The Plant-Endophyte-Synthetic Biology Trinity: A Next-Generation Biorefinery Platform for Lignocellulose Valorization and Precision Polysaccharide Biomanufacturing

Authors

  • Xinyu Wang Tianjin University of Traditional Chinese Medicine, Tianjin 301600, China
  • Xia Li Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China
  • Wenyuan Gao Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China

DOI:

https://doi.org/10.54097/4zg3f345

Keywords:

Lignocellulose, Polysaccharide, Synthetic Biology, Endophyte, Microbial Consortia, Consolidated Bioprocessing (CBP)

Abstract

The establishment of a robust bioeconomy depends on sustainable lignocellulosic biomass valorization and efficient production of high-value functional polysaccharides. The current bio-manufacturing model faces significant hurdles, including high refined sugar costs and energy-intensive pre-treatment. This review proposes an innovative “plant endophytic fungi-synthetic biology” trinity strategy to address these challenges. We describe how engineered plant endophytic fungal systems act as programmable in situ bioreactors to promote the decomposition of lignocellulose through rational design and synthesis of microbial consortia (SynComs) and integrated biological treatment (CBP). At the same time, the framework utilizes a cutting-edge synthetic biology toolbox-cross-genome editing, metabolic engineering, and epigenetic regulation - to achieve precise biomanufacturing of structurally diverse polysaccharides through host metabolic reprogramming. We critically assess industrial bottlenecks, from consortium stability to structural-functional knowledge gaps, while outlining future frontiers such as artificial intelligence-driven rational design and the biological basis of automation. This three-in-one strategy represents a paradigm shift from resource-intensive extraction to intelligent biomanufacturing, providing a theoretical basis and practical roadmap for realizing the full potential of lignocellulose in modern biorefinery.

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References

[1] Wasser, S. (2002). Medicinal mushrooms as a source of antitumor and immunomodulating polysaccharides. Applied Microbiology and Biotechnology, 60(3), 258–274. https://doi. org/ 10. 1007/s00253-002-1076-7.

[2] Schepetkin, I. A., & Quinn, M. T. (2006). Botanical polysaccharides: Macrophage immunomodulation and therapeutic potential. International Immunopharmacology, 6(3), 317–333. https://doi.org/10.1016/j.intimp.2005.10.005.

[3] De Silva, D. D., et al. (2013). Bioactive metabolites from macrofungi: Ethnopharmacology, biological activities and chemistry. Fungal Diversity, 62(1), 1–40. https://doi.org/10. 1007/ s13225-013-0265-2.

[4] Himmel, M. E., et al. (2007). Biomass recalcitrance: Engineering plants and enzymes for biofuels production. Science, 315(5813), 804–807. https://doi.org/ 10.1126/ science. 1137016.

[5] Mahmood, H., Moniruzzaman, M., Iqbal, T., & Khan, M. J. (2019). Recent advances in the pretreatment of lignocellulosic biomass for biofuels and value-added products. Current Opinion in Green and Sustainable Chemistry, 20, 18–24. https://doi.org/10.1016/j.cogsc.2019.08.001.

[6] Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206(4), 1196–1206. https://doi.org/10.1111/nph.13312.

[7] Hardoim, P. R., et al. (2015). The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiology and Molecular Biology Reviews, 79(3), 293–320. https://doi.org/ 10. 1128/ mmbr.00050-14.

[8] Berg, G., et al. (2020). Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8(1), 103. https://doi.org/10.1186/s40168-020-00875-0.

[9] Reinhold-Hurek, B., & Hurek, T. (2011). Living inside plants: Bacterial endophytes. Current Opinion in Plant Biology, 14(4), 435–443. https://doi.org/10.1016/j.pbi.2011.04.004.

[10] Lee, J. S., Cho, J. Y., & Hong, E. K. (2009). Study on macrophage activation and structural characteristics of purified polysaccharides from the liquid culture broth of Hericium erinaceus. Carbohydrate Polymers, 78(1), 162–168. https://doi. org/ 10.1016/j.carbpol.2009.04.036.

[11] Yuan, J., et al. (2019). Comparative transcriptomics and proteomics of Atractylodes lancea in response to endophytic fungus Gilmaniella sp. AL12 reveals regulation in plant metabolism. Frontiers in Microbiology, 10, 1208. https://doi. org/ 10.3389/fmicb.2019.01208.

