|
|
|
| Construction of Synthetic Microbial Consortium and Its Mechanism of Enhancing Plant Tolerance to Cadmium |
| ZHAO Qing1, LI Na1, WANG Jian-Feng2,*, WEI Ting-Ting1, ZHANG Jing1, CHEN Lan-Lan1, TIAN Ming-Zhu1, GONG Ji-Yi1, YI Yin1,* |
1 College of Life Sciences/Key Laboratory of National Forestry and Grassland Administration for Biodiversity Conservation of Southwest Karst Mountains/Key Laboratory of Plant Physiology and Developmental Regulation of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; 2 Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou 730000, China |
|
|
|
|
Abstract Soil cadmium (Cd) contamination has become an increasingly serious environmental problem under intensified industrial and agricultural activities, posing significant threats to crop production and ecological security. Microbial remediation has attracted considerable attention as an environmentally friendly and cost-effective strategy. Synthetic microbial communities (SynComs), which are artificially assembled microbial consortia composed of functionally defined strains, represent controllable microbial systems capable of performing complex ecological functions through cooperative interactions. In recent years, SynComs have emerged as powerful tools for investigating plant-microbe interactions and for developing microbiome-based environmental solutions. This review summarizes the principles and design strategies for constructing SynComs and outlines the main approaches for their optimization and functional regulation. In addition, the potential roles of SynComs in plant-microbe interaction studies and environmental management are discussed, with a particular focus on their application in enhancing plant tolerance to cadmium stress. Overall, this review aims to provide theoretical insights into the ecological and molecular mechanisms underlying SynCom-mediated plant tolerance to heavy metal stress, and to offer new perspectives for the application of SynComs in the remediation of heavy metal-contaminated soils and sustainable agricultural development.
|
|
Received: 03 October 2025
|
|
|
|
Corresponding Authors:
*yiyin@gznu.edu.cn; wangjf12@lzu.edu.cn
|
|
|
|
[1] 白晓晗. 2024. 合成菌群对上海青砷镉吸收的阻控过程与技术[D].博士学位论文, 西北农林科技大学, 导师:方临川, 陈寒松, pp. 26-36. (Bai X H.2024. Processes and techniques for synthetic microbial communities to regulate arsenic and cadmium absorption in Shanghai green vegetables[D]. Thesis for Ph. D., Northwest A&F University, Supervisor:Fang L C, Chen H S, pp. 26-36.) [2] 黄佳城, 张瑷珲, 付友思, 等. 2022. 功能性菌群构建的研究进展[J].合成生物学, 3(01):155-167. (Huang J C, Zhang A H, Fu Y S, et al.2022. Research progress in functional microbiome engineering[J]. Synthetic Biology, 3(01):155-167.) [3] 康育鑫, 廖水兰, 兰婕, 等. 2021. 镉胁迫对不同叶用莴苣品种生长及生理特性的影响[J]. 江苏农业科学, 49(07):149-154. (Kang Y X, Liao S L, Lan J, et al.2021. Effects of cadmium stress on growth and physiological characteristics of different leaf Lactucasativa L. varieties[J]. Jiangsu Agricultural Sciences, 49(07):149-154. [4] 李敏, 陈利顶, 杨小茹, 等. 2021. 城乡复合生态系统土壤微生物群落特征及功能差异:研究进展与展望[J]. 土壤学报, 58(06):1368-1380. (Li M, Chen L, Yang X, et al.2021. Characteristics and functional differences of soil microbial communities in urban-rural composite ecosystems:Research progress and outlook[J]. Acta Pedologica Sinica, 58(06):1368-1380.) [5] 孙韵雅, 陈佳, 王悦, 等. 2020. 根际促生菌促生机理及其增强植物抗逆性研究进展[J].