Closing loop: Systems-level integration of synthetic consortia and process engineering for lignocellulosic microbial lipid biomanufacturing

Changyu Pi; Jinyang Li; Fangting Jiang; Le Gao; Xin Wu

doi:10.1016/j.jobab.2026.100254

Volume 11 Issue 3

Jun. 2026

Turn off MathJax

Article Contents

Article Navigation > Journal of Bioresources and Bioproducts > 2026 > 11(3): 100254

Changyu Pi, Jinyang Li, Fangting Jiang, Le Gao, Xin Wu. Closing loop: Systems-level integration of synthetic consortia and process engineering for lignocellulosic microbial lipid biomanufacturing[J]. Journal of Bioresources and Bioproducts, 2026, 11(3): 100254. doi: 10.1016/j.jobab.2026.100254

Citation:

Changyu Pi, Jinyang Li, Fangting Jiang, Le Gao, Xin Wu. Closing loop: Systems-level integration of synthetic consortia and process engineering for lignocellulosic microbial lipid biomanufacturing[J]. Journal of Bioresources and Bioproducts, 2026, 11(3): 100254. doi: 10.1016/j.jobab.2026.100254

Citation:

Changyu Pi, Jinyang Li, Fangting Jiang, Le Gao, Xin Wu. Closing loop: Systems-level integration of synthetic consortia and process engineering for lignocellulosic microbial lipid biomanufacturing[J]. Journal of Bioresources and Bioproducts, 2026, 11(3): 100254. doi: 10.1016/j.jobab.2026.100254

PDF( 4040 KB)

Closing loop: Systems-level integration of synthetic consortia and process engineering for lignocellulosic microbial lipid biomanufacturing

doi: 10.1016/j.jobab.2026.100254

State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China

More Information

Corresponding author: E-mail address: gao_l@tib.cas.cn (L. Gao); E-mail address: wuxin@tib.cas.cn (X. Wu)
Received Date: 2026-01-19
Accepted Date: 2026-03-28
Rev Recd Date: 2026-03-21

Available Online: 2026-04-19

Publish Date: 2026-06-01

Abstract

Abstract

Amidst the urgent quest for carbon neutrality, lignocellulosic biomass has emerged as a key feedstock for sustainable biomanufacturing. However, the commercial viability of converting this recalcitrant resource into microbial lipids remains constrained by fragmented unit operations, particularly the trade-offs between biomass deconstruction efficiency and downstream inhibitor toxicity. This review moves beyond a linear technological summary to propose an integrated roadmap for next-generation biorefineries. We analyze the convergence of flexible and broadly applicable pretreatment strategies across diverse lignocellulosic feedstocks and synthetic biology-driven strain engineering, highlighting how tools such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 and RNA interference enable more precise control of metabolic flux toward lipid precursors. Furthermore, we extend the discussion from monoculture systems to emerging artificial microbial consortia, which offer opportunities for functional division of labor in simultaneous inhibitor detoxification and lipid accumulation, while also presenting challenges in stability and metabolic coordination. In addition, we discuss how data-driven strategies, including machine learning and techno-economic analysis, can help bridge the gap between laboratory-scale advances and industrial implementation. By integrating insights from feedstock chemistry, microbial physiology, and process engineering, this review provides a systems-level perspective on the development of economically viable and low-carbon lipid biomanufacturing platforms.
- Lignocellulosic biomass,
- Microbial lipid,
- Pretreatment,
- Metabolic engineering,
- Fermentation

Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Peer review under the responsibility of Editorial Office of Journal of Bioresources and Bioproducts.

FullText(HTML)

References(209)

References

Abbas, N., Riaz, S., Mazhar, S., Essa, R., Maryam, M., Saleem, Y., Syed, Q., Perveen, I., Bukhari, B., Ashfaq, S., Abidi, S.H.I., 2023. Microbial production of docosahexaenoic acid (DHA): biosynthetic pathways, physical parameter optimization, and health benefits. Arch. Microbiol. 205, 321. doi: 10.1007/s00203-023-03666-x

Adsul, M.G., 2024. Cellulolytic enzymes recycling strategies for the economic conversion of lignocellulosic biomass to fuels. Process. Biochem. 147, 62–74. doi: 10.1016/j.procbio.2024.08.009

Afedzi, A.E.K., Afrakomah, G.S., Gyan, K., Khan, J., Seidu, R., Baidoo, T., Sultan, I.N., Tareen, A.K., Parakulsuksatid, P., 2025. Enhancing economic and environmental sustainability in lignocellulosic bioethanol production: key factors, innovative technologies, policy frameworks, and social considerations. Sustainability 17, 499. doi: 10.3390/su17020499

Agrawal, R., Bhadana, B., singh chauhan, P., Adsul, M., Kumar, R., Gupta, R.P., Satlewal, A., 2022. Understanding the effects of low enzyme dosage and high solid loading on the enzyme inhibition and strategies to improve hydrolysis yields of pilot scale pretreated rice straw. Fuel 327, 125114. doi: 10.1016/j.fuel.2022.125114

Akintunde, M.O., Adebayo-Tayo, B.C., Ishola, M.M., Zamani, A., Horváth, I.S., 2022. Bacterial cellulose production from agricultural residues by two Komagataeibacter sp. strains. Bioengineered 13, 10010–10025. doi: 10.1080/21655979.2022.2062970

Al Azad, S., Madadi, M., Song, G.J., Sun, C.H., Sun, F.B., 2024. New trends in microbial lipid-based biorefinery for fermentative bioenergy production from lignocellulosic biomass. Biofuel Res. J. 11, 2040–2064. doi: 10.18331/brj2024.11.1.5

Andlar, M., Rezić, T., Marđetko, N., Kracher, D., Ludwig, R., Šantek, B., 2018. Lignocellulose degradation: an overview of fungi and fungal enzymes involved in lignocellulose degradation. Eng. Life Sci. 18, 768–778. doi: 10.1002/elsc.201800039

Anthony, W.E., Carr, R.R., DeLorenzo, D.M., Campbell, T.P., Shang, Z.Y., Foston, M., Moon, T.S., Dantas, G., 2019. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. Biotechnol. Biofuels 12, 192. doi: 10.1186/s13068-019-1535-3

Anthony, W.E., Geng, W.T., Diao, J.J., Carr, R.R., Wang, B., Ning, J., Moon, T.S., Dantas, G., Zhang, F.Z., 2024. Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators. Biotechnol. Biofuels Bioprod. 17, 83. doi: 10.1186/s13068-024-02523-3

Arora, N., Patel, A., Mehtani, J., Pruthi, P.A., Pruthi, V., Poluri, K.M., 2019. Co-culturing of oleaginous microalgae and yeast: paradigm shift towards enhanced lipid productivity. Environ. Sci. Pollut. Res. 26, 16952–16973. doi: 10.1007/s11356-019-05138-6

Athoillah, A.Z., Ahmad, F.B., 2022. Biodiesel production from bioremediation of palm oil mill effluent via oleaginous fungi. CLEAN 50, 2200025.

Babu, S.S., Gondi, R., Vincent, G.S., JohnSamuel, G.C., Jeyakumar, R.B., 2022. Microalgae biomass and lipids as feedstock for biofuels: sustainable biotechnology strategies. Sustainability 14, 15070. doi: 10.3390/su142215070

Baksi, S., Saha, D., Saha, S., Sarkar, U., Basu, D., Kuniyal, J.C., 2023. Pre-treatment of lignocellulosic biomass: review of various physico-chemical and biological methods influencing the extent of biomass depolymerization. Int. J. Environ. Sci. Technol. 20, 13895–13922. doi: 10.1007/s13762-023-04838-4

Bao, W.J., Li, Z.F., Wang, X.M., Gao, R.L., Zhou, X.Q., Cheng, S.K., Men, Y., Zheng, L., 2021. Approaches to improve the lipid synthesis of oleaginous yeast Yarrowia lipolytica: a review. Renew. Sustain. Energy Rev. 149, 111386. doi: 10.1016/j.rser.2021.111386

Baptista, M., Cunha, J.T., Domingues, L., 2021. Establishment of Kluyveromyces marxianus as a microbial cell factory for lignocellulosic processes: production of high value furan derivatives. J. Fungi 7, 1047. doi: 10.3390/jof7121047