[12] Manganyi, M. C., & Ateba, C. N. (2020). Untapped potentials of endophytic fungi: A review of novel bioactive compounds with biological applications. Microorganisms, 8(12), 1934. https:// doi.org/10.3390/microorganisms8121934.

[13] Somerville, C. (2006). Cellulose synthesis in higher plants. Annual Review of Cell and Developmental Biology, 22, 53–78. https://doi.org/10.1146/annurev.cellbio.22.022206.160206.

[14] Mohnen, D. (2008). Pectin structure and biosynthesis. Current Opinion in Plant Biology, 11(3), 266–277. https://doi.org/ 10. 1016/ j.pbi.2008.03.006.

[15] Zhong, R., & Ye, Z. H. (2015). Secondary cell walls: Biosynthesis, patterned deposition and transcriptional regulation. Plant & Cell Physiology, 56(2), 195–214. https:// doi. org/ 10.1093/pcp/pcu140.

[16] Purushotham, P., Ho, R., Yu, L., Fincher, G. B., Bulone, V., & Zimmer, J. (2022). Mechanism of mixed-linkage glucan biosynthesis by barley cellulose synthase–like CslF6 (1,3;1,4)-β-glucan synthase. Science Advances, 8(45), eadd1596. https://doi.org/10.1126/sciadv.add1596.

[17] Wang, Y., et al. (2023). Signal molecules regulate the synthesis of secondary metabolites in the interaction between endophytes and medicinal plants. Processes, 11(3), 849. https://doi.org/ 10. 3390/pr11030849.

[18] Biswas, P. R., Roy, N., Ghosh, S., Tayung, K., & Dutta, A. K. (2025). A review of molecular signaling and communication between root tissues and their endophytes. Rhizosphere, 36, 101188. https://doi.org/10.1016/j.rhisph.2025.101188.

[19] Ludwig-Müller, J. (2015). Bacteria and fungi controlling plant growth by manipulating auxin: Balance between development and defense. Journal of Plant Physiology, 172, 4–12. https:// doi. org/10.1016/j.jplph.2014.01.002.

[20] Chen, F., Ren, C. G., Zhou, T., Wei, Y. J., & Dai, C. C. (2016). A novel exopolysaccharide elicitor from endophytic fungus Gilmaniella sp. AL12 on volatile oils accumulation in Atractylodes lancea. Scientific Reports, 6, 34735. https:// doi. org/ 10.1038/srep34735.

[21] Rocafort, M., Fudal, I., & Mesarich, C. H. (2020). Apoplastic effector proteins of plant-associated fungi and oomycetes. Current Opinion in Plant Biology, 56, 9–19. https://doi.org/ 10. 1016/j.pbi.2020.02.004.

[22] Silva, F. R., de Resende, M. L. V., Xavier, K. V., Brawner, J. T., & de Lima Santos, M. (2025). Genome-wide analysis reveals chitinases as putative defense-related proteins against fungi in the genomes of Coffea arabica and its progenitors. Plants, 14(20), 3130. https://doi.org/10.3390/plants14203130.

[23] Hemetsberger, C., et al. (2015). The fungal core effector Pep1 is conserved across smuts of dicots and monocots. New Phytologist, 206(3), 1116–1126. https://doi.org/10.1111/ nph. 13304.

[24] Wang, Y., et al. (2025). Isolation of endophytic fungi and effects on secondary metabolites in hairy roots of Salvia miltiorrhiza. Journal of Microbiology and Biotechnology, 35(4), 1–8. https://doi.org/10.4014/jmb.2411.11051.

[25] Beck, A. E., Kleiner, M., & Garrell, A. K. (2022). Elucidating plant-microbe-environment interactions through omics-enabled metabolic modelling using synthetic communities. Frontiers in Plant Science, 13, 910377. https://doi.org/10. 3389/ fpls.2022.910377.

[26] Ellis, J. R., Bull, J. J., & Rowley, P. A. (2023). Fungal glycoside hydrolases display unique specificities for polysaccharides and Staphylococcus aureus biofilms. Microorganisms, 11(2), 293. https://doi.org/10. 3390/ microorganisms11020293.

[27] Hsin, K. T., et al. (2025). Lignocellulose degradation in bacteria and fungi: Cellulosomes and industrial relevance. Frontiers in Microbiology, 16, 1583746. https://doi. org/1 0.3389/ fmicb.2025.1583746.

