Harnessing Paecilomyces variotii to remove lignocellulose-derived inhibitors: potential evaluation, lignocellulosic biorefining route design, and transcriptome analysis

Abstract

Discovery and identification of robust biodetoxification strain is crucial for the sustainable and efficient operation of lignocellulosic biorefining process. Paecilomyces variotii FN89, a recently isolated mesophilic filamentous fungi, was herein shown to be able to biodegrade lignocellulose-derived inhibitors including furfural (1.5 g/L), 5-hydroxymethylfurfural (4 g/L), acetic acid (4 g/L), hydroxybenzaldehyde (0.2 g/L), syringaldehyde (0.2 g/L), and vanillin (1.5 g/L) efficiently and completely. P. variotii FN89 was adapted to mixed inhibitors and relatively low dissolved oxygen conditions, which can detoxify both the highly viscosity hydrolysate and solid biomass with the well preserve of fermentable sugars and no addition of any nutrients. Two biorefinery chains involving biodetoxification process were thus established to cope with different forms of pretreated biomass for cellulosic lactic acid production. The cellulosic lactic acid titers were above 100 g/L from 25% (w/w) solids loading pretreated wheat straw. The global transcriptome analysis of P. variotii FN89 in the presence of mixed inhibitors suggested that the glycolysis pathway and pentose phosphate pathway were repressed while tricarboxylic acid cycle was enhanced, ensuring the complete degradation of the inhibitors-derived intermediates and efficient energy supply. This study provided a unique and practical biodetoxification strain for lignocellulosic biorefinery, as well as enriched the knowledge of the molecular basis of lignocellulose-derived inhibitors tolerance and carbohydrates metabolism of P. variotii.

Keywords

Biodetoxification / Paecilomyces variotii / Lignocellulose / Lactic acid / Transcriptome analysis

References

[1] ZhaoL, SunZF, ZhangCC, NanJ, RenNQ, LeeDJ, ChenC. Advances in pretreatment of lignocellulosic biomass for bioenergy production: challenges and perspectives. Bioresour Technol, 2022, 343126123.

[2] GuoH, ZhaoY, ChangJS, LeeDJ. Inhibitor formation and detoxification during lignocellulose biorefinery: A review. Bioresour Technol, 2022, 361127666.

[3] RajT, ChandrasekharK, MoryaR, Kumar PandeyA, JungJH, KumarD, SinghaniaRR, KimSH. Critical challenges and technological breakthroughs in food waste hydrolysis and detoxification for fuels and chemicals production. Bioresour Technol, 2022, 360127512.

[4] HouJ, ZhangX, LiuS, ZhangS, ZhangQ. A critical review on bioethanol and Biochar production from lignocellulosic biomass and their combined application in generation of high-value byproducts. Energy Technol, 2020, 852000025.

[5] SinghB, KumarP, YadavA, DattaS. Degradation of fermentation inhibitors from lignocellulosic hydrolysate liquor using immobilized bacterium, Bordetella Sp. BTIITR Chem Eng J, 2019, 361: 1152-60.

[6] XieY, HuQ, FengG, JiangX, HuJ, HeM, HuG, ZhaoS, LiangY, RuanZ, PengN. Biodetoxification of phenolic inhibitors from lignocellulose pretreatment using Kurthia Huakuii LAM0618(T) and subsequent lactic acid fermentation. Molecules, 2018, 232626.

[7] HeY, ZhangJ, BaoJ. Acceleration of biodetoxification on dilute acid pretreated lignocellulose feedstock by aeration and the consequent ethanol fermentation evaluation. Biotechnol Biofuels, 2016, 919.

[8] SinghB, VermaA, Pooja, MandalPK, DattaS. A biotechnological approach for degradation of inhibitory compounds present in lignocellulosic biomass hydrolysate liquor using Bordetella Sp. BTIITR Chem Eng J, 2017, 328: 519-26.

[9] LiuJ, CaiY, LiuL, ZhanR, ZhaoS, LiangY, PengN, ZhuJ, LiH, XiaoN, HuJ, HeM, HuG. Enhanced lactic acid production by Bacillus coagulans through simultaneous saccharification, biodetoxification, and fermentation. Biofuels Bioprod Biorefining, 2020, 14(3): 533-43.

