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Energy and Environment Directorate

Jon Magnuson

Jon Magnuson

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352
(509) 372-4119


Jon Magnuson is a biochemist with more than 20 years of research experience studying enzymes and metabolic pathways in bacteria and fungi. Dr. Magnuson is currently part of a team utilizing filamentous fungi in the development of processes for converting renewable biomass to fuels, chemicals and enzymes. This research involves the discovery and manipulation of genes encoding the enzymes of biosynthetic pathways or the regulation of those pathways. Complementary to this work is his major interest in fungal genomics. He is involved in the annotation and analysis of many fungal genomes with particular focus on the enzymes involved in the breakdown of plant biomass into sugars. Another area of his research is developing tools to assess and understand the diversity of fungi and other eukaryotic microbes found in different natural environments. This research has culminated in the development of a microarray based on a highly variable region of the ribosomal RNA gene, which is useful for the study of the diverse fungi, diatoms and green algae found in soils, sediments and natural biofilms.

Education and Credentials

  • Ph.D., Biochemistry, University of Minnesota, 1993
  • B.S., Biochemistry, University of Minnesota, 1986

PNNL Patents

PNNL Publications


  • Bilbao A., N. Munoz Munoz, J. Kim, D.J. Orton, Y. Gao, K. Poorey, and K.R. Pomraning, et al. 2023. "PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements." Nature Communications 14, no. 2023:2461. PNNL-SA-174727. doi:10.1038/s41467-023-37031-9
  • Dai Z., K.R. Pomraning, S. Deng, J. Kim, K.B. Campbell, A.L. Robles, and B.A. Hofstad, et al. 2023. "Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species." Biotechnology for Biofuels and Bioproducts 16. PNNL-SA-182738. doi:10.1186/s13068-023-02288-1
  • Liu D., H. Hwang, P.B. Otoupal, G.M. Geiselman, J. Kim, K.R. Pomraning, and Y. Kim, et al. 2023. "Engineering Rhodosporidium toruloides for Production of 3-Hydroxypropionic Acid from Lignocellulosic Hydrolysate." Metabolic Engineering 78. PNNL-SA-185285. doi:10.1016/j.ymben.2023.05.001
  • McNaught K.J., E. Kuatsjah, M. Zahn, E. Teixeira Prates, H. Shao, G. Bentley, and A. Pickford, et al. 2023. "Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440." Metabolic Engineering 76. PNNL-SA-179252. doi:10.1016/j.ymben.2023.02.006
  • Yuan G., J.J. Czajka, Z. Dai, D. Hu, K.R. Pomraning, B.A. Hofstad, and J. Kim, et al. 2023. "Rapid and robust squashed spore/colony PCR of industrially important fungi." Fungal Biology and Biotechnology 10. PNNL-SA-186830. doi:10.1186/s40694-023-00163-0


  • Ling C., G. Peabody, D. Salvachua, Y. Kim, C.M. Kneucker, C.H. Calvey, and M.A. Monninger, et al. 2022. "Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering." Nature Communications 13. PNNL-SA-168423. doi:10.1038/s41467-022-32296-y
  • Pomraning K.R., J.K. Magnuson, A.S. Beliaev, E.A. Hill, A.L. Robles, M.R. Garcia, and T.L. Lemmon. 2022. Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater. PNNL-33008. Richland, WA: Pacific Northwest National Laboratory. Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater
  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and T.L. Lemmon, et al. 2022. "Itaconic acid production is regulated by laeA in Aspergillus pseudoterreus." Metabolic Engineering Communications 15. PNNL-SA-171876. doi:10.1016/j.mec.2022.e00203


  • Dai Z., K.R. Pomraning, E.A. Panisko, B.A. Hofstad, K.B. Campbell, J. Kim, and A.L. Robles, et al. 2021. "Genetically engineered oleaginous yeast Lipomyces starkeyi for sesquiterpene a-zingiberene production." ACS Synthetic Biology 10, no. 5:1000-1008. PNNL-SA-156626. doi:10.1021/acssynbio.0c00503
  • Kim J., S.T. Coradetti, Y. Kim, Y. Gao, J. Yaegashi, J.D. Zucker, and N. Munoz Munoz, et al. 2021. "Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156767. doi:10.3389/fbioe.2020.612832
  • Kirby J., G.M. Geiselman, J. Yaegashi, J. Kim, X. Zhuang, M. Tran-Gyamfi, and J. Prahl, et al. 2021. "Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass." Biotechnology for Biofuels 14, no. 1:Article No. 101. PNNL-SA-162406. doi:10.1186/s13068-021-01950-w
  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and J. Kim, et al. 2021. "Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-149911. doi:10.3389/fbioe.2021.603832