[28] Kun, R. S., Gomes, A. C. S., Hildén, K. S., Salazar Cerezo, S., Mäkelä, M. R., & de Vries, R. P. (2019). Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnology Advances, 37(6), 107361. https:// doi. org/ 10.1016/j.biotechadv.2019.02.017.

[29] Guo, X., An, Y., Liu, F., Lu, F., & Wang, B. (2022). Lytic polysaccharide monooxygenase – A new driving force for lignocellulosic biomass degradation. Bioresource Technology, 362, 127803. https://doi.org/10.1016/j.biortech.2022.127803.

[30] Robl, D., et al. (2015). Enhancing of sugar cane bagasse hydrolysis by Annulohypoxylon stygium glycohydrolases. Bioresource Technology, 177, 247–254. https://doi.org/10. 1016/ j. biortech.2014.11.082.

[31] Malik, K., Chen, Z., Saif, I., Chen, T., & Li, C. (2024). Bacterial endophytes-mediated lignin degradation and co-culture fermentation of ryegrass for bioethanol production. Industrial Crops and Products, 222, 119976. https://doi.org/ 10. 1016/ j. indcrop.2024.119976.

[32] Sharma, G., et al. (2024). Developing endophytic Penicillium oxalicum as a source of lignocellulolytic enzymes for enhanced hydrolysis of biorefinery relevant pretreated rice straw. Bioprocess and Biosystems Engineering, 47(12), 2055–2073. https:// doi.org/10.1007/s00449-024-03085-2.

[33] Marchetti, A., et al. (2025). Xylan degradation in the halotolerant bacterium Bacillus altitudinis relies on glycosidic hydrolases from families 11 and 30. Journal of Agricultural and Food Chemistry, 73(43), 27599–27610. https://doi.org/10. 1021/acs.jafc.5c06247.

[34] Hamidi, M., et al. (2022). Fungal exopolysaccharides: Properties, sources, modifications, and biomedical applications. Carbohydrate Polymers, 284, 119152. https://doi.org/ 10. 1016/ j. carbpol.2022.119152.

[35] Zeng, Y. J., Yang, H. R., Wang, H. F., Zong, M. H., & Lou, W. Y. (2019). Immune enhancement activity of a novel polysaccharide produced by Dendrobium officinale endophytic fungus Fusarium solani DO7. Journal of Functional Foods, 53, 266–275. https://doi.org/10.1016/j.jff.2018.12.038.

[36] Zeng, Y. J., Yang, H. R., Zong, M. H., Yang, J. G., & Lou, W. Y. (2019). Novel antibacterial polysaccharides produced by endophyte Fusarium solani DO7. Bioresource Technology, 288, 121596. https://doi.org/10.1016/j.biortech.2019.121596.

[37] Zhang, W., et al. (2025). Exopolysaccharide from endophytic fungi of Cinnamomum burmannii leaves: Structural characterization and hepatoprotective effects. International Journal of Biological Macromolecules, 322, 146703. https:// doi. org/10.1016/j.ijbiomac.2025.146703.

[38] Nyaisaba, B. M., Masalu, R. J., Myovela, H., & Mpinda, C. B. (2025). Unlocking the antioxidant and antibacterial potential of exopolysaccharides produced by endophytic fungi (Aspergillus fumigatus and Preussia isabellae) isolated from Tanzania’s mangroves. BMC Biotechnology, 25(1), 66. https://doi.org/ 10. 1186/s12896-025-01005-0.

[39] Yang, J., Sun, Y., Li, M., & Yu, Q. (2025). Anti-inflammatory potential of extracellular polysaccharide from the moss endophyte Ovatospora brasiliensis during pathogen infection. Microorganisms, 13(9), 2037. https://doi.org/ 10. 3390/ microorganisms 13092037.

[40] Liang, J., et al. (2025). Isolation of endophytes from Taxus cuspidata cv. Nana, preparation of extracellular polysaccharides and study on their functional properties. International Journal of Biological Macromolecules, 309, 142494. https://doi.org/10.1016/j.ijbiomac.2025.142494.

[41] Fu, B., & Yan, Q. (2023). Exopolysaccharide is required for motility, stress tolerance, and plant colonization by the endophytic bacterium Paraburkholderia phytofirmans PsJN. Frontiers in Microbiology, 14, 1218653. https://doi.org/ 10. 3389/ fmicb.2023.1218653.