[10] ZhangD, OngYL, LiZ, WuJC. Biological detoxification of furfural and 5-hydroxyl Methyl furfural in hydrolysate of oil palm empty fruit bunch by Enterobacter sp. FDS8. Biochem Eng J, 2013, 72: 77-82.

[11] FonsecaBG, MateoS, MoyaAJ, RobertoIC. Biotreatment optimization of rice straw hydrolyzates for ethanolic fermentation with Scheffersomyces stipitis. Biomass Bioenerg, 2018, 112: 19-28.

[12] ZanellatiA, SpinaF, BonaterraM, DinuccioE, VareseGC, ScarpeciTE. Screening and evaluation of phenols and furans degrading fungi for the biological pretreatment of lignocellulosic biomass. Int Biodeterior Biodegrad, 2021, 161105246.

[13] FonsecaBG, MouttaRdO, FerrazFdO, VieiraER, NogueiraAS, BaratellaBF, RodriguesLC, Hou-RuiZ, da SilvaSS. Biological detoxification of different hemicellulosic hydrolysates using Issatchenkia occidentalis CCTCC M 206097 yeast. J Ind Microbiol Biotechnol, 2010, 38(1): 199-207.

[14] YanY, HeJ. Clostridium species strain BOH3 tolerates and transforms inhibitors from horticulture waste hydrolysates. Appl Microbiol Biotechnol, 2017, 101(15): 6289-97.

[15] SinghA, BedoreSR, SharmaNK, LeeSA, EitemanMA, NeidleEL. Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces Marxianus. Biotechnol Biofuels, 2019, 1291.

[16] RanH, ZhangJ, GaoQ, LinZ, BaoJ. Analysis of biodegradation performance of furfural and 5-hydroxymethylfurfural by Amorphotheca resinae ZN1. Biotechnol Biofuels, 2014, 7151.

[17] HerreraB, de LagunaI, Toledo MaranteFJ, MiosoR. Enzymes and bioproducts produced by the ascomycete fungus Paecilomyces variotii. J Appl Microbiol, 2015, 119(6): 1455-66.

[18] MadeiraJVJr, MacedoJA, MacedoGA. Detoxification of castor bean residues and the simultaneous production of Tannase and phytase by solid-state fermentation using Paecilomyces variotii. Bioresour Technol, 2011, 102(15): 7343-8.

[19] WangL, LiY, YuP, XieZ, LuoY, LinY. Biodegradation of phenol at high concentration by a novel fungal strain Paecilomyces variotii JH6. J Hazard Mater, 2010, 183(1–3): 366-71.

[20] ZhangB, KhushikFA, ZhanB, BaoJ. Transformation of lignocellulose to starch-like carbohydrates by organic acid-catalyzed pretreatment and biological detoxification. Biotechnol Bioeng, 2021, 118(10): 4105-18.

[21] QiuZ, GaoQ, BaoJ. Engineering Pediococcus acidilactici with xylose assimilation pathway for high titer cellulosic l-lactic acid fermentation. Bioresour Technol, 2018, 249: 9-15.

[22] HanX, BaoJ. General method to correct the fluctuation of acid based pretreatment efficiency of lignocellulose for highly efficient bioconversion. ACS Sustain Chem Eng, 2018, 6(3): 4212-9.

[23] YiX, GaoQ, ZhangL, WangX, HeY, HuF, ZhangJ, ZouG, YangS, ZhouZ, BaoJ. Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn Stover. Biotechnol Biofuels, 2019, 12126.

[24] HoubrakenJ, VerweijPE, RijsAJ, BormanAM, SamsonRA. Identification of Paecilomyces variotii in clinical samples and settings. J Clin Microbiol, 2010, 48(8): 2754-61.

[25] ZhangB, GeberekidanM, YanZ, YiX, BaoJ. Very high thermotolerance of an adaptive evolved Saccharomyces cerevisiae in cellulosic ethanol fermentation. Fermentation, 2023, 9393.