草地学报, 28(05):1203-1215. (Sun Y, Chen J, Wang Y, et al.2020. Advances in growth promotion mechanisms of PGPRs and their effects on improving plant stress tolerance[J]. Acta Agrestia Sinica, 28(5):1203.) [6] 王琼, 冯雪薇, 冯英. 2025. 镉修复微生物菌剂的构建及其作用效果[J].农业环境科学学报, 44(05):1266-1275. (Wang Q, Feng X, Feng Y.2025. Development and efficacy of microbial agents for cadmium remediation[J]. Journal of Agricultural Environmental Sciences, 44(05):1266-1275.) [7] 张娇, 陈江峰, 陈奕璇, 等. 2023. 合成功能菌群的构建及其工程化应用[J]. 生物工程学报, 39(06):2517-2545. (Zhang J, Chen J, Chen Y, et al.2023. Construction of synthetic functional microbial communities and their engineered applications[J]. Chinese Journal of Biotechnology, 39(06):2517-2545.) [8] 周佳新, 刘悦, 徐伟慧, 等. 2024. 合成菌群对大豆根际和根内微生物群落的影响[J].中国生态农业学报(中英文), 32(04):571-581. (Zhou J, Liu Y, Xu W, et al.2024. Effects of synthetic microbial communities on microbial communities in the rhizosphere and root interior of soybean plants[J]. Chinese Journal of Ecological Agriculture (Chinese and English), 32(04):571-581.) [9] Ahmad P, Jaleel C A, Salem M A, et al.2010. Roles of enzymatic and nonenzymatic antioxidants in plants during abiotic stress[J]. Critical Reviews in Biotechnology, 30(3):161-175. [10] Alnahhas R N, Sadeghpour M, Chen Y, et al.2020. Majority sensing in synthetic microbial consortia[J]. Nature Communications, 11(1):3659. [11] Baldini F, Heinken A, Heirendt L, et al.2019. The Microbiome modeling toolbox:From microbial interactions to personalized microbial communities[J]. Bioinformatics, 35(13):2332-2334. [12] Bhanse P, Kumar M, Singh L, et al.2022. Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils:Opportunities, challenges, and prospects[J]. Chemosphere, 303(Pt 1):134954. [13] Blake C, Christensen M N, Kovács Á T.2021. Molecular aspects of plant growth promotion and protection by Bacillus subtilis[J]. Molecular Plant-Microbe Interactions, 34(1):15-25. [14] Bodenhausen N, Bortfeld-Miller M, Ackermann M, et al.2014. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota[J]. PLOS Genetics, 10(4):e1004283. [15] Brenner K, Arnold F H.2011. Self-organization, layered structure, and aggregation enhance persistence of a synthetic biofilm consortium[J]. PLOS ONE, 6(2):e16791. [16] Cai Z, Yu T, Tan W, et al.2024. GmAMT2.1/2.2-dependent ammonium nitrogen and metabolites shape rhizosphere microbiome assembly to mitigate cadmium toxicity[J]. npj Biofilms and Microbiomes, 10(1):60. [17] Chang J D, Huang S, Yamaji N, et al.2020. OsNRAMP1 transporter contributes to cadmium and manganese uptake in rice[J]. Plant, Cell & Environment, 43(10):2476-2491. [18] Chebli Y, Geitmann A.2017. Cellular growth in plants requires regulation of cell wall biochemistry[J]. Current Opinion in Cell Biology, 44:28-35. [19] Chen L, Luo S, Li X, et al.2014. Interaction of Cd-hyperaccumulator Solanum nigrum L. and functional endophyte Pseudomonas sp. Lk9 on soil heavy metals uptake[J]. Soil Biology and Biochemistry, 68:300-308. [20] Chen L, Luo S, Xiao X, et al.2010. Application of plant growth-promoting endophytes (PGPE) isolated from Solanum nigrum L. for phytoextraction of Cd-polluted soils[J]. Applied Soil Ecology, 46(3):383-389. [21] Chi Y, Ma X, Chu S, et al.2025. Nitrogen cycle induced by plant growth-promoting rhizobacteria drives “microbial partners” to enhance cadmium phytoremediation[J]. Microbiome, 13(1):113. [22] Chiboub M, Jebara S H, Saadani O, et al.2018. Physiological responses and antioxidant enzyme changes in Sulla coronaria inoculated by cadmium