  • Chaves J.E., R. Wilton, Y. Gao, N. Munoz Munoz, M.C. Burnet, Z. Schmitz, and J. Rowan, et al. 2020. "Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design." Metabolic Engineering Communications 11. PNNL-SA-155823. doi:10.1016/j.mec.2020.e00139
  • Comyn S., and J.K. Magnuson. 2020. "Molecular and genetic strategies for enhanced production of heterologous lignocellulosic enzymes." In Grand Challenges in Biology and Biotechnology, edited by H. Nevalainen. 281-313. Cham:Springer. PNNL-SA-142603. doi:10.1007/978-3-030-29541-7_10
  • Deng S., Z. Dai, M.S. Swita, K.R. Pomraning, B.A. Hofstad, E.A. Panisko, and S.E. Baker, et al. 2020. "Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359." Applied Microbiology and Biotechnology 104, no. 9:3981-3992. PNNL-SA-144713. doi:10.1007/s00253-020-10418-0
  • Geiselman G.M., X. Zhuang, J. Kirby, M. Tran-Gyamfi, J. Prahl, E.R. Sundstrom, and Y. Gao, et al. 2020. "Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides." Microbial Cell Factories 19, no. 1:Article No. 24. PNNL-SA-150034. doi:10.1186/s12934-020-1293-8
  • Haridas S., R. Albert, M. Binder, J. Bloem, K.M. LaButti, A. Salamov, and W.B. Andreopoulos, et al. 2020. "101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens." Studies in Mycology 96. PNNL-SA-150863. doi:10.1016/j.simyco.2020.01.003
  • Kjaerbolling I., T.C. Vesth, J. Frisvad, J. Nybo, S. Theobald, S. Kildgaard, and T.I. Petersen, et al. 2020. "A comparative genomics study of 23 Aspergillus species from section Flavi." Nature Communications 11, no. 1:Article No. 1106. PNNL-SA-146998. doi:10.1038/s41467-019-14051-y


  • Collett J.R., J.M. Billing, P.A. Meyer, A.J. Schmidt, A.B. Remington, E. Hawley, and B.A. Hofstad, et al. 2019. "Renewable diesel via hydrothermal liquefaction of oleaginous yeast and residual lignin from bioconversion of corn stover." Applied Energy 233. PNNL-SA-133222. doi:10.1016/j.apenergy.2018.09.115
  • Dai Z., K.R. Pomraning, S. Deng, B.A. Hofstad, E.A. Panisko, D. Rodriguez, and M.G. Butcher, et al. 2019. "Deletion of the ku70 homologue facilitates gene targeting in lipomyces starkeyi strain NRRL Y-11558." Current Genetics 65, no. 1:269-282. PNNL-SA-130042. doi:10.1007/s00294-018-0875-z
  • Leynaud- Kieffer L.M., S.C. Curran, I. Kim, J.K. Magnuson, J.M. Gladden, S.E. Baker, and B.A. Simmons. 2019. "A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable." PLoS One 14, no. 1:Article No. e0210243. PNNL-SA-142504. doi:10.1371/journal.pone.0210243
  • Otoupal P.B., M. Ito, A.P. Arkin, J.K. Magnuson, J.M. Gladden, and J.M. Skerker. 2019. "Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides." mSphere 4, no. 2:Article No. e00099-19. PNNL-SA-142513. doi:10.1128/mSphere.00099-19
  • Pomraning K.R., J.R. Collett, J. Kim, E.A. Panisko, D.E. Culley, Z. Dai, and S. Deng, et al. 2019. "Transcriptomic analysis of the oleaginous yeast Lipomyces starkeyi during lipid accumulation on enzymatically treated corn stover hydrolysate." Biotechnology for Biofuels 12. PNNL-SA-142743. doi:10.1186/s13068-019-1510-z
  • Rodriguez A., N. Ersig, G.M. Geiselman, K. Seibel, B.A. Simmons, J.K. Magnuson, and A. Eudes, et al. 2019. "Conversion of depolymerized sugars and aromatics from engineered feedstocks by two oleaginous red yeasts." Bioresource Technology 286. PNNL-SA-148133. doi:10.1016/j.biortech.2019.121365