Basak, B., Kumar, R., Bharadwaj, A.V.S.L.S., Kim, T.H., Kim, J.R., Jang, M., Oh, S.E., Roh, H.S., Jeon, B.H., 2023. Advances in physicochemical pretreatment strategies for lignocellulose biomass and their effectiveness in bioconversion for biofuel production. Bioresour. Technol. 369, 128413. doi: 10.1016/j.biortech.2022.128413

Batchuluun, B., Pinkosky, S.L., Steinberg, G.R., 2022. Lipogenesis inhibitors: therapeutic opportunities and challenges. Nat. Rev. Drug Discov. 21, 283–305. doi: 10.1038/s41573-021-00367-2

Bellou, S., Triantaphyllidou, I.E., Mizerakis, P., Aggelis, G., 2016. High lipid accumulation in Yarrowia lipolytica cultivated under double limitation of nitrogen and magnesium. J. Biotechnol. 234, 116–126. doi: 10.1016/j.jbiotec.2016.08.001

Bharathiraja, B., Sridharan, S., Sowmya, V., Yuvaraj, D., Praveenkumar, R., 2017. Microbial oil–a plausible alternate resource for food and fuel application. Bioresour. Technol. 233, 423–432. doi: 10.1016/j.biortech.2017.03.006

Bossie, M.A., Martin, C.E., 1989. Nutritional regulation of yeast delta-9 fatty acid desaturase activity. J. Bacteriol. 171, 6409–6413. doi: 10.1128/jb.171.12.6409-6413.1989

Bracharz, F., Beukhout, T., Mehlmer, N., Brück, T., 2017. Opportunities and challenges in the development of Cutaneotrichosporon oleaginosus ATCC 20509 as a new cell factory for custom tailored microbial oils. Microb. Cell Fact. 16, 178. doi: 10.1186/s12934-017-0791-9

Brandenburg, J., Blomqvist, J., Shapaval, V., Kohler, A., Sampels, S., Sandgren, M., Passoth, V., 2021. Oleaginous yeasts respond differently to carbon sources present in lignocellulose hydrolysate. Biotechnol. Biofuels 14, 124. doi: 10.1186/s13068-021-01974-2

Brienza, F., Cannella, D., Montesdeoca, D., Cybulska, I., Debecker, D.P., 2024. A guide to lignin valorization in biorefineries: traditional, recent, and forthcoming approaches to convert raw lignocellulose into valuable materials and chemicals. RSC Sustain. 2, 37–90. doi: 10.1039/d3su00140g

Calvey, C.H., Su, Y.K., Willis, L.B., McGee, M., Jeffries, T.W., 2016. Nitrogen limitation, oxygen limitation, and lipid accumulation in Lipomyces starkeyi. Bioresour. Technol. 200, 780–788. doi: 10.1016/j.biortech.2015.10.104

Carter, B., Squillace, P., Gilcrease, P.C., Menkhaus, T.J., 2011. Detoxification of a lignocellulosic biomass slurry by soluble polyelectrolyte adsorption for improved fermentation efficiency. Biotechnol. Bioeng. 108, 2053–2060. doi: 10.1002/bit.23152

Chang, L.L., Chen, H.Q., Yang, B., Chen, H.Q., Chen, W., 2023. Redistributing carbon flux by impairing saccharide synthesis to enhance lipid yield in oleaginous fungus Mortierella alpina. ACS Synth. Biol. 12, 1750–1760. doi: 10.1021/acssynbio.3c00046

Chemat, F., Vian, M.A., Cravotto, G., 2012. Green extraction of natural products: concept and principles. Int. J. Mol. Sci. 13, 8615–8627. doi: 10.3390/ijms13078615

Chen, L., Yan, W., Qian, X.J., Chen, M.J., Zhang, X.Y., Xin, F.X., Zhang, W.M., Jiang, M., Ochsenreither, K., 2021. Increased lipid production in Yarrowia lipolytica from acetate through metabolic engineering and cosubstrate fermentation. ACS Synth. Biol. 10, 3129–3138. doi: 10.1021/acssynbio.1c00405

Chen, W., Dong, T.T., Bai, F.T., Wang, J.L., Li, X.S., 2022. Lignin–carbohydrate complexes, their fractionation, and application to healthcare materials: a review. Int. J. Biol. Macromol. 203, 29–39. doi: 10.1016/j.ijbiomac.2022.01.132

Chen, Y.J., Yang, Y., Liu, X., Shi, X.Y., Wang, C.L., Zhong, H., Jin, F.M., 2023. Sustainable production of formic acid and acetic acid from biomass. Mol. Catal. 545, 113199.

Chisti, Y., 2007. Biodiesel from microalgae. Biotechnol. Adv. 25, 294–306. doi: 10.1016/j.biotechadv.2007.02.001

Chuengcharoenphanich, N., Watsuntorn, W., Qi, W., Wang, Z.M., Hu, Y.Z., Chulalaksananukul, W., 2023. The potential of biodiesel production from grasses in Thailand through consolidated bioprocessing using a cellulolytic oleaginous yeast, Cyberlindnera rhodanensis CU-CV7. Energy 263, 125759. doi: 10.1016/j.energy.2022.125759

Cianchetta, S., Ceotto, E., Galletti, S., 2023. Microbial oil production from alkali pre-treated giant reed (Arundo donax L.) by selected fungi. Energies 16, 5398. doi: 10.3390/en16145398

Cronan, J.E., 2021. The classical, yet controversial, first enzyme of lipid synthesis: Escherichia coli acetyl-CoA carboxylase. Microbiol. Mol. Biol. Rev. 85 e00032–e00021.

Cross, E.M., Adams, F.G., Waters, J.K., Aragão, D., Eijkelkamp, B.A., Forwood, J.K., 2021. Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases. Sci. Rep. 11, 7050. doi: 10.1038/s41598-021-86400-1

Cunha, J.T., Soares, P.O., Romaní, A., Thevelein, J.M., Domingues, L., 2019. Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways. Biotechnol. Biofuels 12, 20. doi: 10.1186/s13068-019-1360-8

David, F., Nielsen, J., Siewers, V., 2016. Flux control at the malonyl-CoA node through hierarchical dynamic pathway regulation in Saccharomyces cerevisiae. ACS Synth. Biol. 5, 224–233. doi: 10.1021/acssynbio.5b00161

de Jesus, S.S., Ferreira, G.F., Moreira, L.S., Wolf Maciel, M.R., Maciel Filho, R., 2019. Comparison of several methods for effective lipid extraction from wet microalgae using green solvents. Renew. Energy 143, 130–141. doi: 10.1016/j.renene.2019.04.168

DebRoy, S., Aliaga-Tobar, V., Galvez, G., Arora, S., Liang, X.W., Horstmann, N., Maracaja-Coutinho, V., Latorre, M., Hook, M., Flores, A.R., Shelburne, S.A., 2021. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus. Mol. Microbiol. 115, 1207–1228. doi: 10.1111/mmi.14667

Deshavath, N.N., Woodruff, W., Eller, F., Susanto, V., Yang, C., Rao, C.V., Singh, V., 2024. Scale-up of microbial lipid and bioethanol production from oilcane. Bioresour. Technol. 399, 130594. doi: 10.1016/j.biortech.2024.130594

Donzella, S., Serra, I., Fumagalli, A., Pellegrino, L., Mosconi, G., Lo Scalzo, R., Compagno, C., 2022. Recycling industrial food wastes for lipid production by oleaginous yeasts Rhodosporidiobolus azoricus and Cutaneotrichosporon oleaginosum. Biotechnol. Biofuels Bioprod. 15, 51. doi: 10.1186/s13068-022-02149-3

dos S Costa, G., Martinez-Burgos, W.J., dos Reis, G.A., Puche, Y.P., Vega, F.R., Rodrigues, C., Serra, J.L., de M Campos, S., Soccol, C.R., 2024. Advances in biomass and microbial lipids production: trends and prospects. Processes 12, 2903. doi: 10.3390/pr12122903

Duan, Y., Chen, L.M., Ma, L.X., Amin, F.R., Zhai, Y.D., Chen, G.F., Li, D.M., 2024. From lignocellulosic biomass to single cell oil for sustainable biomanufacturing: current advances and prospects. Biotechnol. Adv. 77, 108460. doi: 10.1016/j.biotechadv.2024.108460

Duan, Y., Chen, L.M., Ma, L.X., Zhai, Y.D., Hu, Y., Li, G.H., Chen, G.F., Li, D.M., 2025. CRISPR/Cas9-mediated metabolic engineering for enhanced PUFA production in Schizochytrium limacinum. Chem. Eng. J. 517, 164320. doi: 10.1016/j.cej.2025.164320

Fabiszewska, A., Misiukiewicz-Stępień, P., Paplińska-Goryca, M., Zieniuk, B., Białecka-Florjańczyk, E., 2019. An insight into storage lipid synthesis by Yarrowia lipolytica yeast relating to lipid and sugar substrates metabolism. Biomolecules 9, 685. doi: 10.3390/biom9110685.

