SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils

Abstract

Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%−99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10⁴ cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.

Keywords

black soil / carbon metabolism / herbicide degradation / keystone species / synthetic microbial community

References

[1] USDA. 1999. Soil Taxonomy: A Basic System of Soil Classification for Making and Interpreting Soil Surveys. Washington, DC: USDA Soil Conservation Service.

[2] 1998. National Soil Survey Office, Soils of China. Beijing: China Agriculture Press.

[3] Xuan, Fu, Yi Dong, Jiayu Li, Xuecao Li, Wei Su, Xianda Huang, Jianxi Huang, et al. 2023. “Mapping Crop Type in Northeast China During 2013-2021 Using Automatic Sampling and Tile-Based Image Classification.” International Journal of Applied Earth Observations and Geoinformation 117: 103178. https://doi.org/10.1016/j.jag.2022.103178

[4] Fang, Haiyan, Liying Sun, Deli Qi, and Qiangguo Cai. 2012. “Using 137Cs Technique to Quantify Soil Erosion and Deposition Rates in an Agricultural Catchment in the Black Soil Region, Northeast China.” Geomorphology 169-170: 142-150. https://doi.org/10.1016/j.geomorph.2012.04.019

[5] Xu, Xiang-Zhou, Yi Xu, Su-Chin Chen, Shi-Guo Xu, and Huawei Zhang. 2010. “Soil Loss and Conservation in the Black Soil Region of Northeast China: A Retrospective Study.” Environmental Science & Policy 13(8): 793-800. https://doi.org/10.1016/j.envsci.2010.07.004

[6] Zhang, Ying, Zhigang Wang, Huosheng Guo, Dongfang Meng, Yang Wang, and Po-keung Wong. 2015. “Interaction Between Microbes DNA and Atrazine in Black Soil Analyzed by Spectroscopy.” CLEAN - Soil, Air, Water 43(6): 867-871. https://doi.org/10.1002/clen.201400006

[7] Wang, Yifan, Xinyuan Zhang, Xing Zhang, Qingjuan Meng, Fengjie Gao, and Ying Zhang. 2017. “Characterization of Spectral Responses of Dissolved Organic Matter (DOM) for Atrazine Binding During the Sorption Process Onto Black Soil.” Chemosphere 180: 531-539. https://doi.org/10.1016/j.chemosphere.2017.04.063

[8] Rama Krishna, K., and Ligy Philip. 2008. “Adsorption and Desorption Characteristics of Lindane, Carbofuran and Methyl Parathion on Various Indian Soils.” Journal of Hazardous Materials 160: 559-567. https://doi.org/10.1016/j.jhazmat.2008.03.107

[9] Rotich, Henry K., Zhuoyong Zhang, Yongsheng Zhao, and Jinchang Li. 2004. “The Adsorption Behavior of Three Organophosphorus Pesticides in Peat and Soil Samples and Their Degradation in Aqueous Solutions at Different Temperatures and pH Values.” International Journal of Environmental Analytical Chemistry 84: 289-301. https://doi.org/10.1080/03067310310001637694

[10] Chang, Jianning, Wei Fang, Le Chen, Panyue Zhang, Guangming Zhang, Haibo Zhang, Jinsong Liang, Qingyan Wang, and Weifang Ma. 2022. “Toxicological Effects, Environmental Behaviors and Remediation Technologies of Herbicide Atrazine in Soil and Sediment: A Comprehensive Review.” Chemosphere 307: 136006. https://doi.org/10.1016/j.chemosphere.2022.136006

[11] Li, Zilu, Xingyu Zhang, Yue Wang, Zirui Zheng, Chenhui Zhang, Tianyue Wu, Yanling Wu, Yuxia Gao, and Fengpei Du. 2023. “Improved Method to Characterize Leaf Surfaces, Guide Adjuvant Selection, and Improve Glyphosate Efficacy.” Journal of Agricultural and Food Chemistry 71(3): 1348-1359. https://doi.org/10.1021/acs.jafc.2c05622

[12] NBS. National Bureau of Statistics of China. 2023. http://www.stats.gov.cn/

[13] Bast, Aalt, Khrystyna O. Semen, and Marjolein Drent. 2021. “Pulmonary Toxicity Associated With Occupational and Environmental Exposure to Pesticides and Herbicides.” Current Opinion in Pulmonary Medicine 27(4): 278-283. https://doi.org/10.1097/MCP.0000000000000777

