinus</i> and <i>Methylomonas</i>, while <i>mcrA</i> gene was observed in <i>Methanospirillum</i> and <i>Methanofollis</i>. Moreover, nitrogenase structural genes, such as <i>nifHDK,</i> were found in <i>Methylosinus</i> (Methylocystaceae) and <i>Methylomonas</i> (Methylococcaceae). Minor nitrogenase genes were detected in <i>Cyanothece</i>, <i>Lyngbya</i>, <i>Pelobacter</i> and <i>Smithella</i> of Cyanobacteriaceae family. In addition, N<sub>2</sub> fixing activity of <i>P. australis</i> was determined by analyzing the natural abundance of δ<sup>15</sup>N from June to August. The N<sub>2</sub> fixing activity of <i>P. australis</i> increased in presence of CH<sub>4</sub> in root system under <sup>15</sup>N-N<sub>2</sub> feeding. Metatranscriptomic analysis revealed that not only type II methanotrophs, but also type I methanotrophs oxidize CH<sub>4</sub> and fix N<sub>2</sub>.</p>\",\"PeriodicalId\":9210,\"journal\":{\"name\":\"Biology and Fertility of Soils\",\"volume\":\"11 1\",\"pages\":\"\"},\"PeriodicalIF\":5.1000,\"publicationDate\":\"2024-10-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Biology and Fertility of Soils\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1007/s00374-024-01869-y\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"SOIL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biology and Fertility of Soils","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s00374-024-01869-y","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"SOIL SCIENCE","Score":null,"Total":0}
引用次数: 0
摘要
与根相关的 II 型甲烷营养体对依赖于 CH4 氧化的 N2 固定有很大贡献。然而,目前还不清楚 I 型甲烷营养体是否参与了 CH4 氧化和 N2 固定,尤其是在自然湿地中。迄今为止,人们对与根相关的活性微生物关注有限。本文通过对根相关微生物的元转录组学分析,揭示了生长在天然湿地中的葭萌植物根系中促进 CH4 和氮循环的需氧甲烷营养体。结果表明,在转录水平上,甲囊菌科(II 型甲烷营养体)和甲球菌科(I 型甲烷营养体)是主要类群(相对丰度为 14%)。然而,根据 16S rRNA 基因测序,这些类群在 DNA 水平上的贡献率为 1%。在甲基单胞菌(pmoCBA)和甲基单胞菌(mmoXYZCB)中检测到了编码甲烷单氧化酶(负责 CH4 氧化第一步的酶)的基因。此外,在甲基单胞菌(Methylosinus)和甲基单胞菌(Methylomonas)中还检测到与甲醇脱氢酶、甲醛脱氢酶和甲酸脱氢酶有关的基因,而在甲烷螺旋体(Methanospirillum)和甲烷磷脂菌(Methanofollis)中则观察到 mcrA 基因。此外,在甲基单胞菌(Methylocystaceae)和甲基单胞菌(Methylococcaceae)中发现了氮酶结构基因,如 nifHDK。在蓝藻科的 Cyanothece、Lyngbya、Pelobacter 和 Smithella 中发现了次要的氮酶基因。此外,通过分析 6 月至 8 月δ15N 的自然丰度,确定了 P. australis 的 N2 固定活性。在15N-N2喂养条件下,当根系中存在CH4时,奥氏囊藻的N2固定活性增加。转录组分析表明,不仅 II 型甲烷营养体,I 型甲烷营养体也氧化 CH4 并固定 N2。
Metatranscriptomic analysis to reveal the coupling between nitrogen fixation and CH4 oxidation in root tissues of Phragmites australis
The root-associated type II methanotrophs significantly contribute to CH4 oxidation-dependent N2 fixation. However, it is unclear whether type I methanotrophs are involved in CH4 oxidation and N2 fixation, especially in natural wetlands. So far, limited attention has given to root-associated active microorganisms. Here, metatranscriptomic analysis of root-associated microbes has been proposed to reveal the aerobic methanotrophs contributing to CH4 and nitrogen cycles in the roots of Phragmites australis grown in a natural wetland. Results showed Methylocystaceae (type II methanotrophs) and Methylococcaceae (type I methanotrophs) as major taxa (relative abundance, 14%) at transcription level. However, based on 16S rRNA gene sequencing, contribution of these taxa was < 1% at DNA level. Genes encoding methane monooxygenase (enzyme responsible for the first step of CH4 oxidation) were detected in Methylomonas (pmoCBA) and Methylosinus (mmoXYZCB). Furthermore, genes related to methanol dehydrogenase, formaldehyde dehydrogenase, and formate dehydrogenase were also detected in Methyosinus and Methylomonas, while mcrA gene was observed in Methanospirillum and Methanofollis. Moreover, nitrogenase structural genes, such as nifHDK, were found in Methylosinus (Methylocystaceae) and Methylomonas (Methylococcaceae). Minor nitrogenase genes were detected in Cyanothece, Lyngbya, Pelobacter and Smithella of Cyanobacteriaceae family. In addition, N2 fixing activity of P. australis was determined by analyzing the natural abundance of δ15N from June to August. The N2 fixing activity of P. australis increased in presence of CH4 in root system under 15N-N2 feeding. Metatranscriptomic analysis revealed that not only type II methanotrophs, but also type I methanotrophs oxidize CH4 and fix N2.
期刊介绍:
Biology and Fertility of Soils publishes in English original papers, reviews and short communications on all fundamental and applied aspects of biology – microflora and microfauna - and fertility of soils. It offers a forum for research aimed at broadening the understanding of biological functions, processes and interactions in soils, particularly concerning the increasing demands of agriculture, deforestation and industrialization. The journal includes articles on techniques and methods that evaluate processes, biogeochemical interactions and ecological stresses, and sometimes presents special issues on relevant topics.