People
Research Fellow
Jie Cheng
Title
Research Fellow
Degree
PhD
Research Interests
Living Materials, Bioelectronics
Research Group
Office Location
S9-08-01
I-FIM Publications:
2025 |
Huang, Xiaowei; Yang, Xueling; Chen, Yuxuan; Cheng, Jie; Cheng, Zhongyi; Shi, Jiachun; He, Yan; Xu, Jianming Genome-resolved metagenomics reveal soil and viral drivers of keystone bacterial traits shaping nutrient cycling and soybean yield across agroecosystems SOIL ECOLOGY LETTERS, 7 (4), 2025, DOI: 10.1007/s42832-025-0346-7. @article{WOS:001590083800001, title = {Genome-resolved metagenomics reveal soil and viral drivers of keystone bacterial traits shaping nutrient cycling and soybean yield across agroecosystems}, author = {Xiaowei Huang and Xueling Yang and Yuxuan Chen and Jie Cheng and Zhongyi Cheng and Jiachun Shi and Yan He and Jianming Xu}, doi = {10.1007/s42832-025-0346-7}, times_cited = {0}, issn = {2662-2289}, year = {2025}, date = {2025-10-01}, journal = {SOIL ECOLOGY LETTERS}, volume = {7}, number = {4}, publisher = {SPRINGERNATURE}, address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND}, abstract = {Keystone bacteria's effect on soil health was found by genome-resolved metagenomics.Soil pH and C/N content were important for affecting keystone communities.Available phosphorus lacked a significant effect on keystone bacteria.Lysogenic virus-host dynamics help keystone bacteria adaption by P-acquisition AMGs.Soil microbes are crucial for agricultural sustainability, yet the genomic evidence of their interactions with soil abiotic and biotic factors remains unclear. Herein, we evaluated the contribution of soil bacteria to soil functions and soybean yields by analyzing 4 281 bacterial metagenomic assembled genomes (MAGs) recovered from 113 natural fields across China, integrated 12 enzymic activities and 58 quantified nutrient-cycling genes. Genome-resolved metagenomics revealed the diverse genic traits of keystone bacteria, and their roles in nutrient accumulation, fungal pathogen suppression, and herbicide biodegradation, thereby promoting soybean yields. Soil pH and C/N content were important abiotic factors that determined the dominant life history strategy of keystone communities, thus affecting nutrient-cycling genes abundance. We proposed agricultural management suggestions based on diversified planting aligned with the soil environmental preferences of keystone bacteria, verified in two long-term cropping fields. By recovering 7 803 vMAGs, we found the lysogenic virus-host dynamics could promote keystone bacteria adaptation by providing P-acquisition auxiliary metabolic genes (AMGs), leading to ecological advantages. We reported a novel P-acquisition strategy involving phnA-associated phosphonate hydrolysis employed by viruses, significantly influencing keystone-host phosphorus cycling. Overall, our study significantly advances the understanding of keystone bacteria in supporting crop production, with implications for precision microbiome management in agroecosystems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Keystone bacteria's effect on soil health was found by genome-resolved metagenomics.Soil pH and C/N content were important for affecting keystone communities.Available phosphorus lacked a significant effect on keystone bacteria.Lysogenic virus-host dynamics help keystone bacteria adaption by P-acquisition AMGs.Soil microbes are crucial for agricultural sustainability, yet the genomic evidence of their interactions with soil abiotic and biotic factors remains unclear. Herein, we evaluated the contribution of soil bacteria to soil functions and soybean yields by analyzing 4 281 bacterial metagenomic assembled genomes (MAGs) recovered from 113 natural fields across China, integrated 12 enzymic activities and 58 quantified nutrient-cycling genes. Genome-resolved metagenomics revealed the diverse genic traits of keystone bacteria, and their roles in nutrient accumulation, fungal pathogen suppression, and herbicide biodegradation, thereby promoting soybean yields. Soil pH and C/N content were important abiotic factors that determined the dominant life history strategy of keystone communities, thus affecting nutrient-cycling genes abundance. We proposed agricultural management suggestions based on diversified planting aligned with the soil environmental preferences of keystone bacteria, verified in two long-term cropping fields. By recovering 7 803 vMAGs, we found the lysogenic virus-host dynamics could promote keystone bacteria adaptation by providing P-acquisition auxiliary metabolic genes (AMGs), leading to ecological advantages. We reported a novel P-acquisition strategy involving phnA-associated phosphonate hydrolysis employed by viruses, significantly influencing keystone-host phosphorus cycling. Overall, our study significantly advances the understanding of keystone bacteria in supporting crop production, with implications for precision microbiome management in agroecosystems.