[14] Kumar, Vanish, and Ki-Hyun Kim. 2022. “Use of Molecular Imprinted Polymers as Sensitive/Selective Luminescent Sensing Probes for Pesticides/Herbicides in Water and Food Samples.” Environmental Pollution 299: 118824. https://doi.org/10.1016/j.envpol.2022.118824

[15] Richardson, Jason R., Vanessa Fitsanakis, Remco H. S. Westerink, and Anumantha G. Kanthasamy. 2019. “Neurotoxicity of Pesticides.” Acta Neuropathologica 138(3): 343-362. https://doi.org/10.1007/s00401-019-02033-9

[16] Cai, Lin. 2017. “Residues and risk identification of pesticides in soil in northeast agricultural region of China.” Master's thesis, Dalian University of Technology. In Chinese.

[17] Zhang, Kaixin, Jinyan Zhang, and Yafei Wang. 2020. “The Spatial Distribution of Herbicide Residues in Soybean Fields in Mishan Area.” Agrochemicals 59(1): 56-59. https://doi.org/10.16820/j.cnki.1006-0413.2020.01.016

[18] Yao, Ting, Lejun Liu, Shuo Tan, Hui Li, Xiangying Liu, Aiping Zeng, Lang Pan, et al. 2021. “Can the Multi-Walled Carbon Nanotubes be Used to Alleviate the Phytotoxicity of Herbicides in Soils?” Chemosphere 283: 131304. https://doi.org/10.1016/j.chemosphere.2021.131304

[19] Kumari, Pratibha, Alka Sanjay Alka, Sanjay Kumar, Kharu Nisa, and Devinder Kumar Sharma. 2019. “Efficient System for Encapsulation and Removal of Paraquat and Diquat From Aqueous Solution: 4-Sulfonatocalix[n]arenes and Its Magnetite Modified Nanomaterials.” Journal of Environmental Chemical Engineering 7: 103130. https://doi.org/10.1016/j.jece.2019.103130

[20] Malato, S., J. Caceres, A. Agüera, M. Mezcua, D. Hernando, J. Vial, and A. R. Fernández-Alba. 2001. “Degradation of Imidacloprid in Water by Photo-Fenton and TiO₂ Photocatalysis at a Solar Pilot Plant: A Comparative Study.” Environmental Science & Technology 35(21): 4359-4366. https://doi.org/10.1021/es000289k

[21] Landrigan, Philip J., Richard Fuller, Nereus J. R. Acosta, Olusoji Adeyi, Robert Arnold, Niladri (Nil) Basu, Abdoulaye Bibi Baldé, et al. 2018. “The Lancet Commission on Pollution and Health.” The Lancet 391(10119): 462-512. https://doi.org/10.1016/S0140-6736(17)32345-0

[22] Braga, Renan Rodrigues, José Barbosa dos Santos, José Cola Zanuncio, Camila Silva Bibiano, Evander Alves Ferreira, Maxwel Coura Oliveira, Daniel Valadão Silva, and José Eduardo Serrão. 2016. “Effect of Growing Brachiria brizantha on Phytoremediation of Picloram Under Different pH Environments.” Ecological Engineering 94: 102-106. https://doi.org/10.1016/j.ecoleng.2016.05.050

[23] Joly, Pierre, Frédérique Bonnemoy, Jean-Christophe Charvy, Jacques Bohatier, and Clarisse Mallet. 2013. “Toxicity Assessment of the Maize Herbicides S-Metolachlor, Benoxacor, Mesotrione and Nicosulfuron, and Their Corresponding Commercial Formulations, Alone and in Mixtures, Using the Microtoxtest.” Chemosphere 93: 2444-2450. https://doi.org/10.1016/j.chemosphere.2013.08.074

[24] Hagner, Marleena, Juha Mikola, Irma Saloniemi, Kari Saikkonen, and Marjo Helander. 2019. “Effects of a Glyphosate-Based Herbicide on Soil Animal Trophic Groups and Associated Ecosystem Functioning in a Northern Agricultural Field.” Scientific Reports 9(1): 8540. https://doi.org/10.1038/s41598-019-44988-5

