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学者姓名：刘星
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Abstract ：
Biological nitrogen fixation (BNF) represents a sustainable alternative to the capital- and energy-intensive Haber-Bosch process, which dominates industrial fertilizer production but contributes significantly to global carbon emissions. While Geobacter sulfurreducens has been identified as a promising diazotroph, its BNF efficiency remains untapped. Here, we engineered G. sulfurreducens by deleting the ammonium transporter gene amtB (strain Delta amtB), achieving a record-high BNF rate of 20.57 +/- 0.87 mg N L-1 day-1, approximately twice that of the wild-type strain and exceeding those of all reported free-living diazotrophs and synthetic catalysts for ambient nitrogen fixation. 15N isotope labeling and nitrogenase activity assays confirmed enhanced fixation, whereas biofertilizer trials demonstrated the ability of Delta amtB as a biofertilizer to support Arabidopsis thaliana growth. Mechanistic studies revealed that amtB deletion (1) amplified cellular nitrogen assimilation, (2) alleviated ammonium-mediated suppression of nitrogenase activity, and (3) disrupted energy-intensive futile ammonium cycling, conserving cell energy. This study establishes Delta amtB as a scalable BNF platform for sustainable agriculture, offering a viable pathway to decarbonize fertilizer production.
Keyword ：
ammonium transporter amtB ammonium transporter amtB artificial nitrogen fixation artificial nitrogen fixation biofertilizer production biofertilizer production free-living nitrogen fixation free-living nitrogen fixation genetic engineering genetic engineering
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| GB/T 7714 | Yang, Wei , Jing, Xianyue , Lai, Shuyao et al. Engineered Geobacter sulfurreducens Achieves a Record-High Rate of Biological Nitrogen Fixation [J]. | ENVIRONMENTAL SCIENCE & TECHNOLOGY , 2025 , 59 (35) : 18605-18615 . |
| MLA | Yang, Wei et al. "Engineered Geobacter sulfurreducens Achieves a Record-High Rate of Biological Nitrogen Fixation" . | ENVIRONMENTAL SCIENCE & TECHNOLOGY 59 . 35 (2025) : 18605-18615 . |
| APA | Yang, Wei , Jing, Xianyue , Lai, Shuyao , Wang, Hui , Wang, Jun , Liu, Xing et al. Engineered Geobacter sulfurreducens Achieves a Record-High Rate of Biological Nitrogen Fixation . | ENVIRONMENTAL SCIENCE & TECHNOLOGY , 2025 , 59 (35) , 18605-18615 . |
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Energy acquisition presents a fundamental constraint for microbial survival in oligotrophic environments. Although heterotrophic organohalide-respiring bacteria (OHRB) are known to perform reductive dehalogenation in organohalide-contaminated oligotrophic ecosystems, their energy metabolism remains poorly understood. Here, we report that Pseudomonas sp. CP-1, an organohalide-respiring bacterium, can directly oxidize humin from diverse oligotrophic aquifers to drive organohalide respiration. Spectroscopy, electrochemistry, and metabolic profiling demonstrated that electrons stored in phenolic hydroxyl and amino groups of humin were utilized by strain CP-1 for organohalide respiration. Mutational and chemical inhibition studies identified an extracellular electron uptake pathway involving a multiheme cytochrome EeuP, which transfers extracellular electrons into the organohalide-respiratory chain, thereby coupling humin oxidation with reductive dehalogenation. Phylogenetic analyses revealed the widespread distribution of EeuP homologs across environmental bacterial taxa, implying a broader ecological relevance. This discovery sheds light on the hidden world of subsurface microbiology, with implications for understanding microbial energy metabolism in the energy-scarce environments.
