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学者姓名：余林鹏
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Abstract ：
Biological nitrogen fixation (BNF) as the primarily nitrogen supply for rice growth has lately been linked to Fe(III) reduction in paddy field. Rice root iron plaque (IP) is crucial in rhizosphere elements cycling and retaining pollutants, but the synergistic interaction between rhizospheric Fe cycle and BNF remains elusive. Herein, rice seedlings with and without IP on rice root were cultured under hydroponic conditions to explore the extent and the underlying mechanism of IP influencing BNF using acetylene reduction assay and N-15 labeling DNA-based stable isotope probing (DNA-SIP) combined with metagenomics. IP on rice root surface exhibited a diurnal Fe(III)/Fe(II) redox rhythm. In the presence of IP, the nifH gene abundance and nitrogenase activity were significantly increased by 1.15 x 10(8)similar to 1.15 x 10(11) copies/g.dw and 134 similar to 566 mu mol C2H4/(L.h), which enhanced the N-15 abundance in rice shoot and root by 36.4% and 23.1% and further facilitated 2.13 and 1.87 times more biomass accumulation than that without IP. The BNF activity was significantly inhibited by dissociating IP or breaking diurnal Fe redox rhythm. DNA-SIP revealed the enrichment of diazotrophic Azotobacter, Burkholderia, Phytobacter and Dechlormonas by IP and metagenomic binning identified the presence of genes related to BNF and extracellular electron transfer in such diazotrophs, suggesting their genetic potential to mediate synergetic BNF and Fe(III) reduction.
Keyword ：
Biological nitrogen fixation Biological nitrogen fixation DNA-SIP DNA-SIP Fe redox cycle Fe redox cycle Metagenomic binning Metagenomic binning Rice rhizosphere Rice rhizosphere
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| GB/T 7714 | Jia, Rong , Yu, Linpeng , Wang, Mengyi et al. Unveiling the crucial role of rice root iron plaque in enhancing biological nitrogen fixation via 15N-labeling DNA-SIP and metagenomics in a model study [J]. | BIOLOGY AND FERTILITY OF SOILS , 2025 , 61 (7) : 1183-1196 . |
| MLA | Jia, Rong et al. "Unveiling the crucial role of rice root iron plaque in enhancing biological nitrogen fixation via 15N-labeling DNA-SIP and metagenomics in a model study" . | BIOLOGY AND FERTILITY OF SOILS 61 . 7 (2025) : 1183-1196 . |
| APA | Jia, Rong , Yu, Linpeng , Wang, Mengyi , Wu, Yulu , Liu, Shiqi , Zhong, Sining et al. Unveiling the crucial role of rice root iron plaque in enhancing biological nitrogen fixation via 15N-labeling DNA-SIP and metagenomics in a model study . | BIOLOGY AND FERTILITY OF SOILS , 2025 , 61 (7) , 1183-1196 . |
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Abstract ：
Iron plaque (IP) on rice root surfaces has been extensively documented as a natural barrier that effectively reduces contaminant bioavailability and accumulation. However, its regulatory mechanisms in rhizospheric methane oxidation and biological nitrogen fixation (BNF) remain elusive. This study reveals a previously unrecognized function of IP: mediating methanotrophic nitrogen fixation through coupled aerobic methane oxidation and IP reduction (Fe-MOX). Using a hydroponic coculture system integrating methane-oxidizing bacteria and rice seedlings, we demonstrated that IP enhanced microbial methane oxidation by 46.8% and significantly stimulated BNF rate by 33.6%, with methane-derived carbon accounting for 89.1% of the BNF energy source. Notably, dissolved iron removal did not diminish the BNF enhancement, excluding mediation by soluble iron species. Intriguingly, ferrihydrite supplementation at equivalent iron concentrations failed to replicate the BNF stimulation observed with IP, suggesting the indispensability of root-associated iron redox cycling. Mechanistic analyses identified that Methylosinus/Methylocystis species mediated Fe(III) reduction, synergistically collaborating with specific rhizobial strains to execute Fe-MOX-dependent BNF. These findings uncover a previously overlooked yet pronounced contribution of IP to BNF, providing novel insights for developing dual-strategy approaches to mitigate methane emissions and reduce nitrogen fertilizer dependency in paddy ecosystems.