[25] Rabelo, Jordana Stein, Edson Aparecido dos Santos, Edmar Isaías de Melo, Marcelo Gomes Marçal Vieira Vaz, and Gilberto de Oliveira Mendes. 2023. “Tolerance of Microorganisms to Residual Herbicides Found in Eucalyptus Plantations.” Chemosphere 329: 138630. https://doi.org/10.1016/j.chemosphere.2023.138630

[26] Namiki, Sayuri, Takashi Otani, Yutaka Motoki, Nobuyasu Seike, and Takashi Iwafune. 2018. “Differential Uptake and Translocation of Organic Chemicals by Several Plant Species From Soil.” Journal of Pesticide Science 43(2): 96-107. https://doi.org/10.1584/jpestics.D17-088

[27] Pang, Nannan, Yu Cui, and Jiye Hu. 2016. “Weather Dependent Dynamics of the Herbicides Florasulam, Carfentrazone-Ethyl, Fluroxypyrmeptyl and Fluroxypyr in Wheat Fields Through Field Studies and Computational Simulation.” Chemosphere 165: 320-328. https://doi.org/10.1016/j.chemosphere.2016.09.026

[28] Caceres-Jensen, Lizethly, Jorge Rodriguez-Becerra, Mauricio Escudey, Jorge Joo-Nagata, Cristian A. Villagra, Valentina Dominguez-Vera, Angelo Neira-Albornoz, and Maribel Cornejo-Huentemilla. 2020. “Nicosulfuron Sorption Kinetics and Sorption/Desorption on Volcanic Ash-Derived Soils: Proposal of Sorption and Transport Mechanisms.” Journal of Hazardous Materials 385: 121576. https://doi.org/10.1016/j.jhazmat.2019.121576

[29] Gao, Jianpeng, Peipei Song, Guanying Wang, Jinhua Wang, Lusheng Zhu, and Jun Wang. 2018. “Responses of Atrazine Degradation and Native Bacterial Community in Soil to Arthrobacter sp. Strain HB-5.” Ecotoxicology and Environmental Safety 159: 317-323. https://doi.org/10.1016/j.ecoenv.2018.05.017

[30] Zhu, Jiangwei, Li Fu, Caihua Jin, Zili Meng, and Ning Yang. 2019. “Study on the Isolation of Two Atrazine-Degrading Bacteria and the Development of a Microbial Agent.” Microorganisms 7: 80. https://doi.org/10.3390/microorganisms7030080

[31] Liu, Jingyuan, Xiaoli Zhou, Tong Wang, Lingling Fan, Shixun Liu, Nan Wu, Anming Xu, et al. 2022. “Construction and Comparison of Synthetic Microbial Consortium System (SMCs) by Non-Living or Living Materials Immobilization and Application in Acetochlor Degradation.” Journal of Hazardous Materials 438: 129460. https://doi.org/10.1016/j.jhazmat.2022.129460

[32] Wahla, Abdul Qadeer, Samina Anwar, Jochen A. Mueller, Muhammad Arslan, and Samina Iqbal. 2020. “Immobilization of Metribuzin Degrading Bacterial Consortium MB3R on Biochar Enhances Bioremediation of Potato Vegetated Soil and Restores Bacterial Community Structure.” Journal of Hazardous Materials 390: 121493. https://doi.org/10.1016/j.jhazmat.2019.121493

[33] Zhong, Jianfeng, Siyi Wu, Wen-Juan Chen, Yaohua Huang, Qiqi Lei, Sandhya Mishra, Pankaj Bhatt, and Shaohua Chen. 2023. “Current Insights Into the Microbial Degradation of Nicosulfuron: Strains, Metabolic Pathways, and Molecular Mechanisms.” Chemosphere 326: 138390. https://doi.org/10.1016/j.chemosphere.2023.138390

[34] Szewczyk, Rafał, Sylwia Różalska, Julia Mironenka, and Przemysław Bernat. 2020. “Atrazine Biodegradation by Mycoinsecticide Metarhizium robertsii: Insights Into Its Amino Acids and Lipids Profile.” Journal of Environmental Management 262: 110304. https://doi.org/10.1016/j.jenvman.2020.110304