Keyword ：
humin oxidation humin oxidation multiheme cytochrome multiheme cytochrome oligotrophic survival oligotrophic survival organohalide biotransformation organohalide biotransformation
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| GB/T 7714 | Zhang, Zimeng , Liu, Xing , Li, Zhiling et al. Humin oxidation drives microbial dehalogenation in oligotrophic environments [J]. | ISME JOURNAL , 2025 , 19 (1) . |
| MLA | Zhang, Zimeng et al. "Humin oxidation drives microbial dehalogenation in oligotrophic environments" . | ISME JOURNAL 19 . 1 (2025) . |
| APA | Zhang, Zimeng , Liu, Xing , Li, Zhiling , Chen, Xueqi , Zu, Yunxia , Ho, Shih-Hsin et al. Humin oxidation drives microbial dehalogenation in oligotrophic environments . | ISME JOURNAL , 2025 , 19 (1) . |
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Identifying the factors that affect the nitrate reduction partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification is crucial for mitigating nitrogen loss in ecosystems. Conventionally, the nutrient status of the environment (e.g., the carbon-to-nitrogen ratio) is recognized as the key determinant of nitrogen conversion pathways. Here, we report that the availability of Fe(III) regulates the nitrate reduction partitioning in Geobacter metallireducens and Alcaligenes faecalis co-culture. We controlled the availability of Fe(III) in the coculture medium and tracked nitrogen conversion dynamics and community composition. The results demonstrated that the coculture performed DNRA, contributed mainly by G. metallireducens under Fe(III)-replete conditions, while performing interspecies synergistic denitrification between both species under Fe(III)-depleted conditions. Nitrate/nitrite reductase activity calculations and mutation analyses indicated that nitrate reduction partitioning in the coculture was governed by the nitrite reductase (Nrf) activity of G. metallireducens, which was Fe(III)-dependent. Further validation in urban river water confirmed that Fe(III) supplementation significantly enhances DNRA activity. Our findings establish Fe(III) as a previously unrecognized regulator of microbial nitrogen retention, showing insights into strategies for managing nitrogen fluxes in agricultural and aquatic systems.IMPORTANCENitrogen is essential for life, but its loss from ecosystems through microbial processes like denitrification harms agricultural productivity and contributes to greenhouse gas emissions. Retaining nitrogen as ammonium via microbial dissimilatory nitrate reduction to ammonium (DNRA) could mitigate these issues, but the factors governing microbial prioritization of DNRA over denitrification remain unclear. Our study reveals that Fe(III) plays a critical, previously unrecognized role in steering this process. We show that Fe(III) availability determines whether the nitrate-reducing community conserves nitrogen as ammonium or releases it as gas, with implications for managing nitrogen in soils and waterways. By demonstrating Fe(III)'s ability to enhance nitrogen retention in environmental systems like urban rivers, our findings offer a new lever for sustainable agriculture and pollution control. This work bridges microbial ecology and environmental management, highlighting how trace metals shape nutrient cycles in ways that can be harnessed to protect ecosystem health.
Keyword ：
denitrification denitrification dissimilatory nitrate reduction to ammonium dissimilatory nitrate reduction to ammonium Fe(III) cofactor Fe(III) cofactor interspecies synergistic denitrification interspecies synergistic denitrification nitrite reductase nitrite reductase nitrogen conversion nitrogen conversion
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| GB/T 7714 | Zhan, Ji , Zhang, Lu , Lai, Shuyao et al. Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities [J]. | MBIO , 2025 , 16 (11) . |
| MLA | Zhan, Ji et al. "Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities" . | MBIO 16 . 11 (2025) . |
| APA | Zhan, Ji , Zhang, Lu , Lai, Shuyao , Guo, Junhui , Lin, Tianqi , Liu, Guohong et al. Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities . | MBIO , 2025 , 16 (11) . |
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In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.
Keyword ：
Fe(III)-reducing bacteria Fe(III)-reducing bacteria Geothrix campi sp. nov. Geothrix campi sp. nov. Geothrix mesophila sp. nov. Geothrix mesophila sp. nov. Paddy soil Paddy soil Polyphasic taxonomy Polyphasic taxonomy
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| GB/T 7714 | Han, Shuang , Yang, Shang , Tang, Rong et al. Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils [J]. | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY , 2024 , 117 (1) . |
| MLA | Han, Shuang et al. "Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils" . | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY 117 . 1 (2024) . |
| APA | Han, Shuang , Yang, Shang , Tang, Rong , Xie, Cheng-Jie , Liu, Xing , Liu, Guo-Hong et al. Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils . | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY , 2024 , 117 (1) . |