[42] Ashajyothi, M., Balamurugan, A., Patel, C., Krishnappa, R., Kumar, R., & Kumar, A. (2023). Cell wall polysaccharides of endophytic Pseudomonas putida elicit defense against rice blast disease. Journal of Applied Microbiology, 134(2), lxac042. https://doi.org/10.1093/jambio/lxac042.

[43] Kalimuthu, A. K., et al. (2023). Drug delivery applications of exopolysaccharides from endophytic bacteria Pseudomonas otitidis from Tribulus terrestris L. Journal of Polymers and the Environment, 31(8), 3632–3649. https://doi.org/10. 1007/ s 10924-023-02848-4.

[44] Zuroff, T. R., Xiques, S. B., & Curtis, W. R. (2013). Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture. Biotechnology for Biofuels, 6(1), 59. https://doi.org/10.1186/1754-6834-6-59.

[45] Tariq, A., Guo, S., Farhat, F., & Shen, X. (2025). Engineering synthetic microbial communities: Diversity and applications in soil for plant resilience. Agronomy, 15(3), 513. https://doi. org/ 10. 3390/agronomy15030513.

[46] Vieira, R. I. M., et al. (2025). Fungal coculture: Unlocking the potential for efficient bioconversion of lignocellulosic biomass. Journal of Fungi, 11(6), 458. https://doi.org/10. 3390/ jof11 060458.

[47] Chen, S., Liu, Q., & Li, D. (2025). Synthetic microbial community enhances lignocellulose degradation at the composting thermophilic phase: Metagenomic and metabolic pathway insights. Chemical Engineering Journal, 520, 165847. https://doi.org/10.1016/j.cej.2025.165847.

[48] Lynd, L. R., van Zyl, W. H., McBride, J. E., & Laser, M. (2005). Consolidated bioprocessing of cellulosic biomass: An update. Current Opinion in Biotechnology, 16(5), 577–583. https:// doi. org/ 10.1016/j.copbio.2005.08.009.

[49] Hasunuma, T., & Kondo, A. (2012). Consolidated bioprocessing and simultaneous saccharification and fermentation of lignocellulose to ethanol with thermotolerant yeast strains. Process Biochemistry, 47(9), 1287–1294. https:// doi. org/10.1016/j.procbio.2012.05.004.

[50] Wan, C., et al. (2026). MDG1-mediated transcriptional reprogramming enhances cellulase production and alters thermal activity in recombinant Saccharomyces cerevisiae. Metabolic Engineering, 93, 24–34. https://doi.org/10.1016/j. ymben. 2025.09.002.

[51] Wang, Z., et al. (2023). Compound probiotics producing cellulase could replace cellulase preparations during solid-state fermentation of millet bran. Bioresource Technology, 385, 129457. https://doi.org/10.1016/j.biortech.2023.129457.

[52] Ko, C. H., Chen, W. L., Tsai, C. H., Jane, W. N., Liu, C. C., & Tu, J. (2007). Paenibacillus campinasensis BL11: A wood material-utilizing bacterial strain isolated from black liquor. Bioresource Technology, 98(14), 2727–2733. https://doi. org/ 10. 1016/j.biortech.2006.09.034.

[53] Wang, G., Xie, L., Huang, Z., & Xie, J. (2024). Recent advances in polysaccharide biomodification by microbial fermentation: Production, properties, bioactivities, and mechanisms. Critical Reviews in Food Science and Nutrition, 64 (33), 12999–13023. https://doi.org/10.1080/ 10408398. 2023. 2259461.

[54] Gong, M., et al. (2021). Key metabolism pathways and regulatory mechanisms of high polysaccharide yielding in Hericium erinaceus. BMC Genomics, 22(1), 160. https:// doi. org/ 10.1186/s12864-021-07480-x.

[55] Sha, Y., et al. (2019). Investigation of glutamate dependence mechanism for poly-γ-glutamic acid production in Bacillus subtilis on the basis of transcriptome analysis. Journal of Agricultural and Food Chemistry, 67(22), 6263–6274. https://doi.org/10.1021/acs.jafc.9b01755.

[56] Lee, H. M., Vo, P. N. L., & Na, D. (2018). Advancement of metabolic engineering assisted by synthetic biology. Catalysts, 8(12), 619. https://doi.org/10.3390/catal8120619.