resistant bacteria[J]. Journal of Plant Research, 131(1):99-110. [23] De Vrieze J, Christiaens M E R, Verstraete W.2017. The microbiome as engineering tool:Manufacturing and trading between microorganisms[J]. New Biotechnology, 39:206-214. [24] El-Ballat E M, Elsilk S E, Ali H M, et al.2023. Metal-resistant PGPR strain azospirillum brasilense EMCC1454 enhances growth and chromium stress tolerance of chickpea (Cicer arietinum L.) by modulating redox potential, osmolytes, antioxidants, and stress-related gene expression[J]. Plants, 12(11):2110. [25] Gilbert E S, Walker A W, Keasling J D.2003. A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion[J]. Applied Microbiology and Biotechnology, 61:77-81. [26] Gilmore S P, Lankiewicz T S, Wilken S E, et al.2019. Top-down enrichment guides in formation of synthetic microbial consortia for biomass degradation[J]. ACS Synthetic Biology, 8(9):2174-2185. [27] Glick B R.2012. Plant growth‐promoting bacteria:Mechanisms and applications[J]. Scientifica, 2012(1):963401. [28] Gollop N, Zakin V, Weinberg Z G.2005. Antibacterial activity of lactic acid bacteria included in inoculants for silage and in silages treated with these inoculants[J]. Journal of Applied Microbiology, 98(3):662-666. [29] Haider F U, Liqun C, Coulter J A, et al.2021. Cadmium toxicity in plants:Impacts and remediation strategies[J]. Ecotoxicology and Environmental Safety, 211:111887. [30] Han H, Cai H, Wang X, et al.2020. Heavy metal-immobilizing bacteria increase the biomass and reduce the Cd and Pb uptake by pakchoi (Brassica chinensis L.) in heavy metal-contaminated soil[J]. Ecotoxicology and Environmental Safety, 195:110375. [31] Han H, Wang Q, He L, et al.2018. Increased biomass and reduced rapeseed Cd accumulation of oilseed rape in the presence of Cd-immobilizing and polyamine-producing bacteria[J]. Journal of Hazardous Materials, 353:280-289. [32] Huang L, Fan Z, Hu Z, et al.2024. Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation[J]. Microbiome, 12(1):236. [33] Jia H, Fan Y, Feng X, et al.2014. Enhancing stress-resistance for efficient microbial biotransformations by synthetic biology[J]. Frontiers in Bioengineering and Biotechnology, 2:44. [34] Johnston T G, Yuan S F, Wagner J M, et al.2020. Compartmentalized microbes and co-cultures in hydrogels for on-demand bioproduction and preservation[J]. Nature Communications, 11(1):563. [35] Jonguitud-Borrego N.2023. Production of novel taxane intermediates of anticancer drug taxol using microbial consortia[D]. Thesis for Ph. D., The University of Edinburgh, Supervisor:Rios-Solisdoi L, pp. 25-35. [36] Kerner A, Park J, Lin X N.2012. A programmable Escherichia coli consortium via tunable Symbiosis[J]. PLOS ONE, 7(3):e34032. [37] Khanna K, Jamwal V L, Kohli S K, et al.2019. Plant growth promoting rhizobacteria induced Cd tolerance in Lycopersicon esculentum through altered antioxidative defence expression[J]. Chemosphere, 217:463-474. [38] Kolupaev Y E, Karpets Y V, Kabashnikova L F.2019. Antioxidative system of plants:Cellular compartmentalization, protective and signaling functions, mechanisms of regulation[J]. Applied Biochemistry and Microbiology, 55:441-459. [39] Lanquar V, Lelièvre F, Barbier-Brygoo H, et al.2004. Regulation and function of AtNRAMP4 metal transporter protein[J]. Soil Science and Plant Nutrition, 50(7):1141-1150. [40] Lawson C E, Harcombe W R, Hatzenpichler R, et al.2019. Common principles and best practices for engineering microbiomes[J]. Nature Reviews Microbiology, 17(12):725-741. [41] Lei Z, Zhang H, Liu W, et al.2025. Dynamic and stable core microbiota assist plants in enriching selenium and reducing cadmium absorption[J]. Advanced Science (Weinheim, Baden-Wurttemberg, Germany), 12(25):e00862. [42] van der Lelie D, Oka A, Taghavi S, et al.2021. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis[J]. Nature Communications, 12(1):3105. [43] Li F, Deng Y, Liu Y, et al.2023. Arabidopsis transcription factor WRKY45 confers cadmium tolerance via activating PCS1 and PCS2 expression[J]. Journal of Hazardous Materials, 460:132496. [44] Lin Y F, Aarts M G M.2012. The molecular mechanism of zinc and cadmium stress response in plants[J]. Cellular and Molecular Life Sciences, 69:3187-3206. [45] Liu L, Gong Z, Zhang Y, et al.2014. Growth, cadmium uptake and accumulation of maize (Zea mays L.) under the effects of arbuscular mycorrhizal fungi[J]. Ecotoxicology, 23:1979-1986. [46] Liu Y, Ding M, Ling W, et al.2017. A three-species microbial consortium for power generation[J]. Energy & Environmental Science, 10(7):1600-1609. [47] Llorca C M, Potschin M, Zentgraf U.2014. bZIPs and WRKYs:Two large transcription factor families executing two different functional strategies[J]. Frontiers in Plant Science, 5:169. [48] Luo J, Gu S, Guo X, et al.2022. Core microbiota in the rhizosphere of heavy metal accumulators and its contribution to plant performance[J]. Environmental Science & Technology, 56(18):12975-12987. [49] Mantelin S, Touraine B.2004. Plant growth‐promoting bacteria and nitrate availability:Impacts on root development and nitrate uptake[J]. Journal of Experimental Botany, 55(394):27-34. [50] Masset J, Calusinska M, Hamilton C, et al.2012. Fermentative hydrogen production from glucose and starch using pure strains and artificial co-cultures of Clostridium Spp[J]. Biotechnology for Biofuels, 5(1):35. [51] Milner M J, Craft E, Yamaji N, et al.2012. Characterization of the high affinity Zn transporter from Noccaea caerulescens, NcZNT1, and dissection of its promoter for its role in Zn uptake and hyperaccumulation[J]. New Phytologist, 195(1):113-123. [52] Minchev Z, Kostenko O, Soler R, et al.2021. Microbial consortia for effective biocontrol of root and foliar diseases in tomato[J]. Frontiers in Plant Science, 12:756368. [53] Miyadate H, Adachi S, Hiraizumi A, et al.2011. OsHMA3, a P1B‐type of ATPase affects root‐to‐shoot cadmium translocation in rice by mediating efflux into vacuoles[J]. New Phytologist, 189(1):190-199. [54] Muschitz A, Riou C, Mollet J, et al.2015. Modifications of cell wall pectin in tomato cell suspension in response to cadmium and zinc[J]. Acta Physiologiae Plantarum, 37:1-11. [55] Nair R R, Vasse M, Wielgoss S, et al.2019. Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences[J]. Nature Communications, 10(1):4301. [56] Nikel P I, de Lorenzo V.2013. Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1, 3-dichloroprop-1-ene[J]. Metabolic Engineering, 15:98-112. [57] Pacheco A R, Moel M, Segrè D.2019. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems[J]. Nature Communications, 10(1):103. [58] Pal A K, Sengupta C.2019. Isolation of cadmium and lead tolerant plant growth promoting rhizobacteria:Lysinibacillus varians and Pseudomonas putida from Indian agricultural soil[J]. Soil and Sediment Contamination:An International Journal, 28(7):601-629. [59] Pandhal J, Noirel J.2014. Synthetic microbial ecosystems for biotechnology[J]. Biotechnology Letters, 36(6):1141-1151. [60] Pedas P, Ytting C K, Fuglsang A T, et al.2008. Manganese efficiency in barley:Identification and characterization of the metal ion transporter HvIRT1[J]. Plant Physiology, 148(1):455-466. [61] Peng J, Wang Y, Ding G, et al.2017. A pivotal role of cell wall in cadmium accumulation in the Crassulaceae hyperaccumulator Sedum plumbizincicola[J]. Molecular Plant, 10(5):771-774. [62] Puentes-Téllez P E, Salles J F.2018. Construction of effective minimal active microbial consortia for lignocellulose degradation[J]. Microbial Ecology, 76:419-429. [63] Qin S, Zhang H, He Y, et al.2023. Improving radish phosphorus utilization efficiency and inhibiting Cd and Pb uptake by using heavy metal-immobilizing and phosphate-solubilizing bacteria[J]. Science of the Total Environment, 868:161685. [64] Radhakrishnan R, Hashem A, AbdAllah E F.2017. Bacillus:A biological tool for crop improvement through bio-molecular changes in adverse environments[J]. Frontiers in Physiology, 8:667. [65] Ramachandran G, Bikard D.2019. Editing the microbiome the CRISPR way[J]. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 374(1772):20180103. [66] Riggs P J, Chelius M K, Iniguez A L, et al.2001. Enhanced maize productivity by inoculation with diazotrophic bacteria[J]. Functional Plant Biology, 28(9):829-836. [67] Samaras A, Kamou N, Tzelepis G, et al.2022. Root transcriptional and metabolic dynamics induced by the plant growth promoting rhizobacterium (PGPR) Bacillus subtilis Mbi600 on cucumber plants[J]. Plants, 11(9):1218. [68] Santhanam R, Menezes R C, Grabe V, et al.2019. A suite of complementary biocontrol traits allows a native consortium of root-associated bacteria to protect their host plant from a fungal sudden-wilt disease[J]. Molecular Ecology, 28(5):1154-1169. [69] Sasaki A, Yamaji N, Yokosho K, et al.2012. Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice[J]. The Plant Cell, 24(5):2155-2167. [70] Shang C, Wang L, Tian C, et al.2020. Heavy metal tolerance and potential for remediation of heavy metal-contaminated saline soils for the euhalophyte Suaeda salsa[J]. Plant Signaling & Behavior, 15(11):1805902. [71] Tariq S, Zeeshan K, Muhammad A, et al.2024. Synthetic bacterial community derived from Astragalus mongholicus and plant-plant interactions inhibit cadmium uptake by modulating gene expression, antioxidant system and carbohydrate metabolism under cadmium contaminated soil[J]. Journal of Environmental Chemical Engineering,12(1):111619. [72] Ullah I, Al-Johny B O, Al-Ghamdi K M S, et al.2019. Endophytic bacteria isolated from Solanum nigrum L., alleviate cadmium (Cd) stress response by their antioxidant potentials, including SOD synthesis by sodA gene[J]. Ecotoxicology and Environmental Safety, 174:197-207. [73] Valko M, Rhodes C J, Moncol J, et al.2006. Free radicals, metals and antioxidants in oxidative stress-induced cancer[J]. Chemico-Biological Interactions, 160(1):1-40. [74] Vazquez A, Zawoznik M, Benavides M P, et al.2021. Azospirillum brasilense Az39 restricts cadmium entrance into wheat plants and mitigates cadmium stress[J]. Plant Science:An International Journal of Experimental Plant Biology, 312:111056. [75] Verma S, Kuila A.2019. Bioremediation of heavy metals by microbial process[J]. Environmental Technology & Innovation, 14:100369. [76] Vivas