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Long, Min; Cheng, Jie; Zhou, Chen; Rittmann, Bruce E Mechanistic insights into gold (Au) recovery and biosynthesis pathway in a hydrogen (H2)-based denitrifying membrane biofilm RESOURCES CONSERVATION AND RECYCLING, 221 , 2025, DOI: 10.1016/j.resconrec.2025.108394. @article{WOS:001498393200001, title = {Mechanistic insights into gold (Au) recovery and biosynthesis pathway in a hydrogen (H2)-based denitrifying membrane biofilm}, author = {Min Long and Jie Cheng and Chen Zhou and Bruce E Rittmann}, doi = {10.1016/j.resconrec.2025.108394}, times_cited = {1}, issn = {0921-3449}, year = {2025}, date = {2025-07-01}, journal = {RESOURCES CONSERVATION AND RECYCLING}, volume = {221}, publisher = {ELSEVIER}, address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS}, abstract = {Gold (Au) holds a high market value due to its extensive industry, medicine, and jewelry applications. Extracting Au from wastewater streams presents an opportunity to bolster the supply of this precious metal. This study explores a novel application of the H-2-based Membrane Biofilm Reactor (MBfR): reducing Au(III) to recover Au (0) nanoparticles (Au degrees NPs) by a denitrifying biofilm. During long-term operation, >90 % of the soluble Au(III) was reduced to Au degrees NPs through enzymatic processes. Au(III) recovery was primarily conducted by denitrifiers such as Stenotrophomonas, Pannonibacter, and Thermomonas. Most Au degrees NPs were retained within the biofilm matrix, while some Au degrees NPs were released into the liquid. Continued biofilm activity with higher concentrations of influent Au(III) resulted in increasingly larger Au degrees NPs, eventually leading to the formation of high-purity Au (0) foil. This study demonstrates microbially driven Au(0) recovery in MBfR in which the reduction of Au(III) was linked to a core set of denitrifying genera and their genes encoding nitrate and metal reductases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gold (Au) holds a high market value due to its extensive industry, medicine, and jewelry applications. Extracting Au from wastewater streams presents an opportunity to bolster the supply of this precious metal. This study explores a novel application of the H-2-based Membrane Biofilm Reactor (MBfR): reducing Au(III) to recover Au (0) nanoparticles (Au degrees NPs) by a denitrifying biofilm. During long-term operation, >90 % of the soluble Au(III) was reduced to Au degrees NPs through enzymatic processes. Au(III) recovery was primarily conducted by denitrifiers such as Stenotrophomonas, Pannonibacter, and Thermomonas. Most Au degrees NPs were retained within the biofilm matrix, while some Au degrees NPs were released into the liquid. Continued biofilm activity with higher concentrations of influent Au(III) resulted in increasingly larger Au degrees NPs, eventually leading to the formation of high-purity Au (0) foil. This study demonstrates microbially driven Au(0) recovery in MBfR in which the reduction of Au(III) was linked to a core set of denitrifying genera and their genes encoding nitrate and metal reductases.
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Long, Min; Cheng, Jie; Zhou, Chen; Rittmann, Bruce E Enhanced long-term reduction of high-level Au(III) with the presence of NO3- in a H2-based membrane biofilm reactor WATER RESEARCH, 274 , 2025, DOI: 10.1016/j.watres.2024.123013. @article{WOS:001421120800001, title = {Enhanced long-term reduction of high-level Au(III) with the presence of NO3- in a H2-based membrane biofilm reactor}, author = {Min Long and Jie Cheng and Chen Zhou and Bruce E Rittmann}, doi = {10.1016/j.watres.2024.123013}, times_cited = {3}, issn = {0043-1354}, year = {2025}, date = {2025-04-01}, journal = {WATER RESEARCH}, volume = {274}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {Increased mining and ore processing of gold (Au) are leading to waters contaminated with Au(III) ions, and a common co-contaminant is nitrate (NO3-). Here, we demonstrate that a hydrogen (H-2)-based membrane biofilm reactor (MBfR) enabled synergistic co-reductions of NO3- to N-2 and Au(III) to elemental Au degrees for over 250 days of continuous operation. Au(III) was reduced to Au-0 nanoparticles (Au(0)NPs) that were retained within the biofilm's extracellular polymeric substances. NO3- and Au(III) were > 95 % reduced at steady state for a wide range of influent conditions: NO3--N at 1 or 4 mM; Au(III) at 100, 200, or 500 mg/L. Metal-tolerant denitrifiers Azonexus, Pannoibacter, Thermomonas, and Cupriavidus were enriched, as were genes encoding metal reductases. The rate of Au(III) reduction was positively correlated with the abundance of NO3- and NO2- reductases, which supports the role of these reductases in Au(III) reduction. Remarkably, the Au(III)-reduction efficiency remained above 90 % in the highly acidic condition, despite NO2- accumulation due to incomplete NO3- reduction; thus, the microbial community was resilient against environmental perturbation. By providing a mechanistic basis for Au recovery using the MBfR, this study establishes the MBfR as a promising and sustainable technology for treating wastewaters containing valuable metals, such as gold, in coordination with microbial denitrification.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Increased mining and ore processing of gold (Au) are leading to waters contaminated with Au(III) ions, and a common co-contaminant is nitrate (NO3-). Here, we demonstrate that a hydrogen (H-2)-based membrane biofilm reactor (MBfR) enabled synergistic co-reductions of NO3- to N-2 and Au(III) to elemental Au degrees for over 250 days of continuous operation. Au(III) was reduced to Au-0 nanoparticles (Au(0)NPs) that were retained within the biofilm's extracellular polymeric substances. NO3- and Au(III) were > 95 % reduced at steady state for a wide range of influent conditions: NO3--N at 1 or 4 mM; Au(III) at 100, 200, or 500 mg/L. Metal-tolerant denitrifiers Azonexus, Pannoibacter, Thermomonas, and Cupriavidus were enriched, as were genes encoding metal reductases. The rate of Au(III) reduction was positively correlated with the abundance of NO3- and NO2- reductases, which supports the role of these reductases in Au(III) reduction. Remarkably, the Au(III)-reduction efficiency remained above 90 % in the highly acidic condition, despite NO2- accumulation due to incomplete NO3- reduction; thus, the microbial community was resilient against environmental perturbation. By providing a mechanistic basis for Au recovery using the MBfR, this study establishes the MBfR as a promising and sustainable technology for treating wastewaters containing valuable metals, such as gold, in coordination with microbial denitrification.