[57] Liu, Z., Zhang, Z., Rawat, S., Wang, L., Cao, P., & Zhao, L. (2024). Editorial: Plant chassis for synthetic biology and its application in biomanufacturing. Frontiers in Plant Science, 15, 1460378. https://doi.org/10.3389/fpls.2024.1460378.

[58] Chowdhary, K., Arora, H., & Sharma, S. (2022). CRISPR/Cas9-based genome editing as a way ahead for inducing production of bioactive metabolites in endophytes. National Academy Science Letters, 45(3), 275–280. https://doi. org/ 10.1007/s40009-022-01107-9.

[59] Nishida, K., & Kondo, A. (2021). CRISPR-derived genome editing technologies for metabolic engineering. Metabolic Engineering, 63, 141–147. https://doi.org/10.1016/j. ymben. 2020. 12.002.

[60] Zhao, D., et al. (2021). CRISPR-based metabolic pathway engineering. Metabolic Engineering, 63, 148–159. https:// doi. org/ 10.1016/j.ymben.2020.10.004.

[61] Zhao, S., et al. (2024). Efficient gene editing in the slow-growing, non-sporulating, melanized, endophytic fungus Berkleasmium sp. Dzf12 using a CRISPR/Cas9 system. World Journal of Microbiology and Biotechnology, 40(6), 176. https://doi.org/10.1007/s11274-024-03988-y.

[62] Di Fruscia, L., & Weber, J. M. (2025). Leveraging large language models for enzymatic reaction prediction and characterization. Digital Discovery. https://doi.org/10. 1039/ D5DD00187K.

[63] Lairson, L. L., Henrissat, B., Davies, G. J., & Withers, S. G. (2008). Glycosyltransferases: Structures, functions, and mechanisms. Annual Review of Biochemistry, 77, 521–555. https://doi.org/10.1146/annurev.biochem.76.061005.092322.

[64] Wu, Z., Johnston, K. E., Arnold, F. H., & Yang, K. K. (2021). Protein sequence design with deep generative models. Current Opinion in Chemical Biology, 65, 18–27. https://doi.org/ 10. 1016/j.cbpa.2021.04.004.

[65] Song, H., Ding, M. Z., Jia, X. Q., Ma, Q., & Yuan, Y. J. (2014). Synthetic microbial consortia: From systematic analysis to construction and applications. Chemical Society Reviews, 43(20), 6954–6981. https://doi.org/10.1039/C4CS00114A.

[66] Johns, N. I., Blazejewski, T., Gomes, A. L. C., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current Opinion in Microbiology, 31, 146–153. https://doi.org/10.1016/j.mib.2016.03.010.

[67] Sharma, A., & Bora, P. (2025). Engineering synthetic microbial communities to restructure the phytobiome for plant health and productivity. World Journal of Microbiology and Biotechnology, 41(7), 228. https://doi.org/10.1007/s11274-025-04460-1.

[68] Liu, Q., Xie, Z., Tang, S., Xie, Q., He, X., & Li, D. (2025). Synthetic microbial community enhances lignocellulose degradation during composting by assembling fungal communities. Bioresource Technology, 419, 132068. https:// doi. org/10.1016/j.biortech.2025.132068.

[69] Thakore, P. I., Black, J. B., Hilton, I. B., & Gersbach, C. A. (2016). Editing the epigenome: Technologies for programmable transcription and epigenetic modulation. Nature Methods, 13(2), 127–137. https://doi.org/10.1038/nmeth.3733.

[70] Compant, S., Clément, C., & Sessitsch, A. (2010). Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biology & Biochemistry, 42(5), 669–678. https://doi.org/10.1016/j.soilbio.2009.11.024.

[71] Ganeshan, S., Kim, S. H., & Vujanovic, V. (2021). Scaling-up production of plant endophytes in bioreactors: Concepts, challenges and perspectives. Bioresources and Bioprocessing, 8(1), 63. https://doi.org/10.1186/s40643-021-00417-y.

[72] George, D. R., Danciu, M., Davenport, P. W., Lakin, M. R., Chappell, J., & Frow, E. K. (2024). A bumpy road ahead for genetic biocontainment. Nature Communications, 15(1), 650. https://doi.org/10.1038/s41467-023-44531-1.

[73] Castle, S. D., Stock, M., & Gorochowski, T. E. (2024). Engineering is evolution: A perspective on design processes to engineer biology. Nature Communications, 15(1), 3640. https://doi.org/10.1038/s41467-024-48000-1.