A, Biró B, Ruiz-Lozano J M, et al.2006. Two bacterial strains isolated from a Zn-polluted soil enhance plant growth and mycorrhizal efficiency under Zn-toxicity[J]. Chemosphere, 62(9):1523-1533. [77] Wang J, Li R, Zhang H, et al.2020. Beneficial bacteria activate nutrients and promote wheat growth under conditions of reduced fertilizer application[J]. BMC Microbiology, 20(1):38. [78] Wang L, Maranas C D.2018. MinGenome:An in Silico top-down approach for the synthesis of minimized genomes[J]. ACS Synthetic Biology, 7(2):462-473. [79] Wang X, Fang L, Beiyuan J, et al.2021. Improvement of alfalfa resistance against Cd stress through rhizobia and arbuscular mycorrhiza fungi co-inoculation in Cd-contaminated soil[J]. Environmental Pollution, 277:116758. [80] Wani P A, Khan M S, Zaidi A.2007. Synergistic effects of the inoculation with nitrogen-fixing and phosphate-solubilizing rhizobacteria on the performance of field-grown chickpea[J]. Journal of Plant Nutrition and Soil Science, 170(2):283-287. [81] Wu F, Fan J, Ye X, et al.2022. Unraveling cadmium toxicity in Trifolium repens L. seedling:Insight into regulatory mechanisms using comparative transcriptomics combined with physiological analyses[J]. International Journal of Molecular Sciences, 23(9):4612. [82] Wu X, Tian H, Li L, et al.2021. Higher Cd-accumulating oilseed rape has stronger Cd tolerance due to stronger Cd fixation in pectin and hemicellulose and higher Cd chelation[J]. Environmental Pollution, 285:117218. [83] Xavier J B.2011. Social interaction in synthetic and natural microbial communities[J]. Molecular Systems Biology, 7(1):483. [84] Xiao Y, Wu X, Liu D, et al.2020. Cell wall polysaccharide-mediated cadmium tolerance between two Arabidopsis thaliana ecotypes[J]. Frontiers in Plant Science, 11:473. [85] Xie X, Müller N.2019. Enhanced aniline degradation by Desulfatiglans anilini in a synthetic microbial community with the phototrophic purple sulfur bacterium Thiocapsa roseopersicina[J]. Systematic and Applied Microbiology, 42(5):125998. [86] Xu X, Dou Y, Zhao S, et al.2025. Rhizosphere microbes enhance plant resistance to cadmium through a root ROS-microbial IAA-root DNA methylation interkingdom signaling pathway[J]. Cell Reports, 44(11):116491. [87] Yang W, Wang S, Zhou H, et al.2022. Combined amendment reduces soil Cd availability and rice Cd accumulation in three consecutive rice planting seasons[J]. Journal of Environmental Sciences, 111:141-152. [88] Yao T, Jiang S, Hou K, et al.2022. Cadmium (Cd) accumulation in traditional Chinese medicine materials (TCMMs):A critical review[J]. Ecotoxicology and Environmental Safety, 242:113904. [89] Zamioudis C, Mastranesti P, Dhonukshe P, et al.2013. Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria[J]. Plant Physiology, 162(1):304-318. [90] Zhang F, Deng Y, Peng R, et al.2024. Bioremediation of paddy soil with amphitropic mixture markedly attenuates rice cadmium:Effect of soil cadmium removal and Fe/S-cycling bacteria in rhizosphere[J]. Science of the Total Environment, 915:169876. [91] Zentgraf U, Laun T, Miao Y.2010. The complex regulation of WRKY53 during leaf senescence of Arabidopsis thaliana[J]. European Journal of Cell Biology, 89(2-3):133-137. [92] Zhuang L, Li Y, Wang Z, et al.2021. Synthetic community with six Pseudomonas strains screened from garlic rhizosphere microbiome promotes plant growth[J]. Microbial Biotechnology, 14:488-502. |
|
|
|