Keyword ：
iron oxyhydroxide plaque iron oxyhydroxide plaque metagenomic sequencing metagenomic sequencing methane-oxidizing bacteria methane-oxidizing bacteria nitrogen fixation nitrogen fixation
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| GB/T 7714 | Yu, Linpeng , Jia, Rong , Liu, Shiqi et al. Rice Root Iron Plaque as a Mediator to Stimulate Methanotrophic Nitrogen Fixation [J]. | ENVIRONMENTAL SCIENCE & TECHNOLOGY , 2025 , 59 (38) : 20411-20420 . |
| MLA | Yu, Linpeng et al. "Rice Root Iron Plaque as a Mediator to Stimulate Methanotrophic Nitrogen Fixation" . | ENVIRONMENTAL SCIENCE & TECHNOLOGY 59 . 38 (2025) : 20411-20420 . |
| APA | Yu, Linpeng , Jia, Rong , Liu, Shiqi , Li, Shuan , Shen, Yanxi , Rensing, Christopher et al. Rice Root Iron Plaque as a Mediator to Stimulate Methanotrophic Nitrogen Fixation . | ENVIRONMENTAL SCIENCE & TECHNOLOGY , 2025 , 59 (38) , 20411-20420 . |
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【目的】铁还原依赖的甲烷厌氧氧化（Fe-AOM）是厌氧环境中甲烷减排的重要途径，然而在缺氮条件下甲烷氧化微生物如何进行Fe-AOM仍不清楚。【方法】选取甲烷氧化培养物和水铁矿为研究对象，通过氮同位素示踪、三维荧光光谱分析、电化学分析和高通量测序等方法，探究缺氮条件下Fe-AOM的效率及其耦合生物固氮的可能性。【结果】在缺氮条件下，甲烷氧化培养物能够催化Fe-AOM，将水铁矿还原转化为菱铁矿等矿物。当添加甲烷时，甲烷氧化培养物的固氮酶活性和
Keyword ：
厌氧甲烷氧化 厌氧甲烷氧化 生物固氮 生物固氮 铁还原 铁还原 高通量测序 高通量测序
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| GB/T 7714 | 李书安 , 余林鹏 , 杨琳 et al. 甲烷氧化菌群介导的Fe(Ⅲ)还原和生物固氮及其耦合机制 [J]. | 微生物学报 , 2025 , 65 (06) : 2449-2462 . |
| MLA | 李书安 et al. "甲烷氧化菌群介导的Fe(Ⅲ)还原和生物固氮及其耦合机制" . | 微生物学报 65 . 06 (2025) : 2449-2462 . |
| APA | 李书安 , 余林鹏 , 杨琳 , 沈彦汐 , 周顺桂 . 甲烷氧化菌群介导的Fe(Ⅲ)还原和生物固氮及其耦合机制 . | 微生物学报 , 2025 , 65 (06) , 2449-2462 . |
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Iron (Fe) plaque is a concentrated form of microbially available Fe oxide that coats rice plant root surfaces, representing a high density of Fe oxide and which potentially mediates paddy soil CH4 emissions. Using a combination of methods including Fe plaque induction, isotopic labeling, pure microbial strains, and Fe oxide addition experiments, we investigated the impact of Fe plaque on methane (CH4) emissions from paddy soils and explored the associated mechanisms underlying the influence of Fe plaque on CH4 emissions. A 13C-CH4 isotopic labeling experiment showed that Fe plaque did not significantly affect CH4 oxidation and associated gene expression, whereas Fe plaque significantly enriched methanogenic archaea and their expression of genes associated with methanogenesis. Pure microbial strain and Fe oxide addition experiments showed that the enhancement of CH4 production in the presence of Fe plaque was caused by the (semi) conductive minerals within the Fe plaque, specifically, hematite, which promoted the extracellular electron transfer between the methanogenic archaea and their syntrophic bacteria, resulting in enhancement of methanogenesis. Our results imply that the presence of Fe plaque will accelerate CH4 emissions from paddy soils and suppressing Fe plaque has the potential to mitigate CH4 emissions.