[74] Wang, D., Jin, S., Lu, Q., & Chen, Y. (2023). Advances and challenges in CRISPR/Cas-based fungal genome engineering for secondary metabolite production: A review. Journal of Fungi, 9(3), 362. https://doi.org/10.3390/jof9030362.

[75] Verma, V., et al. (2023). Bioengineering of fungal endophytes through the CRISPR/Cas9 system. Frontiers in Microbiology, 14, 1146650. https://doi.org/10.3389/fmicb.2023.1146650.

[76] Koonin, E. V., Gootenberg, J. S., & Abudayyeh, O. O. (2023). Discovery of diverse CRISPR-Cas systems and expansion of the genome engineering toolbox. Biochemistry, 62(24), 3465–3487. https://doi.org/10.1021/acs.biochem.3c00159.

[77] Piskunen, P., Latham, R., West, C. E., Castronovo, M., & Linko, V. (2022). Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience, 25(6), 104389. https://doi.org/ 10.1016/j. isci. 2022. 104389.

[78] Li, X. H., Lu, H. Z., Yao, J. B., Zhang, C., Shi, T. Q., & Huang, H. (2025). Recent advances in the application of CRISPR/Cas-based gene editing technology in filamentous fungi. Biotechnology Advances, 81, 108561. https://doi.org/10.1016/j. biotechadv. 2025. 108561.

[79] Konstantakos, V., Nentidis, A., Krithara, A., & Paliouras, G. (2022). CRISPR–Cas9 gRNA efficiency prediction: An overview of predictive tools and the role of deep learning. Nucleic Acids Research, 50(7), 3616–3637. https://doi.org/10. 1093/ nar/gkac192.

[80] Gavrilescu, M. (2024). From pollutants to products: Microbial cell factories driving sustainable biomanufacturing and environmental conservation. Chemical Engineering Journal, 500, 157152. https://doi.org/10.1016/j.cej.2024.157152.

[81] Zhang, J., Wen, C., Zhang, H., Duan, Y., & Ma, H. (2020). Recent advances in the extraction of bioactive compounds with subcritical water: A review. Trends in Food Science & Technology, 95, 183–195. https://doi.org/10. 1016/j.tifs. 2019. 11. 018.

[82] Wasalathanthri, D. P., et al. (2020). Technology outlook for real-time quality attribute and process parameter monitoring in biopharmaceutical development-A review. Biotechnology and Bioengineering, 117(10), 3182–3198. https://doi.org/10.1002/ bit. 27461.

[83] Ali, S. S., et al. (2024). A review of the fungal polysaccharides as natural biopolymers: Current applications and future perspective. International Journal of Biological Macromolecules, 273, 132986. https://doi.org/10. 1016/ j. ijbiomac. 2024.132986.

[84] Tiemeyer, M., et al. (2017). GlyTouCan: An accessible glycan structure repository. Glycobiology, 27(10), 915–919. https:// doi. org/10.1093/glycob/cwx066.

[85] Li, X., Xu, Z., Hong, X., Zhang, Y., & Zou, X. (2020). Databases and bioinformatic tools for glycobiology and glycoproteomics. International Journal of Molecular Sciences, 21(18), 6727. https://doi.org/10.3390/ijms21186727.

[86] Vacheron, J., et al. (2013). Plant growth-promoting rhizobacteria and root system functioning. Frontiers in Plant Science, 4, 356. https://doi.org/10.3389/fpls.2013.00356.

[87] Schiemann, J., Dietz-Pfeilstetter, A., Hartung, F., Kohl, C., Romeis, J., & Sprink, T. (2019). Risk assessment and regulation of plants modified by modern biotechniques: Current status and future challenges. Annual Review of Plant Biology, 70, 699–726. https://doi.org/10.1146/annurev-arplant-050718-100025.

[88] Kim, H., Lee, J., Cho, Y., Kim, H., Kim, H. Y., & Sung, B. H. (2025). Governing synthetic biology: A co-evolutionary framework for sustainable innovation. Journal of Microbiology and Biotechnology, 35, e2508001. https://doi.org/ 10. 4014/ jmb. 2508.08001.

[89] Radivojević, T., Costello, Z., Workman, K., & Garcia Martin, H. (2020). A machine learning automated recommendation tool for synthetic biology. Nature Communications, 11(1), 4879. https://doi.org/10.1038/s41467-020-18008-4.