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土壤胞外呼吸是驱动元素生物地球化学循环的引擎，而微生物纳米导线是实现土壤胞外呼吸的重要途径。微生物纳米导线是一类生长于微生物表面，可长达数十微米的具有导电性的纤维状结构。它直接作用于微生物与土壤矿物、产甲烷与甲烷氧化微生物间的电子传递，从而影响了土壤矿物的迁移转化及温室气体减排。Geobacter sulfurreducens是研究微生物纳米导线的模式微生物。长久以来，基于分子生物学实验证据表明，G. sulfurreducens纳米导线是PilA-N菌毛。而最近基于冷冻电镜技术的纳米导线结构分析发现，G. sulfurreducens实际上表达着各种形式的细胞色素c纳米导线。自此，关于“纳米导线本质”的问题成为学术界争论的焦点。以G. sulfurreducens纳米导线理论发展为主线，综述了不同时期对纳米导线结构与功能的认识，并系统分析了作为“纳米导线本质”争议的证据基础，将推动该争议的早日解决，并助力土壤胞外呼吸理论的成熟及微生物纳米导线的应用研究。
Keyword ：
Geobacter Geobacter 微生物纳米导线 微生物纳米导线 胞外呼吸 胞外呼吸 胞外电子传递 胞外电子传递
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| GB/T 7714 | 叶银 , 周顺桂 , 刘星 . 微生物纳米导线的结构与功能：争议及进展 [J]. | 土壤学报 , 2024 , 61 (02) : 297-307 . |
| MLA | 叶银 et al. "微生物纳米导线的结构与功能：争议及进展" . | 土壤学报 61 . 02 (2024) : 297-307 . |
| APA | 叶银 , 周顺桂 , 刘星 . 微生物纳米导线的结构与功能：争议及进展 . | 土壤学报 , 2024 , 61 (02) , 297-307 . |
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Extracellular electron transfer (EET) of microorganisms is a major driver of the microbial growth and metabolism, including reactions involved in the cycling of C, N, and Fe in anaerobic environments such as soils and sediments. Understanding the mechanisms of EET, as well as knowing which organisms are EET-capable (or can become so) is fundamental to electromicrobiology and geomicrobiology. In general, Gram-positive bacteria very seldomly perform EET due to their thick non-conductive cell wall. Here, we report that a Gram-positive Clostridium intestinale (C.i) attained EET-capability for ethanol metabolism only after forming chimera with electroactive Geobacter sulfurreducens (G.s). Mechanism analyses demonstrated that the EET was possible after the cell fusion of the two species was achieved. Under these conditions, the ethanol metabolism pathway of C.i was integrated by the EET pathway of G.s, by which achieved the oxidation of ethanol for the subsequent reduction of extracellular electron acceptors in the coculture. Our study displays a new approach to perform EET for Gram-positive bacteria via recruiting the EET pathway of an electroactive bacterium, which suggests a previously unanticipated prevalence of EET in the microbial world. These findings also provide new perspectives to understand the energetic coupling between bacterial species and the ecology of interspecies mutualisms. Graphical Abstract
Keyword ：
electroactive bacteria electroactive bacteria energetic coupling energetic coupling energy metabolism energy metabolism extracellular electron transfer extracellular electron transfer Gram-positive bacteria Gram-positive bacteria interspecies electron transfer interspecies electron transfer interspecies mutualism interspecies mutualism
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| GB/T 7714 | Liu, Xing , Ye, Yin , Yang, Naiming et al. Nonelectroactive clostridium obtains extracellular electron transfer-capability after forming chimera with Geobacter [J]. | ISME COMMUNICATIONS , 2024 , 4 (1) . |
| MLA | Liu, Xing et al. "Nonelectroactive clostridium obtains extracellular electron transfer-capability after forming chimera with Geobacter" . | ISME COMMUNICATIONS 4 . 1 (2024) . |
| APA | Liu, Xing , Ye, Yin , Yang, Naiming , Cheng, Chen , Rensing, Christopher , Jin, Chao et al. Nonelectroactive clostridium obtains extracellular electron transfer-capability after forming chimera with Geobacter . | ISME COMMUNICATIONS , 2024 , 4 (1) . |
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Electroactive biofilms show great promise in bioenergy production, bioremediation, wastewater treatment, and bioelectronics. However, their applicability is impeded by energy dissipation owing to the electron transfer resistance in electroactive biofilms. Herein, we tuned the structure of a Geobacter sulfurreducens anode biofilm in situ to reduce the electron transfer resistance. Therein, the pili of G. sulfurreducens were genetically engineered with six-histidine tags, and nickel(II) ions were supplied thereafter to trigger the formation of histidine:nickel biohybrid pili via histidine-nickel coordination bonds. We reported that these treatments resulted in the intertwining of pili from different cells, which contributed to the formation of a highly structured biofilm and increased the concentration of electroactive sites in the microenvironments of the biofilm. Electrochemical analyses demonstrated that the treatments decreased the electron diffusion resistance as well as the interface electron transfer resistance and mass transfer resistance, all of which contributed to an approximately 2.4 times increase in current generation. Considering the universality of pili in microorganisms and the strong coordination interaction between histidine tags and nickel(II) ions, this study provides a general method to reduce energy dissipation in electroactive biofilms and suggests a technique to manipulate the biofilm structure, which is significant in biofilm-based technologies.