Fang, H., Zhao, C., Chen, S.L., 2016. Single cell oil production by Mortierella isabellina from steam exploded corn stover degraded by three-stage enzymatic hydrolysis in the context of on-site enzyme production. Bioresour. Technol. 216, 988–995. doi: 10.1016/j.biortech.2016.06.051

Farese, R.V., Walther, T.C., 2023. Glycerolipid synthesis and lipid droplet formation in the endoplasmic reticulum. Cold Spring Harb. Perspect. Biol. 15, a041246. doi: 10.1101/cshperspect.a041246

Fei, Q., O’Brien, M., Nelson, R., Chen, X.W., Lowell, A., Dowe, N., 2016. Enhanced lipid production by Rhodosporidium toruloides using different fed-batch feeding strategies with lignocellulosic hydrolysate as the sole carbon source. Biotechnol. Biofuels 9, 130. doi: 10.1186/s13068-016-0542-x

Feofilova, E.P., Sergeeva, Y.E., Ivashechkin, A.A., 2010. Biodiesel-fuel: content, production, producers, contemporary biotechnology (Review). Appl. Biochem. Microbiol. 46, 369–378. doi: 10.1134/S0003683810040010

Ferreira, D., Nobre, A., Silva, M.L., Faria-Oliveira, F., Tulha, J., Ferreira, C., Lucas, C., 2013. XYLH encodes a xylose/H⁺ symporter from the highly related yeast species Debaryomyces fabryi and Debaryomyces hansenii. FEMS Yeast Res. 13, 585–596. doi: 10.1111/1567-1364.12061

Francois, J.M., Alkim, C., Morin, N., 2020. Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives. Biotechnol. Biofuels 13, 118. doi: 10.1186/s13068-020-01744-6

Gálvez-López, D., Chávez-Meléndez, B., Vázquez-Ovando, A., Rosas-Quijano, R., 2019. The metabolism and genetic regulation of lipids in the oleaginous yeast Yarrowia lipolytica. Braz. J. Microbiol. 50, 23–31. doi: 10.1007/s42770-018-0004-7

Gan, Q., Zhang, J.L., Gong, X.Y., Zou, Y.S., Yan, Y.J., 2025. Advancing lignocellulosic conversion though biosensor-enabled metabolic engineering. Green Chem. 27, 9862–9873. doi: 10.1039/d5gc03618f

Gao, L., Jiang, F.T., Zhang, Z.K., Bao, T.T., Zhu, D.C., Wu, X., 2025a. Unlocking lignin valorization and harnessing lignin-based raw materials for bio-manufacturing. Sci. China Life Sci. 68, 994–1009. doi: 10.1007/s11427-024-2792-x

Gao, L., Khoo, S.C., Zhang, Z.K., Wu, X., 2025b Trends in sustainable single-cell protein from non-grain feedstocks. Trends Biotechnol. 44, 65–78.

Gardeli, C., Athenaki, M., Xenopoulos, E., Mallouchos, A., Koutinas, A.A., Aggelis, G., Papanikolaou, S., 2017. Lipid production and characterization by Mortierella (Umbelopsis) isabelline cultivated on lignocellulosic sugars. J. Appl. Microbiol. 123, 1461–1477. doi: 10.1111/jam.13587

Gautam, D., Rana, V., Sharma, S., Kumar Walia, Y., Kumar, K., Umar, A., Ibrahim, A.A., Baskoutas, S., 2025. Hemicelluloses: a review on extraction and modification for various applications. ChemistrySelect 10, e06050. doi: 10.1002/slct.202406050

Gedela, R., Vantaku, V.R., Dasu, V.V., Pakshirajan, K., 2025. Artificial intelligence and machine learning-assisted metabolite profiling of oleaginous yeast Rhodotorula mucilaginosa. Bioresour. Technol. Rep. 32, 102431. doi: 10.1016/j.biteb.2025.102431

Gong, G.P., Wu, B., Liu, L.P., Li, J.T., He, M.X., 2024. Engineering oleaginous red yeasts as versatile chassis for the production of oleochemicals and valuable compounds: current advances and perspectives. Biotechnol. Adv. 76, 108432. doi: 10.1016/j.biotechadv.2024.108432

Gong, G.P., Wu, B., Liu, L.P., Li, J.T., He, M.X., Hu, G.Q., 2022. Enhanced biomass and lipid production by light exposure with mixed culture of Rhodotorula glutinis and Chlorella vulgaris using acetate as sole carbon source. Bioresour. Technol. 364, 128139. doi: 10.1016/j.biortech.2022.128139

Günenc, A.N., Graf, B., Stark, H., Chari, A., 2022. Fatty acid synthase: structure, function, and regulation. In: Harris, J.R., Marles-Wright, J. (Eds.), Macromolecular Protein Complexes Ⅳ: Structure and Function. Springer International Publishing, Cham, pp. 1–33.

Günerken, E., D’Hondt, E., Eppink, M.H.M., Garcia-Gonzalez, L., Elst, K., Wijffels, R.H., 2015. Cell disruption for microalgae biorefineries. Biotechnol. Adv. 33, 243–260. doi: 10.1016/j.biotechadv.2015.01.008

Hatakeyama, H., Hatakeyama, T., 2010. Lignin structure, properties, and applications. In: Abe, A., Dusek, K., Kobayashi, S. (Eds.), Biopolymers: Lignin, Proteins, Bioactive Nanocomposites. Springer, Berlin, Heidelberg, pp. 1–63.

Hu, R., Zhan, J.H., Zhao, Y.Y., Xu, X.Y., Luo, G., Fan, J.J., Clark, J.H., Zhang, S.C., 2023a. Bio-based platform chemicals synthesized from lignin biorefinery. Green Chem. 25, 8970–9000. doi: 10.1039/d3gc02927a

Hu, S.H., Zhang, T.W., Jiang, B., Huang, C.X., Wei, W.Q., Wu, W.J., Jin, Y.C., 2023b Achieving high enzymatic hydrolysis sugar yield of sodium hydroxide-pretreated wheat straw with a low cellulase dosage by adding sulfomethylated tannic acid. Bioresour. Technol. 384, 129276. doi: 10.1016/j.biortech.2023.129276

Huang, C., Chen, X.F., Xiong, L., Chen, X.D., Ma, L.L., Chen, Y., 2013. Single cell oil production from low-cost substrates: the possibility and potential of its industrialization. Biotechnol. Adv. 31, 129–139. doi: 10.1016/j.biotechadv.2012.08.010

Huang, C., Luo, M.T., Chen, X.F., Qi, G.X., Xiong, L., Lin, X.Q., Wang, C., Li, H.L., Chen, X.D., 2017. Combined “de novo” and “ex novo” lipid fermentation in a mix-medium of corncob acid hydrolysate and soybean oil by Trichosporon dermatis. Biotechnol. Biofuels 10, 147. doi: 10.1186/s13068-017-0835-8

Hunkeler, M., Hagmann, A., Stuttfeld, E., Chami, M., Guri, Y., Stahlberg, H., Maier, T., 2018. Structural basis for regulation of human acetyl-CoA carboxylase. Nature 558, 470–474. doi: 10.1038/s41586-018-0201-4

Hwangbo, M., Chu, K.H., 2020. Recent advances in production and extraction of bacterial lipids for biofuel production. Sci. Total Environ. 734, 139420. doi: 10.1016/j.scitotenv.2020.139420

Intasit, R., Cheirsilp, B., Louhasakul, Y., Boonsawang, P., 2020. Consolidated bioprocesses for efficient bioconversion of palm biomass wastes into biodiesel feedstocks by oleaginous fungi and yeasts. Bioresour. Technol. 315, 123893. doi: 10.1016/j.biortech.2020.123893

Isikgor, F.H., Becer, C.R., 2015. Lignocellulosic biomass: a sustainable platform for the production of bio-based chemicals and polymers. Polym. Chem. 6, 4497–4559. doi: 10.1039/C5PY00263J

Ivančić Šantek, M., Grubišić, M., Galić Perečinec, M., Beluhan, S., Šantek, B., 2021. Lipid production by Mortierella isabellina from pretreated corn cobs and effect of lignocellulose derived inhibitors on growth and lipid synthesis. Process. Biochem. 109, 46–58. doi: 10.1016/j.procbio.2021.06.021

Jarboe, L.R., Khalid, A., Rodriguez Ocasio, E., Noroozi, K.F., 2022. Extrapolation of design strategies for lignocellulosic biomass conversion to the challenge of plastic waste. J. Ind. Microbiol. Biotechnol. 49, kuac001. doi: 10.1093/jimb/kuac001

Jeffries, T., 2022. Compositions and methods for producing lipids and other biomaterials from grain ethanol stillage and stillage derivatives. INFORM 33, 36.