[90] Gonçalves, O. S., Creevey, C. J., & Santana, M. F. (2023). Designing a synthetic microbial community through genome metabolic modeling to enhance plant–microbe interaction. Environmental Microbiome, 18(1), 81. https://doi.org/10. 1186/ s40793-023-00536-3.

[91] Lawson, C. E., et al. (2019). Common principles and best practices for engineering microbiomes. Nature Reviews Microbiology, 17(12), 725–741. https://doi.org/10. 1038/ s41 579-019-0255-9.

[92] Ma, J., Qiao, J., Cao, Y., & Cheng, Z. (2025). Harnessing artificial intelligence to decode the rhizosphere microbiome. aBIOTECH, 100005. https://doi.org/10. 1016/j.abiote. 2025. 100005.

[93] Fujiwara, F., Miyazawa, K., Nihei, N., & Ichihashi, Y. (2022). Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data. Bioscience, Biotechnology, and Biochemistry, 87(1), 21–27. https://doi. org/ 10. 1093/ bbb/zbac191.

[94] Tian, L., Chen, F., & Macosko, E. Z. (2023). The expanding vistas of spatial transcriptomics. Nature Biotechnology, 41(6), 773–782. https://doi.org/10.1038/s41587-022-01448-2.

[95] Ståhl, P. L., et al. (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science, 353(6294), 78–82. https://doi.org/10.1126/science.aaf2403.

[96] Singh, S., Praveen, A., Dudha, N., Sharma, V. K., & Bhadrecha, P. (2024). Single-cell transcriptomics: A new frontier in plant biotechnology research. Plant Cell Reports, 43(12), 294. https://doi. org/ 10. 1007/s00299-024-03383-9.

[97] Asin-Garcia, E., Fawcett, J. D., Batianis, C., & Martins dos Santos, V. A. P. (2025). A snapshot of biomanufacturing and the need for enabling research infrastructure. Trends in Biotechnology, 43(5), 1000–1014. https://doi.org/10.1016/j. tibtech. 2024.10.014.

[98] Lee, D. H., Kim, H., Sung, B. H., Cho, B. K., & Lee, S. G. (2023). Biofoundries: Bridging automation and biomanufacturing in synthetic biology. Biotechnology and Bioprocess Engineering, 28(6), 892–904. https://doi.org/ 10. 1007/ s12257-023-0226-x.

[99] Chen, J., Singh, N., Lu, J., Lane, S. T., & Zhao, H. (2025). Artificial intelligence–powered biofoundries for protein engineering and metabolic engineering. Current Opinion in Biotechnology, 96, 103380. https://doi.org/ 10.1016/j. copbio. 2025.103380.

[100] Pérez, S., & Bertoft, E. (2010). The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review. Starch Stärke, 62(8), 389–420. https://doi.org/10.1002/star.201000013.

[101] Bacalzo, N. P., Jr., et al. (2023). Quantitative bottom-up glycomic analysis of polysaccharides in food matrices using liquid chromatography–tandem mass spectrometry. Analytical Chemistry, 95(2), 1008–1015. https://doi.org/10. 1021/ acs. analchem.2c03707.

[102] Marvin, H. J. P., et al. (2025). “Digitalisation and artificial intelligence for sustainable food systems” [Trends in Food Science & Technology 120, (2022) 344–348]. Trends in Food Science & Technology, 160, 104973. https://doi.org/10. 1016/j. tifs.2025.104973.

[103] Ullah, M. W., et al. (2025). Bacterial polysaccharides in the food industry: Synthesis-structure-properties relationships, AI-driven innovations, regulatory challenges, and bioeconomy prospects. Carbohydrate Polymers, 370, 124343. https:// doi. org/ 10.1016/j. carbpol. 2025.124343.

[104] Osterne, V. J. S., Nascimento, K. S., Cavada, B. S., & Van Damme, E. J. M. (2025). The future of plant lectinology: Advanced technologies and computational tools. BBA Advances, 7, 100145. https://doi.org/10. 1016/j. bbadva. 2025. 100145.

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29-06-2026

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Wang, X., Li, X., & Gao, W. (2026). The Plant-Endophyte-Synthetic Biology Trinity: A Next-Generation Biorefinery Platform for Lignocellulose Valorization and Precision Polysaccharide Biomanufacturing. International Journal of Biology and Life Sciences, 15(1), 27-40. https://doi.org/10.54097/4zg3f345