[35] Caron, Emmanuelle, Pierre Lafrance, Jean-Christian Auclair, and Marc Duchemin. 2010. “Impact of Grass and Grass With Poplar Buffer Strips on Atrazine and Metolachlor Losses in Surface Runoff and Subsurface Infiltration From Agricultural Plots.” Journal of Environmental Quality 39: 617-629. https://doi.org/10.2134/jeq2009.0041

[36] Johnston, Trevor G., Shuo-Fu Yuan, James M. Wagner, Xiunan Yi, Abhijit Saha, Patrick Smith, Alshakim Nelson, and Hal S. Alper. 2020. “Compartmentalized Microbes and Co-Cultures in Hydrogels for On-Demand Bioproduction and Preservation.” Nature Communications 11: 563. https://doi.org/10.1038/s41467-020-14371-4

[37] Scott, Spencer R., M. Omar Din, Philip Bittihn, Liyang Xiong, Lev S. Tsimring, and Jeff Hasty. 2017. “A Stabilized Microbial Ecosystem of Self-Limiting Bacteria Using Synthetic Quorum-Regulated Lysis.” Nature Microbiology 2: 17083. https://doi.org/10.1038/nmicrobiol.2017.83

[38] Jiao, Shuo, Yunfeng Yang, Yiqin Xu, Jie Zhang, and Yahai Lu. 2020. “Balance Between Community Assembly Processes Mediates Species Coexistence in Agricultural Soil Microbiomes Across Eastern China.” The ISME Journal 14(1): 202-216. https://doi.org/10.1038/s41396-019-0522-9

[39] Fuhrman, Jed A. 2009. “Microbial Community Structure and Its Functional Implications.” Nature 459(7244): 193-199. https://doi.org/10.1038/nature08058

[40] Gilmore, Sean P., Thomas S. Lankiewicz, St. Elmo Wilken, Jennifer L. Brown, Jessica A. Sexton, John K. Henske, Michael K. Theodorou, David L. Valentine, and Michelle A. O'Malley. 2019. “Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation.” ACS Synthetic Biology 8(9): 2174-2185. https://doi.org/10.1021/acssynbio.9b00271

[41] Bairey, Eyal, Eric D. Kelsic, and Roy Kishony. 2016. “High-Order Species Interactions Shape Ecosystem Diversity.” Nature Communications 7: 12285. https://doi.org/10.1038/ncomms12285

[42] Yu, Xiaofei, Sijia Zheng, Meijuan Zheng, Xiaofan Ma, Guoping Wang, and Yuanchun Zou. 2018. “Herbicide Accumulations in the Xingkai Lake Area and the Use of Restored Wetland for Agricultural Drainage Treatment.” Ecological Engineering 120: 260-265. https://doi.org/10.1016/j.ecoleng.2018.06.009

[43] Wang, Xiaochun, and Qinglong Liu. 2020. “Spatial and Temporal Distribution Characteristics of Triazine Herbicides in Typical Agricultural Regions of Liaoning, China.” Bulletin of Environmental Contamination and Toxicology 105(6): 899-905. https://doi.org/10.1007/s00128-020-03049-8

[44] Gfrerer, Marion, Thomas Wenzl, Xie Quan, Bernhard Platzer, and Ernst Lankmayr. 2002. “Occurrence of Triazines in Surface and Drinking Water of Liaoning Province in Eastern China.” Journal of Biochemical and Biophysical Methods 53(1-3): 217-228. https://doi.org/10.1016/S0165-022X(02)00110-0

[45] Shi, Rongguang, Jungang Lv, and Jimin Feng. 2011. “Assessment of Pesticide Pollution in Suburban Soil in South Shenyang, China.” Bulletin of Environmental Contamination and Toxicology 87(5): 567-573. https://doi.org/10.1007/s00128-011-0401-1

[46] Lee, H. J., M. V. Duke, and S. O. Duke. 1993. “Cellular Localization of Protoporphyrinogen-Oxidizing Activities of Etiolated Barley (Hordeum Vulgare L.) Leaves (Relationship to Mechanism of Action of Protoporphyrinogen Oxidase-Inhibiting Herbicides).” Plant Physiology 102: 881-889. https://doi.org/10.1104/pp.102.3.881

[47] Liang, Bo, Peng Lu, Huihui Li, Rong Li, Shunpeng Li, and Xing Huang. 2009. “Biodegradation of Fomesafen by Strain Lysinibacillus sp. ZB-1 Isolated From Soil.” Chemosphere 77: 1614-1619. https://doi.org/10.1016/j.chemosphere.2009.09.033