Ji, X.J., Ledesma-Amaro, R., 2020. Microbial lipid biotechnology to produce polyunsaturated fatty acids. Trends Biotechnol. 38, 832–834. doi: 10.1016/j.tibtech.2020.02.003

Jia, Y.L., Li, J., Nong, F.T., Yan, C.X., Ma, W., Zhu, X.F., Zhang, L.H., Sun, X.M., 2023. Application of adaptive laboratory evolution in lipid and terpenoid production in yeast and microalgae. ACS Synth. Biol. 12, 1396–1407. doi: 10.1021/acssynbio.3c00179

Jia, Y.L., Zhang, Q.M., Du, F., Yang, W.Q., Zhang, Z.X., Xu, Y.S., Ma, W., Sun, X.M., Huang, H., 2024a. Identification of lipid synthesis genes in Schizochytrium sp. and their application in improving eicosapentaenoic acid synthesis in Yarrowia lipolytica. Biotechnol. Biofuels Bioprod. 17, 32. doi: 10.1186/s13068-024-02471-y

Jia, Y.L., Zhang, Y., Xu, L.W., Zhang, Z.X., Xu, Y.S., Ma, W., Gu, Y., Sun, X.M., 2024b Enhanced fatty acid storage combined with the multi-factor optimization of fermentation for high-level production of docosahexaenoic acid in Schizochytrium sp. Bioresour. Technol. 398, 130532. doi: 10.1016/j.biortech.2024.130532

Jiang, T., Montgomery, V.A., Jetty, K., Ganesan, V., Incha, M.R., Gladden, J.M., Hillson, N.J., Liu, D., 2025. Metabolic engineering and synthetic biology for the environment: from perspectives of biodetection, bioremediation, and biomanufacturing. Biotechnol. Environ. 2, 14. doi: 10.1186/s44314-025-00029-2

Jiang, X.Y., Liu, L., Chen, J.H., Wei, D., 2018. Effects of Xanthophyllomyces dendrorhous on cell growth, lipid, and astaxanthin production of Chromochloris zofingiensis by mixed culture strategy. J. Appl. Phycol. 30, 3009–3015. doi: 10.1007/s10811-018-1553-8

Jilani, S.B., Olson, D.G., 2023. Mechanism of furfural toxicity and metabolic strategies to engineer tolerance in microbial strains. Microb. Cell Fact. 22, 221. doi: 10.1186/s12934-023-02223-x

Jin, M.J., Slininger, P.J., Dien, B.S., Waghmode, S., Moser, B.R., Orjuela, A., da Costa Sousa, L., Balan, V., 2015. Microbial lipid-based lignocellulosic biorefinery: feasibility and challenges. Trends Biotechnol. 33, 43–54. doi: 10.1016/j.tibtech.2014.11.005

Jørgensen, H., Pinelo, M., 2017. Enzyme recycling in lignocellulosic biorefineries. Biofuels Bioprod. Biorefin. 11, 150–167. doi: 10.1002/bbb.1724

Joshi, M., Manjare, S., 2024. Chemical approaches for the biomass valorisation: a comprehensive review of pretreatment strategies. Environ. Sci. Pollut. Res. 31, 48928–48954. doi: 10.1007/s11356-024-34473-6

Juanssilfero, A.B., Kahar, P., Amza, R.L., Yopi, Sudesh, K., Ogino, C., Prasetya, B., Kondo, A., 2019. Lipid production by Lipomyces starkeyi using sap squeezed from felled old oil palm trunks. J. Biosci. Bioeng. 127, 726–731. doi: 10.1016/j.jbiosc.2018.12.002

Kamal, R., Liu, Y.X., Li, Q., Huang, Q.T., Wang, Q., Yu, X., Zhao, Z.K., 2020. Exogenous l-proline improved Rhodosporidium toruloides lipid production on crude glycerol. Biotechnol. Biofuels 13, 159. doi: 10.1186/s13068-020-01798-6

Karim, A., Islam, M.A., Bin Khalid, Z., Yousuf, A., Khan, M.M.R., Mohammad Faizal, C.K., 2021. Microbial lipid accumulation through bioremediation of palm oil mill effluent using a yeast-bacteria co-culture. Renew. Energy 176, 106–114. doi: 10.1016/j.renene.2021.05.055

Kim, J., Son, H.F., Hwang, S., Gong, G., Ko, J.K., Um, Y., Han, S.O., Lee, S.M., 2022. Improving lipid production of Yarrowia lipolytica by the aldehyde dehydrogenase-mediated furfural detoxification. Int. J. Mol. Sci. 23, 4761. doi: 10.3390/ijms23094761

Kitamoto, D., Fukuoka, T., Saika, A., Morita, T., 2021. Glycolipid biosurfactants, mannosylerythritol lipids: distinctive interfacial properties and applications in cosmetic and personal care products. J. Oleo Sci. 71, 1–13. doi: 10.5650/jos.ess21358

Koppram, R., Tomás-Pejó, E., Xiros, C., Olsson, L., 2014. Lignocellulosic ethanol production at high-gravity: challenges and perspectives. Trends Biotechnol. 32, 46–53. doi: 10.1016/j.tibtech.2013.10.003

Krasznai, D.J., Champagne Hartley, R., Roy, H.M., Champagne, P., Cunningham, M.F., 2018. Compositional analysis of lignocellulosic biomass: conventional methodologies and future outlook. Crit. Rev. Biotechnol. 38, 199–217. doi: 10.1080/07388551.2017.1331336

Kraus, A., Hillen, W., 1997. Analysis of CcpA mutations defective in carbon catabolite repression in Bacillus megaterium. FEMS Microbiol. Lett. 153, 221–226. doi: 10.1016/s0378-1097(97)00264-4

Lazar, Z., Neuvéglise, C., Rossignol, T., Devillers, H., Morin, N., Robak, M., Nicaud, J.M., Crutz-Le Coq, A.M., 2017. Characterization of hexose transporters in Yarrowia lipolytica reveals new groups of sugar Porters involved in yeast growth. Fungal Genet. Biol. 100, 1–12.

Leber, C., Choi, J.W., Polson, B., Da Silva, N.A., 2016. Disrupted short chain specific β-oxidation and improved synthase expression increase synthesis of short chain fatty acids in Saccharomyces cerevisiae. Biotechnol. Bioeng. 113, 895–900. doi: 10.1002/bit.25839

Ledesma-Amaro, R., Nicaud, J.-M., 2016. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. Prog. Lipid Res. 61, 40–50. doi: 10.1016/j.plipres.2015.12.001.