Keyword ：
CH4 emission CH4 emission Extracellular electron transfer Extracellular electron transfer Fe plaque Fe plaque Global warming Global warming
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| GB/T 7714 | Yao, Jinzhi , Xie, Minghui , Yu, Linpeng et al. Rice root Fe plaque increases paddy soil CH4 emissions via the promotion of electron transfer for syntrophic methanogenesis [J]. | SOIL BIOLOGY & BIOCHEMISTRY , 2024 , 191 . |
| MLA | Yao, Jinzhi et al. "Rice root Fe plaque increases paddy soil CH4 emissions via the promotion of electron transfer for syntrophic methanogenesis" . | SOIL BIOLOGY & BIOCHEMISTRY 191 (2024) . |
| APA | Yao, Jinzhi , Xie, Minghui , Yu, Linpeng , Liu, Ting , Clough, Tim J. , Wrage-Moennig, Nicole et al. Rice root Fe plaque increases paddy soil CH4 emissions via the promotion of electron transfer for syntrophic methanogenesis . | SOIL BIOLOGY & BIOCHEMISTRY , 2024 , 191 . |
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Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 mu mol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones. Graphical Abstract
Keyword ：
biological nitrogen fixation biological nitrogen fixation iron reduction iron reduction metagenomics metagenomics methane oxidation methane oxidation methane-oxidizing bacteria methane-oxidizing bacteria
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| GB/T 7714 | Yu, Linpeng , Jia, Rong , Liu, Shiqi et al. Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia [J]. | ISME COMMUNICATIONS , 2024 , 4 (1) . |
| MLA | Yu, Linpeng et al. "Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia" . | ISME COMMUNICATIONS 4 . 1 (2024) . |
| APA | Yu, Linpeng , Jia, Rong , Liu, Shiqi , Li, Shuan , Zhong, Sining , Liu, Guohong et al. Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia . | ISME COMMUNICATIONS , 2024 , 4 (1) . |
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本发明公开了一种促进甲烷氧化固氮和水稻生长的方法，涉及诱导水稻幼苗形成根表铁膜，然后将形成根表铁膜的水稻幼苗移栽到含有甲烷氧化菌的环境中培养，使根表铁膜与环境中的甲烷氧化菌起到协同增效作用，增强了甲烷氧化菌的甲烷氧化固氮作用，同时耦合铁还原过程，减少了稻田甲烷排放，促使水稻的生长量、多糖含量、蛋白含量、叶绿素含量等生理指标明显提高，降低氮肥的使用量。本发明提供的方法是一种原位条件下环境友好型的技术，实际可操作性强，能够富集甲烷氧化铁还原固氮微生物，并能增强生物固氮作用以促进水稻生长，还能减少氮肥的使用，减少稻田甲烷的排放，对于响应生态环境可持续发展的理念和节能减排具有重要意义。
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| GB/T 7714 | 余林鹏 , 贾蓉 , 刘世奇 et al. 一种促进甲烷氧化固氮和水稻生长的方法 : CN202410120545.X[P]. | 2024-01-29 . |
| MLA | 余林鹏 et al. "一种促进甲烷氧化固氮和水稻生长的方法" : CN202410120545.X. | 2024-01-29 . |
| APA | 余林鹏 , 贾蓉 , 刘世奇 , 周顺桂 , 唐家桓 . 一种促进甲烷氧化固氮和水稻生长的方法 : CN202410120545.X. | 2024-01-29 . |
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本发明公开了一种促进稻田土壤中甲烷氧化耦合铁还原及固氮过程的方法，选取长期未施用或少施用氮肥的水稻田土壤，淹水耗竭土壤中的有机碳氮，加入水铁矿，富集甲烷氧化固氮微生物及铁还原微生物，以及该方法在富集甲烷氧化固氮微生物及铁还原微生物方面、在减少稻田甲烷排放及氮肥施用方面的应用。本发明提供了一种环境友好型的技术，能够富集铁依赖型甲烷氧化耦合生物固氮的相关微生物，适用于铁氧化物含量低并且施氮肥少的的稻田土壤，并且实际可操作性强，能够增强稻田的生物固氮作用，并耦合铁还原过程，从而减少氮肥的使用及其对环境的污染。
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| GB/T 7714 | 周顺桂 , 余林鹏 , 贾蓉 et al. 一种促进稻田土壤中甲烷氧化耦合铁还原及固氮过程的方法 : CN202410120400.X[P]. | 2024-01-29 . |
| MLA | 周顺桂 et al. "一种促进稻田土壤中甲烷氧化耦合铁还原及固氮过程的方法" : CN202410120400.X. | 2024-01-29 . |
| APA | 周顺桂 , 余林鹏 , 贾蓉 , 刘世奇 . 一种促进稻田土壤中甲烷氧化耦合铁还原及固氮过程的方法 : CN202410120400.X. | 2024-01-29 . |