[48] Singh, Simranjeet, Vijay Kumar, Niraj Upadhyay, and Joginder Singh. 2020. “The Effects of Fe(II), Cu(II) and Humic Acid on Biodegradation of Atrazine.” Journal of Environmental Chemical Engineering 8(2): 103539. https://doi.org/10.1016/j.jece.2019.103539

[49] Hofman, Jakub, Ivana Hovorková, and Kirk T. Semple. 2014. “The Variability of Standard Artificial Soils: Behaviour, Extractability and Bioavailability of Organic Pollutants.” Journal of Hazardous Materials 264: 514-520. https://doi.org/10.1016/j.jhazmat.2013.10.039

[50] Song, Ning Hui, Liang Chen, and Hong Yang. 2008. “Effect of Dissolved Organic Matter on Mobility and Activation of Chlorotoluron in Soil and Wheat.” Geoderma 146(1/2): 344-352. https://doi.org/10.1016/j.geoderma.2008.05.031

[51] Scelza, Rosalia, Maria Antonietta Rao, and Liliana Gianfreda. 2008. “Response of an Agricultural Soil Topentachlorophenol (PCP) Contamination and the Addition of Compost or Dissolved Organic Matter.” Soil Biology and Biochemistry 40(90): 2162-2169. https://doi.org/10.1016/j.soilbio.2008.05.005

[52] Moon, Jung-Won, Mark N. Goltz, Kyu-Hong Ahn, and Jae-Woo Park. 2003. “Dissolved Organic Matter Effects on the Performance of a Barrier to Polycyclic Aromatic Hydrocarbon Transport by Groundwater.” Journal of Contaminant Hydrology 60(3/4): 307-326. https://doi.org/10.1016/S0169-7722(02)00084-0

[53] Govantes, Fernando, Vicente García-González, Odil Porrúa, Ana Isabel Platero, Alicia Jiménez-Fernández, and Eduardo Santero. 2010. “Regulation of the Atrazine-Degradative Genes in Pseudomonas sp. Strain ADP.” FEMS Microbiology Letters 310: 1-8. https://doi.org/10.1111/j.1574-6968.2010.01991.x

[54] Han, Lingxi, Tong Liu, Kuan Fang, Xianxu Li, Xiangwei You, Yiqiang Li, Xiuguo Wang, and Jun Wang. 2022. “Indigenous Functional Microbial Communities for the Preferential Degradation of Chloroacetamide Herbicide S-Enantiomers in Soil.” Journal of Hazardous Materials 423: 127135. https://doi.org/10.1016/j.jhazmat.2021.127135

[55] Spangenberg, Jorge E., and Vivian Zufferey. 2023. “Soil Management Affects Carbon and Nitrogen Concentrations and Stable Isotope Ratios in Vine Products.” Science of the Total Environment 873: 162410. https://doi.org/10.1016/j.scitotenv.2023.162410

[56] Zhang, Yuanqing, Jingwen Zhang, Baihui Shi, Bing Li, Zhongkun Du, Jun Wang, Lusheng Zhu, and Jinhua Wang. 2021. “Effects of Cloransulam-Methyl and Diclosulam on Soil Nitrogen and Carbon Cycle-Related Microorganisms.” Journal of Hazardous Materials 418: 126395. https://doi.org/10.1016/j.jhazmat.2021.126395

[57] Cui, Ning, Saige Wang, Mahdi Safaei Khorram, Hua Fang, and Yunlong Yu. 2018. “Microbial Degradation of Fomesafen and Detoxification of Fomesafen-Contaminated Soil by the Newly Isolated Strain Bacillus sp. FE-1 Via a Proposed Biochemical Degradation Pathway.” Science of the Total Environment 616-617: 1612-1619. https://doi.org/10.1016/j.scitotenv.2017.10.151

[58] Lee, Dong Hyeon, and Seung Bum Kim. 2024. “Quorum Quenching Potential of Reyranella sp. Isolated From Riverside Soil and Description of Reyranella humidisoli sp. Nov.” Journal of Microbiology 62: 449-461. https://doi.org/10.1007/s12275-024-00131-2