Lee, S.Y., Weingarten, M., Ottenheim, C., 2024. Current upstream and downstream process strategies for sustainable yeast lipid production. Bioresour. Technol. 414, 131601. doi: 10.1016/j.biortech.2024.131601

Lei, C.R., Guo, X.P., Zhang, M.M., Zhou, X., Ding, N., Ren, J.L., Liu, M.H., Jia, C.L., Wang, Y.J., Zhao, J.R., Dong, Z.Y., Lu, D., 2024. Regulating the metabolic flux of pyruvate dehydrogenase bypass to enhance lipid production in Saccharomyces cerevisiae. Commun. Biol. 7, 1399. doi: 10.1038/s42003-024-07103-7

Li, J.Y., Pi, C.Y., Zhang, J.T., Jiang, F.T., Bao, T.T., Gao, L., Wu, X., 2025. Fungal bioconversion of lignin-derived aromatics: pathways, enzymes, and biotechnological potential. Biotechnol. Adv. 83, 108624. doi: 10.1016/j.biotechadv.2025.108624

Liang, Y., Ma, A.Z., Zhuang, G.Q., 2022. Construction of environmental synthetic microbial consortia: based on engineering and ecological principles. Front. Microbiol. 13, 829717. doi: 10.3389/fmicb.2022.829717

Lin, Z.N., Zhou, Y.J., Wu, J., Liu, H.J., Zhang, J.N., 2017. Effect of multiple inhibitions in corncob hydrolysate on the lipid production by Rhodotorula glutinis. Energy Fuels 31, 12247–12255. doi: 10.1021/acs.energyfuels.7b02159

Liu, C.S., Choi, B., Efimova, E., Nygård, Y., Santala, S., 2024. Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. Biotechnol. Biofuels Bioprod. 17, 61. doi: 10.1186/s13068-024-02510-8

Liu, H., Marsafari, M., Wang, F., Deng, L., Xu, P., 2019. Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metab. Eng. 56, 60–68. doi: 10.1016/j.ymben.2019.08.017

Liu, T.T., Li, P.D., Ou, Z.Q., Feng, Y.M., Wang, B.H., Yu, T.Y., Zhu, Y.M., Yu, L.J., 2025. Insights into the special physiology of Mortierella alpina cultured by agar supported solid state fermentation in enhancing arachidonic acid enriched lipid production. Sci. Rep. 15, 15967. doi: 10.1038/s41598-025-00965-9

Liu, Z.J., Natalizio, F., Dragone, G., Mussatto, S.I., 2021. Maximizing the simultaneous production of lipids and carotenoids by Rhodosporidium toruloides from wheat straw hydrolysate and perspectives for large-scale implementation. Bioresour. Technol. 340, 125598. doi: 10.1016/j.biortech.2021.125598

Lu, Q., Ma, C.Y., Guo, L., Lu, Y.J., Li, H.K., 2023. Co-fermentation of Chlorella vulgaris with oleaginous yeast in starch processing effluent as a carbon-reducing strategy for wastewater treatment and biofuel feedstock production. Fermentation 9, 476. doi: 10.3390/fermentation9050476

Lu, Q.L., Wu, J.Y., Li, Y.G., Huang, B., 2021. Isolation of thermostable cellulose Ⅱ nanocrystals and their molecular bridging for electroresponsive and pH-sensitive bio-nanocomposite. Ind. Crops Prod. 173, 114127. doi: 10.1016/j.indcrop.2021.114127

Lu, Y.J., Zhang, Y.M., Rock, C.O., 2004. Product diversity and regulation of type Ⅱ fatty acid synthases. Biochem. Cell Biol. 82, 145–155. doi: 10.1139/o03-076

Lyu, L.T., Chu, Y.D., Zhang, S.F., Zhang, Y., Huang, Q.T., Wang, S., Zhao, Z.K., 2021. Engineering the oleaginous yeast Rhodosporidium toruloides for improved resistance against inhibitors in biomass hydrolysates. Front. Bioeng. Biotechnol. 9, 768934. doi: 10.3389/fbioe.2021.768934

Lyu, Q.W., Ahmad Dar, R., Baganz, F., Smoliński, A., Rasmey, A.M., Liu, R.H., Zhang, L., 2025. Effects of lignocellulosic biomass-derived hydrolysate inhibitors on cell growth and lipid production during microbial fermentation of oleaginous microorganisms: a review. Fermentation 11, 121. doi: 10.3390/fermentation11030121

Ma, X.M., Mi, Y.W., Zhao, C., Wei, Q., 2022. A comprehensive review on carbon source effect of microalgae lipid accumulation for biofuel production. Sci. Total Environ. 806, 151387. doi: 10.1016/j.scitotenv.2021.151387

Madadi, M., Kargaran, E., Al Azad, S., Saleknezhad, M., Zhang, E.Z., Sun, F.B., 2025a. Machine learning-driven optimization of biphasic pretreatment conditions for enhanced lignocellulosic biomass fractionation. Energy 326, 136241. doi: 10.1016/j.energy.2025.136241

Madadi, M., Kargaran, E., Hashemi, S.S., Sun, C.H., Denayer, J.F.M., Karimi, K., Sun, F.B., Gupta, V.K., 2025b Scalable lignin monomer production via machine learning-guided reductive catalytic fractionation of lignocellulose. Adv. Sci. 12, e10496. doi: 10.1002/advs.202510496

Madadi, M., Saleknezhad, M., Hashemi, S.S., Kargaran, E., Abbasi-Riyakhuni, M., Cai, D., Priyadarshini, A., Elsayed, M., Sun, C.H., Sun, F.B., 2025c. Sustainable poplar biorefinery producing butanol-rich solvents, furfural, and lignin-derived compounds with environmental and economic benefits. Biofuel Res. J. 12, 2554–2568. doi: 10.18331/brj2025.12.4.4

Maddi, B., 2019. Extraction methods used to separate lipids from microbes. In: Balan, V. (Ed.), Microbial Lipid Production: Methods and Protocols. Springer, New York, pp. 151–159.

Malik, K., Sharma, P., Yang, Y.L., Zhang, P., Zhang, L.H., Xing, X.H., Yue, J.W., Song, Z.Z., Nan, L., Su, Y.J., El-Dalatony, M.M., Salama, E.S., Li, X.K., 2022. Lignocellulosic biomass for bioethanol: insight into the advanced pretreatment and fermentation approaches. Ind. Crops Prod. 188, 115569. doi: 10.1016/j.indcrop.2022.115569

Manandhar-Shrestha, K., Hildebrand, M., 2015. Characterization and manipulation of a DGAT2 from the diatom Thalassiosira pseudonana: improved TAG accumulation without detriment to growth, and implications for chloroplast TAG accumulation. Algal Res. 12, 239–248. doi: 10.1016/j.algal.2015.09.004

Mashima, T., Seimiya, H., Tsuruo, T., 2009. De novo fatty-acid synthesis and related pathways as molecular targets for cancer therapy. Br. J. Cancer 100, 1369–1372. doi: 10.1038/sj.bjc.6605007

McNeil, B.A., Stuart, D.T., 2018. Optimization of C16 and C18 fatty alcohol production by an engineered strain of Lipomyces starkeyi. J. Ind. Microbiol. Biotechnol. 45, 1–14. doi: 10.1007/s10295-017-1985-1

Milanesio, J., Hegel, P., Medina-González, Y., Camy, S., Condoret, J.S., 2013. Extraction of lipids from Yarrowia lipolytica. J. Chem. Technol. Biotechnol. 88, 378–387. doi: 10.1002/jctb.3840

Milke, L., Marienhagen, J., 2020. Engineering intracellular malonyl-CoA availability in microbial hosts and its impact on polyketide and fatty acid synthesis. Appl. Microbiol. Biotechnol. 104, 6057–6065. doi: 10.1007/s00253-020-10643-7

Mohamed, E.T., Werner, A.Z., Salvachúa, D., Singer, C.A., Szostkiewicz, K., Rafael Jiménez-Díaz, M., Eng, T., Radi, M.S., Simmons, B.A., Mukhopadhyay, A., Herrgård, M.J., Singer, S.W., Beckham, G.T., Feist, A.M., 2020. Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metab. Eng. Commun. 11, e00143. doi: 10.1016/j.mec.2020.e00143

da Costa Nogueira, C., De Araújo Padilha, C.E., de Medeiros Dantas, J.M., de Medeiros, F.G.M., de Araújo Guilherme, A., de Santana Souza, D.F., dos Santos, E.S., 2021. In-situ detoxification strategies to boost bioalcohol production from lignocellulosic biomass. Renew. Energy 180, 914–936. doi: 10.1016/j.renene.2021.09.012

Ochsenreither, K., Glück, C., Stressler, T., Fischer, L., Syldatk, C., 2016. Production strategies and applications of microbial single cell oils. Front. Microbiol. 7, 1539.