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Fe(III) has been recognized as a potential electron sink for the anaerobic oxidation of methane (Fe-AOM) in diverse environments. However, most of previous Fe-AOM processes are limited to ANME archaea and the Fe-AOM mechanism remains unclear. Here we investigate, for the first time, the Fe-AOM performance and mechanisms by a single methanogen Methanosarcina barkeri. The results showed that M. barkeri was capable of oxidizing methane to CO2 and reducing ferrihydrite to siderite simultaneously. The presence of methane enhanced both the abundances of redox-active species (such as cytochromes) and electrochemical activity of M. barkeri. The proteomic analyses revealed that M. barkeri up-regulated the expressions of a number of methanogenic enzymes during Fe-AOM, and significantly enriched metabolic pathways of amino acid synthesis and nitrogen fixation. Metabolic inhibition experiments indicated that membrane-bound redox-active components (cytochromes, methanophenazine and F420H2:quinone oxidoreductase) were probably involved in extracellular electron transfer (EET) from cells to ferrihydrite. Overall, these results provide a deep insight into the single-carbon metabolism and survival strategy for methanogens and suggest that methanogens may play an important role in linking methane and iron cycling in the substrate-limited environments.
Keyword ：
Anaerobic methane oxidation Anaerobic methane oxidation Extracellular electron transfer Extracellular electron transfer Ferrihydrite reduction Ferrihydrite reduction Methanosarcina barkeri Methanosarcina barkeri Redox-active components Redox-active components
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| GB/T 7714 | Yu, Linpeng , He, Dan , Yang, Lin et al. Anaerobic methane oxidation coupled to ferrihydrite reduction by Methanosarcina barkeri [J]. | SCIENCE OF THE TOTAL ENVIRONMENT , 2022 , 844 . |
| MLA | Yu, Linpeng et al. "Anaerobic methane oxidation coupled to ferrihydrite reduction by Methanosarcina barkeri" . | SCIENCE OF THE TOTAL ENVIRONMENT 844 (2022) . |
| APA | Yu, Linpeng , He, Dan , Yang, Lin , Rensing, Christopher , Zeng, Raymond J. , Zhou, Shungui . Anaerobic methane oxidation coupled to ferrihydrite reduction by Methanosarcina barkeri . | SCIENCE OF THE TOTAL ENVIRONMENT , 2022 , 844 . |
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Methane has been demonstrated to be a feasible substrate for electricity generation in mi-crobial fuel cells (MFCs) and denitrifying anaerobic methane oxidation (DAMO). However, these two processes were evaluated separately in previous studies and it has remained unknown whether methane is able to simultaneously drive these processes. Here we in-vestigated the co-occurrence and performance of these two processes in the anodic cham-ber of MFCs. The results showed that methane successfully fueled both electrogenesis and denitrification. Importantly, the maximum nitrate removal rate was significantly enhanced from (1.4 +/- 0.8) to (18.4 +/- 1.2) mg N/(L middotday) by an electrogenic process. In the presence of DAMO, the MFCs achieved a maximum voltage of 610 mV and a maximum power density of 143 +/- 12 mW/m2. Electrochemical analyses demonstrated that some redox substances (e.g. riboflavin) were likely involved in electrogenesis and also in the denitrification process. High-throughput sequencing indicated that the methanogen Methanobacterium, a close rel-ative of Methanobacterium espanolae, catalyzed methane oxidation and cooperated with both exoelectrogens and denitrifiers (e.g., Azoarcus). This work provides an effective strategy for improving DAMO in methane-powered MFCs, and suggests that methanogens and denitri-fiers may jointly be able to provide an alternative to archaeal DAMO for methane-dependent denitrification.(c) 2022 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V.