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2024 |
He, Yan; Li, ShuYao; Yuan, Jing; Cheng, Jie; Dou, JiBo; Yang, XueLing; Xu, JianMing A systematic understanding of microbial reductive dechlorination towards an improved ``one health'' soil bioremediation: A review and perspective SCIENCE CHINA-TECHNOLOGICAL SCIENCES, 67 (10, SI), pp. 3009-3031, 2024, DOI: 10.1007/s11431-024-2664-5. @article{WOS:001302283400001, title = {A systematic understanding of microbial reductive dechlorination towards an improved ``one health'' soil bioremediation: A review and perspective}, author = {Yan He and ShuYao Li and Jing Yuan and Jie Cheng and JiBo Dou and XueLing Yang and JianMing Xu}, doi = {10.1007/s11431-024-2664-5}, times_cited = {5}, issn = {1674-7321}, year = {2024}, date = {2024-10-01}, journal = {SCIENCE CHINA-TECHNOLOGICAL SCIENCES}, volume = {67}, number = {10, SI}, pages = {3009-3031}, publisher = {SCIENCE PRESS}, address = {16 DONGHUANGCHENGGEN NORTH ST, BEIJING 100717, PEOPLES R CHINA}, abstract = {Chlorinated organic pollutants (COPs), both emerging and traditional, are typical persistent pollutants that harm soil health worldwide. Dechlorinators mediated reductive dechlorination is the optimal way to completely remove COPs from anaerobic soil through a redox reaction driven by electron transfer during microbial anaerobic respiration. Generally, the dechlorinated depletion of COPs in situ often interacts with multiple element biogeochemical activities, e.g., methanogenesis, sulfate reduction, iron reduction, and denitrification. Elucidating the relevance of biogeochemical cycles between COPs and multiple elements and the coupled mechanisms involved, thus, helps to develop effective pollution control strategies with the balance between pollution degradation and element cycles in heterogeneous soil, ultimately contributing to ``one health'' goal. In this review, we summarized the microbial-chemical coupling redox processes and the driving factors, elucidated the interspecies metabolites exchange and electron transfer mechanisms within COP-dechlorinating communities, and further proposed a detailed design, construction, and analysis framework of engineering COP-dechlorinating microbiomes via ``top-down'' self-assembly and ``bottom-up'' synthesis to pave the way from laboratory to practical field application. Especially, we delve into the major challenges and perspectives surrounding the design of state-of-the-art synthetic microbial communities. Our goal is to improve the understanding of the microbial-mediated coupling between reductive dechlorination and element biogeochemical cycling, with a particular focus on the implications for health-integrated soil bioremediation under the ``one health'' concept.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chlorinated organic pollutants (COPs), both emerging and traditional, are typical persistent pollutants that harm soil health worldwide. Dechlorinators mediated reductive dechlorination is the optimal way to completely remove COPs from anaerobic soil through a redox reaction driven by electron transfer during microbial anaerobic respiration. Generally, the dechlorinated depletion of COPs in situ often interacts with multiple element biogeochemical activities, e.g., methanogenesis, sulfate reduction, iron reduction, and denitrification. Elucidating the relevance of biogeochemical cycles between COPs and multiple elements and the coupled mechanisms involved, thus, helps to develop effective pollution control strategies with the balance between pollution degradation and element cycles in heterogeneous soil, ultimately contributing to ``one health'' goal. In this review, we summarized the microbial-chemical coupling redox processes and the driving factors, elucidated the interspecies metabolites exchange and electron transfer mechanisms within COP-dechlorinating communities, and further proposed a detailed design, construction, and analysis framework of engineering COP-dechlorinating microbiomes via ``top-down'' self-assembly and ``bottom-up'' synthesis to pave the way from laboratory to practical field application. Especially, we delve into the major challenges and perspectives surrounding the design of state-of-the-art synthetic microbial communities. Our goal is to improve the understanding of the microbial-mediated coupling between reductive dechlorination and element biogeochemical cycling, with a particular focus on the implications for health-integrated soil bioremediation under the ``one health'' concept.
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