Keyword ：
Bioelectrochemcial system Bioelectrochemcial system biohybrids biohybrids Electroactivebiofilm Electroactivebiofilm electrontransfer resistance electrontransfer resistance extracellular electron transfer extracellular electron transfer genetically engineered biofilm genetically engineered biofilm Geobacter species Geobacter species histidine-nickel coordination bonds histidine-nickel coordination bonds
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| GB/T 7714 | Wang, Huitong , Jing, Xianyue , Feng, Kunjia et al. In Situ Tuning the Structure of Geobacter Biofilm for Bioelectricity Enhancement [J]. | ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS , 2024 , 11 (2) : 106-113 . |
| MLA | Wang, Huitong et al. "In Situ Tuning the Structure of Geobacter Biofilm for Bioelectricity Enhancement" . | ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 11 . 2 (2024) : 106-113 . |
| APA | Wang, Huitong , Jing, Xianyue , Feng, Kunjia , Tremblay, Pier-Luc , Wang, Jun , Liu, Xing et al. In Situ Tuning the Structure of Geobacter Biofilm for Bioelectricity Enhancement . | ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS , 2024 , 11 (2) , 106-113 . |
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Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage-host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack. Graphical Abstract
Keyword ：
bioelectrochemical system bioelectrochemical system biofilm decay biofilm decay ecological competition ecological competition electroactive biofilm electroactive biofilm Geobacter species Geobacter species prophage induction prophage induction
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| GB/T 7714 | Ye, Yin , Zhang, Lu , Hong, Xiaohui et al. Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm [J]. | ISME JOURNAL , 2024 , 18 (1) . |
| MLA | Ye, Yin et al. "Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm" . | ISME JOURNAL 18 . 1 (2024) . |
| APA | Ye, Yin , Zhang, Lu , Hong, Xiaohui , Chen, Man , Liu, Xing , Zhou, Shungui . Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm . | ISME JOURNAL , 2024 , 18 (1) . |
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本发明公开了一种基于拉曼光谱技术快速鉴定电缆细菌的方法，包括：将待检测物清洗后，加入低背景噪音的拉曼基底上；获取待检测单细胞的激光拉曼光谱图像；对所测激光拉曼光谱图像进行预处理得到预处理后的激光拉曼图像；使用371cm‑1和492cm‑1波数的峰面积之和与2800～3100cm‑1的C‑H面积之和的比值X％来判断是否为电缆细菌；其中，X％小于0.0001，则判定为其他菌；X％大于0.3，则判定为电缆细菌。本发明提出一种快速、无损伤的活细胞原位鉴定电缆细的新方法，弥补了微电极系统带来的时差性，减少了FISH和电子显微镜制样的复杂性，同时也缩短了表征电缆细菌的时间，适宜进一步推广应用。
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| GB/T 7714 | 刘星 , 张璐 , 程琛 . 一种基于拉曼光谱技术快速鉴定电缆细菌的方法 : CN202410015310.4[P]. | 2024-01-04 . |
| MLA | 刘星 et al. "一种基于拉曼光谱技术快速鉴定电缆细菌的方法" : CN202410015310.4. | 2024-01-04 . |
| APA | 刘星 , 张璐 , 程琛 . 一种基于拉曼光谱技术快速鉴定电缆细菌的方法 : CN202410015310.4. | 2024-01-04 . |
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Nitrogen gas (N-2) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus Geomonas has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of Geomonas in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH4+) in Geomonas. In this study, we determined that a key nitrogenase gene (nifH) was present in 50 isolates from paddy soils. Members of Geomonas contained the minimum nitrogen fixation gene cluster (nifBHDKEN) based on genomic analysis, implying Geomonas species had the potential to fix nitrogen. Acetylene reduction assay (ARA), N-15(2) isotope labeling, and total nitrogen accumulation assays validated that Geomonas was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of Geomonas changed from short rod-shaped (with NH4+) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the Geomonas transcriptome was quantified in response to NH4+. Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH4+ uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N-2 fixation in Geomonas. These results were verified by RT-qPCR. Taken together, our results demonstrate that Geomonas species possess the ability to fix N-2 and expand our understanding on the ecological significance and potential applications of Geomonas in paddy soil ecosystems. IMPORTANCE The ability of Geomonas species to fix nitrogen gas (N-2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N-2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.
Keyword ：
new diazotrophic Geomonas new diazotrophic Geomonas nitrogenase nitrogenase nitrogen fixation nitrogen fixation paddy soil paddy soil RT-qPCR RT-qPCR transcriptome analysis transcriptome analysis
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| GB/T 7714 | Liu, Guo-Hong , Yang, Shang , Han, Shuang et al. Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils [J]. | MBIO , 2023 , 14 (6) . |
| MLA | Liu, Guo-Hong et al. "Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils" . | MBIO 14 . 6 (2023) . |
| APA | Liu, Guo-Hong , Yang, Shang , Han, Shuang , Xie, Cheng-Jie , Liu, Xing , Rensing, Christopher et al. Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils . | MBIO , 2023 , 14 (6) . |
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