Keyword ：
Anaerobic methane oxidation Anaerobic methane oxidation Denitrification Denitrification Electricity generation Electricity generation Electroactive compounds Electroactive compounds Methanobacterium Methanobacterium Microbial fuel cells Microbial fuel cells
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| GB/T 7714 | Yu, Linpeng , Zhang, Eryi , Yang, Lin et al. Combining biological denitrification and electricity generation in methane-powered microbial fuel cells [J]. | JOURNAL OF ENVIRONMENTAL SCIENCES , 2022 , 130 : 212-222 . |
| MLA | Yu, Linpeng et al. "Combining biological denitrification and electricity generation in methane-powered microbial fuel cells" . | JOURNAL OF ENVIRONMENTAL SCIENCES 130 (2022) : 212-222 . |
| APA | Yu, Linpeng , Zhang, Eryi , Yang, Lin , Liu, Shiqi , Rensing, Christopher , Zhou, Shungui . Combining biological denitrification and electricity generation in methane-powered microbial fuel cells . | JOURNAL OF ENVIRONMENTAL SCIENCES , 2022 , 130 , 212-222 . |
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Anaerobic oxidation of methane (AOM) coupled with electron transfer to electrodes has recently showed great promise for energy harvesting in microbial electrochemical reactors. To date this process has been reported limited to the syntrophic cooperation of archaea and bacteria in mixed cultures. It remains unknown whether pure archaea alone can catalyze electricity production from methane. Here we report the performance of AOM-driven electricity generation by a single methanogen Methanosarcina barkeri. M a poised electrode potential of + 300 mV vs. SHE, a maximum current of 649.7 mA m(-2) was achieved from methane with an appreciable Coulombic efficiency up to 86.9%. The electrogenic mechanism analysis demonstrated that M. barkeri donated most of electrons to electrodes directly and secreted soluble redox-active compounds to facilitate indirect extracellular electron transfer (EET). Electrochemical in situ Fourier transform infrared spectra and metabolic inhibitions suggested the methyl-coenzyme M reductase alpha-subunit (McrA), NiFe hydrogenases and cytochrome proteins were involved in the AOM-EET process. This work provides the first proof of concept for AOM-powered electricity production by a single archaeon via reversed methanogenesis and suggests methanogens may play an important role in coupling AOM with the reduction of solid electron acceptors in natural environments.
Keyword ：
Anaerobic methane oxidation Anaerobic methane oxidation Cytochromes Cytochromes Electrogenesis Electrogenesis Extracellular electron transfer Extracellular electron transfer Methanosarcina barkeri Methanosarcina barkeri NiFe hydrogenases NiFe hydrogenases
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| GB/T 7714 | Yu, Linpeng , He, Dan , Zhang, Eryi et al. Electricity from anaerobic methane oxidation by a single methanogenic archaeon Methanosarcina barkeri [J]. | CHEMICAL ENGINEERING JOURNAL , 2021 , 405 . |
| MLA | Yu, Linpeng et al. "Electricity from anaerobic methane oxidation by a single methanogenic archaeon Methanosarcina barkeri" . | CHEMICAL ENGINEERING JOURNAL 405 (2021) . |
| APA | Yu, Linpeng , He, Dan , Zhang, Eryi , He, Qiuxiang , Li, Jibing , Ren, Zhiyong Jason et al. Electricity from anaerobic methane oxidation by a single methanogenic archaeon Methanosarcina barkeri . | CHEMICAL ENGINEERING JOURNAL , 2021 , 405 . |
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