Pabba, M., Shah, A.M., Mettu, S., Talukder, M.M.R., Puniredd, S.R., 2026. Engineering lignocellulosic biomass to single-cell oils: microbial design, process intensification, and techno-economic constraints. Ind. Eng. Chem. Res. 65, 3027–3048. doi: 10.1021/acs.iecr.5c04697

Pant, M., Pant, T., 2023. Maximising biotransformation of pine needles to microbial lipids using Lipomyces starkeyi MTCC 1400T Renew. Energy 206, 574–581. doi: 10.1016/j.renene.2023.02.051

Patel, A., Matsakas, L., 2019. A comparative study on de novo and ex novo lipid fermentation by oleaginous yeast using glucose and sonicated waste cooking oil. Ultrason. Sonochem. 52, 364–374. doi: 10.1016/j.ultsonch.2018.12.010

Patel, A., Mikes, F., Bühler, S., Matsakas, L., 2018. Valorization of brewers’ spent grain for the production of lipids by oleaginous yeast. Molecules 23, 3052. doi: 10.3390/molecules23123052

Pensupa, N., Treebuppachartsakul, T., Pechprasarn, S., 2023. Machine learning models using data mining for biomass production from Yarrowia lipolytica fermentation. Fermentation 9, 239. doi: 10.3390/fermentation9030239

Pereira, H., Azevedo, F., Domingues, L., Johansson, B., 2022. Expression of Yarrowia lipolytica acetyl-CoA carboxylase in Saccharomyces cerevisiae and its effect on in-vivo accumulation of malonyl-CoA. Comput. Struct. Biotechnol. J. 20, 779–787. doi: 10.1016/j.csbj.2022.01.020

Periyasamy, S., Beula Isabel, J., Kavitha, S., Karthik, V., Mohamed, B.A., Gizaw, D.G., Sivashanmugam, P., Aminabhavi, T.M., 2023. Recent advances in consolidated bioprocessing for conversion of lignocellulosic biomass into bioethanol: a review. Chem. Eng. J. 453, 139783. doi: 10.1016/j.cej.2022.139783

Petersson, A., Almeida, J.R.M., Modig, T., Karhumaa, K., Hahn-Hägerdal, B., Gorwa-Grauslund, M.F., Lidén, G., 2006. A 5-hydroxymethyl furfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance. Yeast 23, 455–464. doi: 10.1002/yea.1370

Pi, C.Y., Li, J.Y., Bao, T.T., Gao, L., Wu, X., 2026. Integrated base editing and microfluidics boost microbial lipid production from lignin. Bioresour. Technol. 440, 133441. doi: 10.1016/j.biortech.2025.133441

Poddar, B.J., Nakhate, S.P., Gupta, R.K., Chavan, A.R., Singh, A.K., Khardenavis, A.A., Purohit, H.J., 2022. A comprehensive review on the pretreatment of lignocellulosic wastes for improved biogas production by anaerobic digestion. Int. J. Environ. Sci. Technol. 19, 3429–3456. doi: 10.1007/s13762-021-03248-8

Poontawee, R., Lorliam, W., Polburee, P., Limtong, S., 2023. Oleaginous yeasts: biodiversity and cultivation. Fungal Biol. Rev. 44, 100295. doi: 10.1016/j.fbr.2022.11.003

Poveda-Giraldo, J.A., Cardona Alzate, C.A., 2025. Valorization of lignocellulosic platform products based on biorefinery schemes through sequential pretreatments. Biomass Conv. Bioref. 15, 637–651. doi: 10.1007/s13399-023-05140-6

Qi, F., Shen, P.J., Hu, R.F., Xue, T., Jiang, X.Z., Qin, L.N., Chen, Y.Q., Huang, J.Z., 2020. Carotenoids and lipid production from Rhodosporidium toruloides cultured in tea waste hydrolysate. Biotechnol. Biofuels 13, 74. doi: 10.1186/s13068-020-01712-0

Qiao, K.J., Wasylenko, T.M., Zhou, K., Xu, P., Stephanopoulos, G., 2017. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nat. Biotechnol. 35, 173–177. doi: 10.1038/nbt.3763

Qiao, Y.M., Kargaran, E., Ji, H., Madadi, M., Rafieyan, S., Liu, D., 2025. Data-driven insights for enhanced cellulose conversion to 5-hydroxymethylfurfural using machine learning. Bioresour. Technol. 430, 132582. doi: 10.1016/j.biortech.2025.132582

Qin, J.S., Liu, N., Abid, U., Coleman, S.M., Wang, Y.D., Fu, Q., Yoon, S., Alper, H.S., Xie, D.M., 2025. Metabolic engineering of Yarrowia lipolytica for conversion of waste cooking oil into omega-3 eicosapentaenoic acid. ACS Eng. Au 5, 128–139. doi: 10.1021/acsengineeringau.4c00053

Rahmati, S., Doherty, W., Dubal, D., Atanda, L., Moghaddam, L., Sonar, P., Hessel, V., Ostrikov, K.K., 2020. Pretreatment and fermentation of lignocellulosic biomass: reaction mechanisms and process engineering. React. Chem. Eng. 5, 2017–2047. doi: 10.1039/d0re00241k

Rana Chhetri, B., Acharya, D., Gautam, A., Bajracharya, N., Shrestha, A., Khadka, S., 2022. Microbial pre-treatment of lignocellulosic biomass for biofuel production: a review. Int. J. Appl. Sci. Biotechnol. 10, 140–148. doi: 10.3126/ijasbt.v10i3.47510

Ranjith Kumar, R., Hanumantha Rao, P., Arumugam, M., 2015. Lipid extraction methods from microalgae: a comprehensive review. Front. Energy Res. 2, 61.

Ravindran, R., Jaiswal, A.K., 2016. A comprehensive review on pre-treatment strategy for lignocellulosic food industry waste: challenges and opportunities. Bioresour. Technol. 199, 92–102. doi: 10.1016/j.biortech.2015.07.106

Robles-Iglesias, R., Naveira-Pazos, C., Fernández-Blanco, C., Veiga, M.C., Kennes, C., 2023. Factors affecting the optimisation and scale-up of lipid accumulation in oleaginous yeasts for sustainable biofuels production. Renew. Sustain. Energy Rev. 171, 113043. doi: 10.1016/j.rser.2022.113043

Saini, R.K., Prasad, P., Shang, X.M., Keum, Y.S., 2021. Advances in lipid extraction methods: a review. Int. J. Mol. Sci. 22, 13643. doi: 10.3390/ijms222413643

Sallet, D., Ugalde, G.A., Tres, M.V., Mazutti, M.A., Zabot, G.L., Kuhn, R.C., 2025. Oil and biodiesel production from Mortierella isabellina biomass by a direct near-critical fluid extraction and transesterification method. Biomass 5, 6. doi: 10.3390/biomass5010006

Santala, S., Santala, V., Liu, N., Stephanopoulos, G., 2021. Partitioning metabolism between growth and product synthesis for coordinated production of wax esters in Acinetobacter baylyi ADP1. Biotechnol. Bioeng. 118, 2283–2292. doi: 10.1002/bit.27740

Santos Lopes, H.J., Bonturi,N., Kerkhoven, E.J., Miranda, E.A., Lahtvee, P.J., 2020. C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides. Appl. Microbiol. Biotechnol. 104, 2639–2649. doi: 10.1007/s00253-020-10386-5

Santos-Pereira, C., Sousa, J., Costa, Â.M.A., Santos, A.O., Rito, T., Soares, P., Franco-Duarte, R., Silvério, S.C., Rodrigues, L.R., 2023. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl. Microbiol. Biotechnol. 107, 5379–5401. doi: 10.1007/s00253-023-12627-9

Satya Sagar, P., Kommoji, S., Jayaraj, I., Balakrishnan, D., Shaik, F., Vucha, M., Gnanasekaran, L., 2023. Lipid bioproduction through optimization of thermal diluted acid pretreatment on native grass using Yarrowia lipolytica. Fuel 333, 126475. doi: 10.1016/j.fuel.2022.126475

Schultz, J.C., Mishra, S., Gaither, E., Mejia, A., Dinh, H., Maranas, C., Zhao, H.M., 2022. Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media. Microb. Cell Fact. 21, 26. doi: 10.1186/s12934-022-01750-3

Schweizer, E., Hofmann, J., 2004. Microbial type Ⅰ fatty acid synthases (FAS): major players in a network of cellular FAS systems. Microbiol. Mol. Biol. Rev. 68, 501–517. doi: 10.1128/MMBR.68.3.501-517.2004

Sha, Y.Y., Zhou, L.L., Wang, Z.D., Ding, Y., Lu, M.R., Xu, Z.X., Zhai, R., Jin, M.J., 2023. Adaptive laboratory evolution boosts Yarrowia lipolytica tolerance to vanillic acid. J. Biotechnol. 367, 42–52. doi: 10.1016/j.jbiotec.2023.03.006