  • Butcher M.G., P.A. Meyer, R.T. Hallen, K.O. Albrecht, C.K. Clayton, E. Polikarpov, and K.G. Rappe, et al. 2018. "Fungal Metabolites as Precursors to Renewable Transportation Fuels." Fuel 215. PNNL-SA-126614. doi:10.1016/j.fuel.2017.10.052
  • Deng S., K.R. Pomraning, P. Bohutskyi, and J.K. Magnuson. 2018. "Draft Genome Sequence of Aspergillus oryzae ATCC 12892." Genome Announcements 8, no. 18:Article No. e00251-18. PNNL-SA-132840. doi:10.1128/genomeA.00251-18
  • Kjaerbolling I., T.C. Vesth, J.C. Frisvad, J. Nybo, S. Theobald, A. Kuo, and A. Kuo, et al. 2018. "Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species." Proceedings of the National Academy of Sciences (PNAS) 115, no. 4:E753-E761. PNNL-SA-131168. doi:10.1073/pnas.1715954115
  • Pomraning K.R., E.L. Bredeweg, E.J. Kerkhoven, K.W. Barry, S. Haridas, H. Hundley, and K.M. LaButti, et al. 2018. "Regulation of yeast-to-hyphae transition in Yarrowia lipolytica." mSphere 3, no. 6:Article No. e00541-18. PNNL-SA-131456. doi:10.1128/mSphere.00541-18
  • Reilly M.C., J. Kim, J.J. Lynn, B.A. Simmons, J.M. Gladden, J.K. Magnuson, and S.E. Baker. 2018. "Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger." Applied Microbiology and Biotechnology 102, no. 4:1797-1807. PNNL-SA-132880. doi:10.1007/s00253-017-8717-3
  • Reilly M.C., S.A. Campen, B.A. Simmons, S.E. Baker, J.M. Gladden, and J.K. Magnuson. 2018. "Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger." In Cellulases: Methods and Protocols. Methods in Molecular Biology, edited by M Lubeck. 123-133. New York, New York:Humana Press. PNNL-SA-135995. doi:10.1007/978-1-4939-7877-9_10
  • Vesth T.C., J. Nybo, S. Theobald, J. Frisvad, T.O. Larsen, K.F. Nielsen, and J.B. Hoof, et al. 2018. "Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri." Nature Genetics 50, no. 12:1688-1695. PNNL-SA-133567. doi:10.1038/s41588-018-0246-1


  • Campen S.A., J.J. Lynn, S. Sibert, S. Srikrishnan, P.A. Phatale, T. Feldman, and J. Guenther, et al. 2017. "Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger." PLoS One 12, no. 12:Article No. e0189604. PNNL-SA-132873. doi:10.1371/journal.pone.0189604
  • Dai Z., S. Deng, D.E. Culley, K.S. Bruno, and J.K. Magnuson. 2017. "Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species." Applied Microbiology and Biotechnology 101, no. 15:6099-6110. PNNL-SA-123451. doi:10.1007/s00253-017-8357-7
  • Mondo S.J., R.O. Dannebaum, R.C. Kuo, K.B. Louie, A.J. Bewick, K.M. LaButti, and S. Haridas, et al. 2017. "Widespread Adenine N6-methylation of Active Genes in Fungi." Nature Genetics 49, no. 6:964-968. PNNL-26468. doi:10.1038/ng.3859
  • Unkefer C.J., R.T. Sayre, J.K. Magnuson, D.B. Anderson, I. Baxter, I.K. Blaby, and J.K. Brown, et al. 2017. "Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts." Algal Research 22. PNNL-SA-125672. doi:10.1016/j.algal.2016.06.002


  • Elliott D.C., T.R. Hart, G.G. Neuenschwander, L.J. Rotness, G. Roesijadi, A.H. Zacher, and J.K. Magnuson. 2014. "Hydrothermal Processing of Macroalgal Feedstocks in Continuous-Flow Reactors." ACS Sustainable Chemistry & Engineering 2, no. 2:207-215. PNNL-SA-97137. doi:10.1021/sc400251p
  • Jambovane S.R., S.A. Prost, A.M. Sheen, J.K. Magnuson, and R.T. Kelly. 2014. "ON-DEMAND SERIAL DILUTION USING QUANTIZED NANO/PICOLITER-SCALE DROPLETS." In Proceedings of the 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2014), October 26-30, 2014, San Antonio, Texas, 1247-1249. San Diego, California:Chemical and Biological Microsystems Society. PNNL-SA-107700.