[59] Chuanxiao, Dai, Fang Ma, Weize Wu, Shuzhen Li, Jing Yang, Zhuo Chen, Shengyang Lian, and Yuanyuan Qu. 2023. “Metagenomic Analyses Reveals Indole Signaling Effect on Microbial Community in Sequencing Batch Reactors: Quorum Sensing Inhibition and Antibiotic Resistance Enrichment.” Environmental Research 229: 115897. https://doi.org/10.1016/j.envres.2023.115897

[60] Wang, Yanhui, Jianan Men, Tao Zheng, Yonglin Ma, Weisheng Li, Tomislav Cernava, Lianyang Bai, and Decai Jin. 2023. “Impact of Pyroxasulfone on Sugarcane Rhizosphere Microbiome and Functioning During Field Degradation.” Journal of Hazardous Materials 455: 131608. https://doi.org/10.1016/j.jhazmat.2023.131608

[61] Wu, Haowei, Huiling Cui, Chenxi Fu, Ran Li, Fengyuan Qi, Zhelun Liu, Guang Yang, Keqing Xiao, and Min Qiao. 2024. “Unveiling the Crucial Role of Soil Microorganisms in Carbon Cycling: A Review.” Science of the Total Environment 909: 168627. https://doi.org/10.1016/j.scitotenv.2023.168627

[62] Liu, Sijia, Zhongtang Yu, Huiyue Zhong, Nan Zheng, Sharon Huws, Jiaqi Wang, and Shengguo Zhao. 2023. “Functional Gene-Guided Enrichment Plus in Situ Microsphere Cultivation Enables Isolation of New Crucial Ureolytic Bacteria From the Rumen of Cattle.” Microbiome 11(1): 76. https://doi.org/10.1186/s40168-023-01510-4

[63] Wang, Baorong, Shaoshan An, Chao Liang, Yang Liu, and Yakov Kuzyakov. 2021. “Microbial Necromass as the Source of Soil Organic Carbon in Global Ecosystems.” Soil Biology and Biochemistry 162: 108422. https://doi.org/10.1016/j.soilbio.2021.108422

[64] Kettler, T. A., J. W. Doran, and T. L. Gilbert. 2001. “Simplified Method for Soil Particle-Size Determination to Accompany Soil-Quality Analyses.” Soil & Water Management & Conservation 65: 849-852. https://doi.org/10.2136/sssaj2001.653849x

[65] Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. 2019. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology 37: 852-857. https://doi.org/10.1038/s41587-019-0209-9

[66] Callahan, Benjamin J., Paul J. McMurdie, Michael J. Rosen, Andrew W. Han, Amy Jo A. Johnson, and Susan P. Holmes. 2016. “DADA2: High-Resolution Sample Inference From Illumina Amplicon Data.” Nature Methods 13(7): 581-583. https://doi.org/10.1038/nmeth.3869

[67] Zhou, Shu-Yi-Dan, Zhiyang Lie, Xujun Liu, Yong-Guan Zhu, Josep Peñuelas, Roy Neilson, Xiaoxuan Su, et al. 2023. “Distinct Patterns of Soil Bacterial and Fungal Community Assemblages in Subtropical Forest Ecosystems Under Warming.” Global Change Biology 29: 1501-1513. https://doi.org/10.1111/gcb.16541

[68] Sun, Yuanze, Mengjun Zhang, Chongxue Duan, Na Cao, Weiqian Jia, Zelong Zhao, Changfeng Ding, Yi Huang, and Jie Wang. 2021. “Contribution of Stochastic Processes to the Microbial Community Assembly on Field-Collected Microplastics.” Environmental Microbiology 23: 6707-6720. https://doi.org/10.1111/1462-2920.15713

[69] Jiao, Shuo, Weimin Chen, and Gehong Wei. 2022. “Core Microbiota Drive Functional Stability of Soil Microbiome in Reforestation Ecosystems.” Global Change Biology 28: 1038-1047. https://doi.org/10.1111/gcb.16024

[70] Zhang, Yuxiao, Zixiao Xu, Jingxin Li, Deli Liu, Yongze Yuan, Zhengjun Chen, and Gejiao Wang. 2019. “Cooperation Between Two Strains of Enterobacter and Klebsiella in the Simultaneous Nitrogen Removal and Phosphate Accumulation Processes.” Bioresource Technology 291: 121854. https://doi.org/10.1016/j.biortech.2019.121854