Shahab, R.L., Brethauer, S., Davey, M.P., Smith, A.G., Vignolini, S., Luterbacher, J.S., Studer, M.H., 2020. A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose. Science 369, eabb1214. doi: 10.1126/science.abb1214

Sharma, K.K., Schuhmann, H., Schenk, P.M., 2012. High lipid induction in microalgae for biodiesel production. Energies 5, 1532–1553. doi: 10.3390/en5051532

Sharma, T., Sailwal, M., Dasgupta, D., Hazra, S., Bhaskar, T., Ghosh, D., 2021. Effect of lignocellulosic biomass inhibitors on oleaginous yeast cultivation in multistage fermentation system. Bioresour. Technol. Rep. 15, 100791. doi: 10.1016/j.biteb.2021.100791

Shin, S., Go, J.H., Moon, M., Park, G.W., 2023. Automatic fed-batch cultivation enhances microbial lipid production from volatile fatty acids. Energies 16, 1996. doi: 10.3390/en16041996

Shukla, A., Kumar, D., Girdhar, M., Kumar, A., Goyal, A., Malik, T., Mohan, A., 2023. Strategies of pretreatment of feedstocks for optimized bioethanol production: distinct and integrated approaches. Biotechnol. Biofuels Bioprod. 16, 44. doi: 10.33545/26633329.2023.v5.i1a.120

Singh, P., Kumari, S., Guldhe, A., Misra, R., Rawat, I., Bux, F., 2016. Trends and novel strategies for enhancing lipid accumulation and quality in microalgae. Renew. Sustain. Energy Rev. 55, 1–16.

Song, B., Zhao, S., Shen, W., Collings, C., Ding, S.Y., 2020. Direct measurement of plant cellulose microfibril and bundles in native cell walls. Front. Plant Sci. 11, 479. doi: 10.3389/fpls.2020.00479

Songdech, P., Intasit, R., Yingchutrakul, Y., Butkinaree, C., Ratanakhanokchai, K., Soontorngun, N., 2022. Activation of cryptic xylose metabolism by a transcriptional activator Znf1 boosts up xylitol production in the engineered Saccharomyces cerevisiae lacking xylose suppressor BUD21 gene. Microb. Cell Fact. 21, 32. doi: 10.1186/s12934-022-01757-w

Sonyeam, J., Chaipanya, R., Suksomboon, S., Khan, M.J., Amatariyakul, K., Wibowo, A., Posoknistakul, P., Charnnok, B., Liu, C.G., Laosiripojana, N., Sakdaronnarong, C., 2024. Process design for acidic and alcohol based deep eutectic solvent pretreatment and high pressure homogenization of palm bunches for nanocellulose production. Sci. Rep. 14, 7550. doi: 10.1038/s41598-024-57631-9

Spagnuolo, M., Shabbir Hussain, M., Gambill, L., Blenner, M., 2018. Alternative substrate metabolism in Yarrowia lipolytica. Front. Microbiol. 9, 1077. doi: 10.3389/fmicb.2018.01077

Srinivasan, N., Thangavelu, K., Sekar, A., Sanjeev, B., Uthandi, S., 2021. Aspergillus caespitosus ASEF14, an oleaginous fungus as a potential candidate for biodiesel production using sago processing wastewater (SWW). Microb. Cell Fact. 20, 179. doi: 10.1186/s12934-021-01667-3

Stovicek, V., Holkenbrink, C., Borodina, I., 2017. CRISPR/Cas system for yeast genome engineering: advances and applications. FEMS Yeast Res. 17, fox030.

Syguła, E., Ciolkosz, D., Białowiec, A., 2024. The significance of structural components of lignocellulosic biomass on volatile organic compounds presence on biochar: a review. Wood Sci. Technol. 58, 859–886. doi: 10.1007/s00226-024-01557-y

Tadioto, V., Deoti, J.R., Müller, C., de Souza, B.R., Fogolari, O., Purificação, M., Giehl, A., Deoti, L., Lucaroni, A.C., Matsushika, A., Treichel, H., Stambuk, B.U., Alves, S.L. Jr, 2023. Prospecting and engineering yeasts for ethanol production under inhibitory conditions: an experimental design analysis. Bioprocess Biosyst. Eng. 46, 1133–1145. doi: 10.1007/s00449-022-02812-x

Tanis, M.H., Wallberg, O., Galbe, M., Al-Rudainy, B., 2024. Lignin extraction by using two-step fractionation: a review. Molecules 29, 98.

Thanapimmetha, A., Peawsuphon, N., Chisti, Y., Saisriyoot, M., Srinophakun, P., 2021. Lipid production by the yeast Lipomyces starkeyi grown on sugars and oil palm empty fruit bunch hydrolysate. Biomass Conv. Bioref. 11, 1197–1210. doi: 10.1007/s13399-019-00532-z

Troiano, D.T., Studer, M.H., 2025. Microbial consortia for the conversion of biomass into fuels and chemicals. Nat. Commun. 16, 6712. doi: 10.1038/s41467-025-61957-x

Ujor, V.C., Okonkwo, C.C., 2022. Microbial detoxification of lignocellulosic biomass hydrolysates: biochemical and molecular aspects, challenges, exploits and future perspectives. Front. Bioeng. Biotechnol. 10, 1061667. doi: 10.3389/fbioe.2022.1061667

Valdés, G., Mendonça, R.T., Aggelis, G., 2020. Lignocellulosic biomass as a substrate for oleaginous microorganisms: a review. Appl. Sci. 10, 7698. doi: 10.3390/app10217698

Vasaki, M., Sithan, M., Ravindran, G., Paramasivan, B., Ekambaram, G., Karri, R.R., 2022. Biodiesel production from lignocellulosic biomass using Yarrowia lipolytica. Energy Convers. Manag. X 13, 100167.

Vladisavljević, G., 2024. Droplet microfluidics for high-throughput screening and directed evolution of biomolecules. Micromachines (Basel) 15, 971. doi: 10.3390/mi15080971

Wang, H., Peng, X.D., Zhang, H., Yang, S., Li, H., 2021. Microorganisms-promoted biodiesel production from biomass: a review. Energy Convers. Manag. X 12, 100137.

Wang, L., Kong, F., Chen, H., 2024a. Steam explosion pretreatment and saccharification of lignocellulosic biomass. In: Handbook of Biorefinery Research and Technology: Biomass Logistics to Saccharification. Springer, Dordrecht, pp. 341–354.

Wang, X.M., Wang, Y.N., He, Q.N., Liu, Y.T., Zhao, M., Liu, Y., Zhou, W.T., Gong, Z.W., 2022a. Highly efficient fed-batch modes for enzymatic hydrolysis and microbial lipogenesis from alkaline organosolv pretreated corn stover for biodiesel production. Renew. Energy 197, 1133–1143. doi: 10.1109/tvlsi.2022.3168783

Wang, Y.L., Gui, C.J., Wu, J.Y., Gao, X., Huang, T., Cui, F.J., Liu, H., Sethupathy, S., 2022b Spatio-temporal modification of lignin biosynthesis in plants: a promising strategy for lignocellulose improvement and lignin valorization. Front. Bioeng. Biotechnol. 10, 917459. doi: 10.3389/fbioe.2022.917459

Wang, Y.L., Zhang, Y.D., Cui, Q., Feng, Y.G., Xuan, J.S., 2024b Composition of lignocellulose hydrolysate in different biorefinery strategies: nutrients and inhibitors. Molecules 29, 2275. doi: 10.3390/molecules29102275

Wankhede, L., Price, B.S., Osorio-González, C.S., Saini, R., Brar, S.K., 2025. Fed-batch lipid production by Rhodosporidium toruloides-7191 using wood hydrolysate. Bioprocess Biosyst. Eng. 48, 1745–1753. doi: 10.1007/s00449-025-03209-2

Watsuntorn, W., Chuengcharoenphanich, N., Srimongkol, P., Alagappan, R.P., James, A., Rene, E.R., Chulalaksananukul, W., 2025. Optimizing lipid production in oleaginous yeasts for sustainable bioenergy: a review of process parameters, cultivation strategies, and machine learning integration. Biomass Bioenergy 197, 107810. doi: 10.1016/j.biombioe.2025.107810

Wolf, M.E., Lalande, A.T., Newman, B.L., Bleem, A.C., Palumbo, C.T., Beckham, G.T., Eltis, L.D., 2024. The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 90. e02155–e02123.