[26] KannistoMS, MangayilRK, Shrivastava-BhattacharyaA, PletschkeBI, KarpMT, SantalaVP. Metabolic engineering of Acinetobacter baylyi ADP1 for removal of clostridium Butyricum growth inhibitors produced from lignocellulosic hydrolysates. Biotechnol Biofuels, 2015, 8198.

[27] RobinsonT, NigamP. Bioreactor design for protein enrichment of agricultural residues by solid state fermentation. Biochem Eng J, 2003, 13(2): 197-203.

[28] BückA, CasciatoriFP, ThoméoJC, TsotsasE. Model-based control of enzyme yield in solid-state fermentation. Procedia Eng, 2015, 102: 362-71.

[29] Santiago AM, Conrado LS, Mélo BCA, Sousa CAB, Oliveira PL, Lima FCS. 2014. Solid state fermentation: Fundamentals and application. in: Transport Phenomena and Drying of Solids and Particulate Materials, editors J.M.P.Q. Delgado, A.G. Barbosa de Lima, Springer International Publishing. Cham, pp. 117–139. https://doi.org/10.1007/978-3-319-04054-7_6

[30] HanT, ZhangB, LiH, ZhangH, YangY, HuL, RenX, WangS, ZhengL, HanX, LiuG, ZhangJ, FeiQ, TangY, YangS, BaoX, BaoJ. Year-round storage operation of three major agricultural crop residue biomasses by performing dry acid pretreatment at regional collection depots. ACS Sustain Chem Eng, 2021, 9(13): 4722-34.

[31] HanT, ZhangB, YangH, LiuX, BaoJ. Changes in pH values allow for a visible detection of the end point in submerged liquid biodetoxification during biorefinery processing. ACS Sustain Chem Eng, 2023, 11(46): 16608-17.

[32] UrquhartAS, MondoSJ, MakelaMR, HaneJK, WiebengaA, HeG, MihaltchevaS, PangilinanJ, LipzenA, BarryK, de VriesRP, GrigorievIV, IdnurmA. Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales). Front Microbiol, 2018, 93058.

[33] MaM, LiuZL. Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC Genomics, 2010, 11660.

[34] BajwaPK, HoC-Y, ChanCK, MartinVJJ, TrevorsJT, LeeH. Transcriptional profiling of Saccharomyces cerevisiae T2 cells upon exposure to hardwood spent sulphite liquor: comparison to acetic acid, furfural and hydroxymethylfurfural. Antonie Van Leeuwenhoek, 2013, 103(6): 1281-95.

[35] WangL, WangX, HeZQ, ZhouSJ, XuL, TanXY, XuT, LiBZ, YuanYJ. Engineering prokaryotic regulator irre to enhance stress tolerance in budding yeast. Biotechnol Biofuels, 2020, 13193.

[36] GuH, ZhuY, PengY, LiangX, LiuX, ShaoL, XuY, XuZ, LiuR, LiJ. Physiological mechanism of improved tolerance of Saccharomyces cerevisiae to lignin-derived phenolic acids in lignocellulosic ethanol fermentation by short-term adaptation. Biotechnol Biofuels, 2019, 12268.

[37] ZhangB, LiJ, LiuX, BaoJ. Continuous simultaneous saccharification and co-fermentation (SSCF) for cellulosic L-lactic acid production. Ind Crop Prod, 2022, 187115527.

[38] ZhangB, RenD, LiuQ, LiuX, BaoJ. Coproduction of single cell protein and lipid from lignocellulose derived carbohydrates and inorganic ammonia salt with soluble ammonia recycling. Bioresour Technol, 2023, 384129345.

[39] ChenA, ZhangB, BaoJ. Adaptive evolution of Paecilomyces variotii enhanced the biodetoxification of high-titer inhibitors in pretreated lignocellulosic feedstock. Bioresour Technol, 2024, 411131351.

Funding

National Key R&D Program of China(2023YFA0914400)

National Natural Science Foundation of China(32301269)

Yangfan Project of Science and Technology Committee of Shanghai Municipality(23YF1409900)

the Key Technology R&D Program of the Science and Technology Commission of Shanghai Municipality(25HC2820200)

RIGHTS & PERMISSIONS

Jiangnan University

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