[71] Zhang, Yuxiao, Qing Xu, Gejiao Wang, and Kaixiang Shi. 2023. “Mixed Enterobacter and Klebsiella Bacteria Enhance Soybean Biological Nitrogen Fixation Ability When Combined With Rhizobia Inoculation.” Soil Biology and Biochemistry 184: 109100. https://doi.org/10.1016/j.soilbio.2023.109100

[72] Zhang, Yuxiao, Qing Xu, Gejiao Wang, and Kaixiang Shi. 2022. “Indole-Acetic Acid Promotes Ammonia Removal Through Heterotrophic Nitrification, Aerobic Denitrification With Mixed Enterobacter sp. Z1 and Klebsiella sp. Z2.” Frontiers in Microbiology 13: 929036. https://doi.org/10.3389/fmicb.2022.929036

[73] Zhang, Xudong, and Wulf Amelung. 1996. “Gas Chromatographic Determination of Muramic Acid, Glucosamine, Mannosamine, and Galactosamine in Soils.” Soil Biology and Biochemistry 28: 1201-1206. https://doi.org/10.1016/0038-0717(96)00117-4

[74] Appuhn, A., and R. Joergensen. 2006. “Microbial Colonisation of Roots as a Function of Plant Species.” Soil Biology and Biochemistry 38: 1040-1051. https://doi.org/10.1016/j.soilbio.2005.09.002

[75] Liang, Chao, Wulf Amelung, Johannes Lehmann, and Matthias Kästner. 2019. “Quantitative Assessment of Microbial Necromass Contribution to Soil Organic Matter.” Global Change Biology 25: 3578-3590. https://doi.org/10.1111/gcb.14781

[76] Zhang, Yuxiao, Zixiao Xu, Zhengjun Chen, and Gejiao Wang. 2020. “Simultaneous Degradation of Triazophos, Methamidophos and Carbofuran Pesticides in Wastewater Using an Enterobacter Bacterial Bioreactor and Analysis of Toxicity and Biosafety.” Chemosphere 261: 128054. https://doi.org/10.1016/j.chemosphere.2020.128054

[77] Chen, Shifu. 2023. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” iMeta 2: e107. https://doi.org/10.1002/imt2.107

[78] Li, Dinghua, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, and Tak-Wah Lam. 2015. “MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct De Bruijn Graph.” Bioinformatics 31: 1674-1676. https://doi.org/10.1093/bioinformatics/btv033

[79] Nielsen, H. Bjørn, Mathieu Almeida, Agnieszka Sierakowska Juncker, Simon Rasmussen, Junhua Li, Shinichi Sunagawa, Damian R. Plichta, et al. 2014. “Identification and Assembly of Genomes and Genetic Elements in Complex Metagenomic Samples Without Using Reference Genomes.” Nature Biotechnology 32: 822-828. https://doi.org/10.1038/nbt.2939

[80] Kang, Dongwan D., Feng Li, Edward Kirton, Ashleigh Thomas, Rob Egan, Hong An, and Zhong Wang. 2019. “MetaBAT 2: An Adaptive Binning Algorithm for Robust and Efficient Genome Reconstruction From Metagenome Assemblies.” PeerJ 7: e7359. https://doi.org/10.7717/peerj.7359

[81] Alneberg, Johannes, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z. Ijaz, Leo Lahti, et al. 2014. “Binning Metagenomic Contigs by Coverage and Composition.” Nature Methods 11: 1144-1146. https://doi.org/10.1038/nmeth.3103

[82] Buchfink, Benjamin, Klaus Reuter, and Hajk-Georg Drost. 2021. “Sensitive Protein Alignments at Tree-of-Life Scale Using DIAMOND.” Nature Methods 18: 366-368. https://doi.org/10.1038/s41592-021-01101-x

[83] Tao, Yue, Lu Shen, Siyue Han, Zixu Li, Yunhe Cui, Yulong Lin, Jianhua Qu, and Ying Zhang. 2023. “Metagenomic Study of Carbon Metabolism in Black Soil Microbial Communities Under Lead-Lanthanum Stress.” Journal of Hazardous Materials 446: 130666. https://doi.org/10.1016/j.jhazmat.2022.130666

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