Woodruff, W., Deshavath, N.N., Susanto, V., Rao, C.V., Singh, V., 2023. Tolerance of engineered Rhodosporidium toruloides to sorghum hydrolysates during batch and fed-batch lipid production. Biotechnol. Biofuels Bioprod. 16, 187. doi: 10.1186/s13068-023-02429-6

Woźniak, A., Kuligowski, K., Świerczek, L., Cenian, A., 2025. Review of lignocellulosic biomass pretreatment using physical, thermal and chemical methods for higher yields in bioethanol production. Sustainability 17, 287. doi: 10.3390/su17010287

Xia, C.J., Zhang, J.G., Zhang, W.D., Hu, B., 2011. A new cultivation method for microbial oil production: cell pelletization and lipid accumulation by Mucor circinelloides. Biotechnol. Biofuels 4, 15. doi: 10.1186/1754-6834-4-15

Xiros, C., Olsson, L., 2014. Comparison of strategies to overcome the inhibitory effects in high-gravity fermentation of lignocellulosic hydrolysates. Biomass Bioenergy 65, 79–90. doi: 10.1016/j.biombioe.2014.03.060

Xu, J.Y., Du, W., Zhao, X.B., Zhang, G.L., Liu, D.H., 2013. Microbial oil production from various carbon sources and its use for biodiesel preparation. Biofuels Bioprod. Biorefin. 7, 65–77. doi: 10.1002/bbb.1372

Xu, P., Li, L.Y., Zhang, F.M., Stephanopoulos, G., Koffas, M., 2014. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc. Natl. Acad. Sci. U. S. A. 111, 11299–11304. doi: 10.1073/pnas.1406401111

Xu, P., Qiao, K.J., Stephanopoulos, G., 2017. Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica. Biotechnol. Bioeng. 114, 1521–1530. doi: 10.1002/bit.26285

Xu, Z.P., Theodoropoulos, C., Pittman, J.K., 2024. Optimization of a Chlorella–Saccharomyces co-culture system for enhanced metabolite productivity. Algal Res. 79, 103455. doi: 10.1016/j.algal.2024.103455

Yang, Q., Tian, M.Z., Dong, P., Zhao, Y.Y., Deng, Y., 2025. Engineering Yarrowia lipolytica to enhance the production of malonic acid via malonyl-CoA pathway at high titer. Adv. Sci. 12, 2411665. doi: 10.1002/advs.202411665

Yellapu, S.K., Bharti, Kaur, R., Kumar, L.R., Tiwari, B., Zhang, X.L., Tyagi, R.D., 2018. Recent developments of downstream processing for microbial lipids and conversion to biodiesel. Bioresour. Technol. 256, 515–528. doi: 10.1016/j.biortech.2018.01.129

Yin, M.Q., Xu, K., Luan, T., Kang, X.L., Yang, X.Y., Li, H.X., Hou, Y.H., Zhao, J.Z., Bao, X.M., 2024. Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae. Microbiol. Res. 286, 127815. doi: 10.1016/j.micres.2024.127815

Yoo, C.G., Meng, X.Z., Pu, Y.Q., Ragauskas, A.J., 2020. The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: a comprehensive review. Bioresour. Technol. 301, 122784. doi: 10.1016/j.biortech.2020.122784

Yu, Q., Liu, R.H., Li, K., Ma, R.J., 2019. A review of crop straw pretreatment methods for biogas production by anaerobic digestion in China. Renew. Sustain. Energy Rev. 107, 51–58. doi: 10.1016/j.rser.2019.02.020

Yu, W.W., Jin, K., Xu, X.H., Liu, Y.F., Li, J.H., Du, G.C., Chen, J., Lv, X.Q., Liu, L., 2025. Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: advances, challenges, and future perspectives. Biotechnol. Adv. 79, 108497. doi: 10.1016/j.biotechadv.2024.108497

Yu, Y., Liu, S.M., Zhang, Y.W., Lu, M.R., Sha, Y.Y., Zhai, R., Xu, Z.X., Jin, M.J., 2022a. A novel fermentation strategy for efficient xylose utilization and microbial lipid production in lignocellulosic hydrolysate. Bioresour. Technol. 361, 127624. doi: 10.1016/j.biortech.2022.127624

Yu, Y., Sha, Y.Y., Yu, J.M., Zhou, L.L., Chen, X.X., Zhai, R., Xu, Z.X., Jin, M.J., 2022b DLC(sa) and DLCA(sa) pretreatments boost the efficiency of microbial lipid production from rice straw via Trichosporon dermatis. Fuel 309, 122117. doi: 10.1016/j.fuel.2021.122117

Yukawa, T., Bamba, T., Guirimand, G., Matsuda, M., Hasunuma, T., Kondo, A., 2021. Optimization of 1, 2, 4-butanetriol production from xylose in Saccharomyces cerevisiae by metabolic engineering of NADH/NADPH balance. Biotechnol. Bioeng. 118, 175–185. doi: 10.1002/bit.27560

Zabed, H.M., Akter, S., Yun, J.H., Zhang, G.Y., Awad, F.N., Qi, X.H., Sahu, J.N., 2019. Recent advances in biological pretreatment of microalgae and lignocellulosic biomass for biofuel production. Renew. Sustain. Energy Rev. 105, 105–128. doi: 10.1016/j.rser.2019.01.048

Zhang, B., Li, J., Guo, L., Chen, Z.P., Li, C., 2018. Photothermally promoted cleavage of β-1, 4-glycosidic bonds of cellulosic biomass on Ir/HY catalyst under mild conditions. Appl. Catal. B Environ. 237, 660–664. doi: 10.1016/j.apcatb.2018.06.041

Zhang, J.L., Wang, Y.N., Gou, Q.L., Zhou, W., Liu, Y.T., Xu, J.K., Liu, Y., Zhou, W.T., Gong, Z.W., 2022. Consolidated bioprocessing of cassava starch into microbial lipid for biodiesel production by the amylolytic yeast Lipomyces starkeyi. Ind. Crops Prod. 177, 114534. doi: 10.1016/j.indcrop.2022.114534

Zhang, L.H., Song, Y.L., Wang, Q., Zhang, X., 2021. Culturing Rhodotorula glutinis in fermentation-friendly deep eutectic solvent extraction liquor of lignin for producing microbial lipid. Bioresour. Technol. 337, 125475. doi: 10.1016/j.biortech.2021.125475

Zhang, Z.R., Chen, X.Y., Gao, L., 2024. New strategy for the biosynthesis of alternative feed protein: single-cell protein production from straw-based biomass. GCB Bioenergy 16, e13120. doi: 10.1111/gcbb.13120

Zhao, M., Zhou, W.T., Wang, Y.N., Wang, J., Zhang, J.L., Gong, Z.W., 2022. Combination of simultaneous saccharification and fermentation of corn stover with consolidated bioprocessing of cassava starch enhances lipid production by the amylolytic oleaginous yeast Lipomyces starkeyi. Bioresour. Technol. 364, 128096. doi: 10.1016/j.biortech.2022.128096

Zhou, Z.Y., Liu, D.H., Zhao, X.B., 2021. Conversion of lignocellulose to biofuels and chemicals via sugar platform: an updated review on chemistry and mechanisms of acid hydrolysis of lignocellulose. Renew. Sustain. Energy Rev. 146, 111169. doi: 10.1016/j.rser.2021.111169

Zhu, Z.W., Zhou, Y.J., Krivoruchko, A., Grininger, M., Zhao, Z.K., Nielsen, J., 2017. Expanding the product portfolio of fungal type Ⅰ fatty acid synthases. Nat. Chem. Biol. 13, 360–362. doi: 10.1038/nchembio.2301

Zhuang, X.Y., Zhang, Y.H., Xiao, A.F., Zhang, A.H., Fang, B.S., 2022. Key enzymes in fatty acid synthesis pathway for bioactive lipids biosynthesis. Front. Nutr. 9, 851402. doi: 10.3389/fnut.2022.851402

Zoghlami, A., Paës, G., 2019. Lignocellulosic biomass: understanding recalcitrance and predicting hydrolysis. Front. Chem. 7, 874. doi: 10.3389/fchem.2019.00874

Relative Articles

Supplements(0)

Cited By

Proportional views