  • Dai Z., U.K. Aryal, A.K. Shukla, W. Qian, R.D. Smith, J.K. Magnuson, and W.S. Adney, et al. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61. PNNL-SA-93855. doi:10.1016/j.fgb.2013.09.004
  • Meyer P., I.J. Tews, J.K. Magnuson, S.A. Karagiosis, and S.B. Jones. 2013. "Techno-economic analysis of corn stover fungal fermentation to ethanol." Applied Energy 111. PNNL-SA-89776. doi:10.1016/j.apenergy.2013.04.085
  • Meyer P.A., I.J. Tews, J.K. Magnuson, S.A. Karagiosis, and S.B. Jones. 2013. "Techno-economic analysis of corn stover fungal fermentation to ethanol." Applied Energy 111. PNNL-SA-93582. doi:10.1016/j.apenergy.2013.04.085
  • Simmons B.A., and J.K. Magnuson. 2013. "A Conversation with Blake Simmons, Vice President, Deconstruction Division, and Jon Magnuson, Director, Fungal Biotechnology Group, Joint BioEnergy Institute, Emeryville, CA." Industrial Biotechnology 9, no. 3:108-112. PNNL-SA-95145. doi:10.1089/ind.2013.1568


  • Andersen M.R., M. Salazar, P. Schaap, P. van de Vondervoort, D.E. Culley, J. Thykaer, and J.C. Frisvad, et al. 2011. "Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88." Genome Research 21, no. 6:885-897. PNNL-SA-78790. doi:10.1101/gr.112169.110
  • Berka R., I.V. Grigoriev, R.P. Otillar, A. Salamov, J. Grimwood, I. Reid, and N. Ishmael, et al. 2011. "Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and thielavia terrestris." Nature Biotechnology 29, no. 10:922-927. PNNL-SA-83457. doi:10.1038/nbt.1976
  • de Vries R.P., I. Benoit, G. Doehlemann, T. Kobayashi, J.K. Magnuson, E.A. Panisko, and S.E. Baker, et al. 2011. "Post-genomic approaches to understanding interactions between fungi and their environment." IMA Fungus 2, no. 1:81-86. PNNL-SA-80280. doi:10.5598/imafungus.2011.02.01.12
  • Grigoriev I.V., D. Cullen, S.X. Goodwin, D. Hibbett, T.W. Jeffries, C.P. Kubicek, and C.R. Kuske, et al. 2011. "Fueling the future with fungal genomics." Mycology 2, no. 3:192-209. PNNL-SA-80132.
  • Ryu J.S., S. Shary, C.J. Houtman, E.A. Panisko, P. Korripally, F.J. St John, and C. Crooks, et al. 2011. "Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood." Applied and Environmental Microbiology 77, no. 22:7933-7941. PNNL-SA-84670. doi:10.1128/AEM.05496-11
  • Zhang F., J. Vierock, O. Yizhar, L.E. Fenno, S. Tsunoda, A. Kianianmomeni, and M. Prigge, et al. 2011. "The Microbial Opsin Family of Optogenetic Tools." Cell 147, no. 7:1446-1457. PNNL-SA-85517. doi:10.1016/j.cell.2011.12.004


  • Ohm R.A., J.F. de Jong, L.G. Lugones, A. Aerts, E. Kothe, J.E. Stajich, and R.P. de Vries, et al. 2010. "Genome sequence of the model mushroom Schizophyllum commune." Nature Biotechnology 28, no. 9:957-963. PNNL-SA-75499. doi:10.1038/nbt.1643
  • Smith D.R., R.W. Lee, J.C. Cushman, J.K. Magnuson, D. Tran, and J.E. Polle. 2010. "The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA." BMC Plant Biology 10. PNNL-SA-73608.


  • Jovanovic I., J.K. Magnuson, F.R. Collart, B. Robbertse, W.S. Adney, M.E. Himmel, and S.E. Baker. 2009. "Fungal glycoside hydrolases for saccharification of lignocellulose: outlook for new discoveries fueled by genomics and functional studies." Cellulose 16, no. 4:687-697. PNNL-SA-66360.
  • Le Crom S., W. Schackwitz, L. Pennacchiod, J.K. Magnuson, D.E. Culley, J.R. Collett, and J.X. Martin, et al. 2009. "Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing." Proceedings of the National Academy of Sciences of the United States of America 106, no. 38:16151-16156. PNNL-SA-67636.
  • Martinez D., J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C.P. Kubicek, and P. Ferreira, et al. 2009. "Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion." Proceedings of the National Academy of Sciences of the United States of America 106, no. 6:1954-1959. PNNL-SA-64450. doi:10.1073/pnas.0809575106
  • Miracle A.L., V.L. Bailey, S.E. Baker, A.L. Bunn, J.K. Magnuson, and B.M. Webb-Robertson. 2009. "Integration of 'omics technologies for characterization of complex microbial ecosystems - 8119." In Waste Management Symposium 2008, 832-841. Tucson, Arizona:WM Symposia. PNNL-SA-58003.


  • Martinez A.D., R. Berka, B. Henrissat, B. Henrissat, M. Saloheimo, M. Arvas, and S.E. Baker, et al. 2008. "Genome Sequencing and Analysis of the Biomass-Degrading Fungus Trichoderma reesei (syn. Hypocrea jecorina)." Nature Biotechnology 26, no. 5:553-560. PNNL-SA-60199.
  • Shary S., A.N. Kapich, A.N. Kapich, E.A. Panisko, J.K. Magnuson, D. Cullen, and K. Hammel, et al. 2008. "Differential Expression in Phanerochaete chrysosporium of Membrane-Associated Proteins Relevant to Lignin Degradation." Applied and Environmental Microbiology 74, no. 23:7252-7257. PNNL-SA-63951. doi:10.1128/AEM.01997-08


  • Baker S.E., C.F. Wend, A.D. Martinez, J.K. Magnuson, E.A. Panisko, Z. Dai, and K.S. Bruno, et al. 2007. "Genome and Proteome Analysis of Industrial Fungi." In Exploitation of Fungi, edited by GD Robson, P van West and G Gadd. 3-9. New York, New York:Cambridge University Press. PNNL-SA-51617. doi:10.1017/CBO9780511902451.002
  • Cuomo C.A., U. Guldener, J.R. Xu, F. Trail, B.G. Turgeon, A. Di Pietro, and A. Di Pietro, et al. 2007. "The Fusarium Graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization." Science 317, no. 5843:1400-1402. PNNL-SA-57387. doi:10.1126/science.1143708


  • Lei C., Y. Shin, J.K. Magnuson, G.E. Fryxell, L.L. Lasure, D.C. Elliott, and J. Liu, et al. 2006. "Characterization of Functionalized Nanoporous Supports for Protein Confinement." Nanotechnology 17, no. 22:5531-5538. PNNL-SA-51297. doi:10.1088/0957-4484/17/22/001


  • Dai Z., X. Mao, J.K. Magnuson, and L.L. Lasure. 2004. "Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization." Applied and Environmental Microbiology 70, no. 4:2474-2485. PNNL-SA-40898.
  • Magnuson J.K., and L.L. Lasure. 2004. "Organic Acid Production by Filamentous Fungi." In ADVANCES IN FUNGAL BIOTECHNOLOGY FOR INDUSTRY, AGRICULTURE, AND MEDICINE, edited by Jan S. Tkacz and Lene Lange. 307-340. New York, New York:Kluwer Academic/Plenum Publishers. PNNL-SA-41208.
  • Syn C.K., J.K. Magnuson, M.T. Kingsley, and S. Swarup. 2004. "Characterization of Pseudomonas putida Genes Responsive to Nutrient Limitation." Microbiology 150. PNNL-SA-40683.


  • de Henestrosa A.R., J. Cune, I. Erill, J.K. Magnuson, and J. Barbe. 2002. "A Green Nonsulfur Bacterium, Dehalococcoides ethenogenes, with the LexA-binding sequence found in Gram-positive organisms." Journal of Bacteriology 184, no. 21:6073-6080. PNWD-SA-5962.


  • Magnuson J.K., M.F. Romine, D.R. Burris, and M.T. Kingsley. 2000. "Trichloroethene Reductive Dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and Substrate Range Characterization." Applied and Environmental Microbiology 66. PNNL-SA-33788.

Energy and Environment

Core Research Areas