Nhu H. NguyenAssociate Professor of Soil Microbial Ecology
Principal Investigator
Office: 221 Sherman Laboratory
Office Phone: 808-956-6593
Lab Phone: 808-956-2634
Email: nhu.nguyen@hawaii.edu
Research Interests
I'm broadly interested in how soil associated organisms functionally interact with each other, with their environment, and the outcomes of these interactions. My approach is grounded in organismal biology, using the best available methods to answer fundamental and mechanistic questions in organismal interactions in both lab and field-based experiments.
Affiliations
Evolutionary Ecology & Conservation Biology (EECB) facultyCourses
BOT430/BIOL430/TPSS432 - Biology of Fungi (Lecture & Lab)TPSS480/BIOL480 - Life in the Soil Environment (Lecture & Lab)
MICR485 - Microbes and their Environment
TPSS604 - Advanced Soil Microbiology (Lecture & Lab)
TPSS711 - Special Topics: Microbiome: From soils to sequences
Publications
*indicates undergraduate author
2024
Lofgren L, Nguyen NH, Kennedy PG, Pérez Pazos E, Fletcher J, Liao H-L, Wang H, Zhang K, Ruytinx J, Smith AH, Ke Y-H, Cotter HVT, Engwall E, Hameed K, Vilgalys R, Branco S. (2024). Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. New Phytologist. doi: 10.1111/nph.19700
2023
Abe JNA*, Dhungana I, Nguyen NH. (2023). Legume-nodulating rhizobia are widespread in soils and plants across the island of O‘ahu, Hawai‘i. PLOS ONE 18(9): e0291250. doi: 10.1371/journal.pone.0291250
Wilson AW, Eberhardt U, Nguyen NH, Noffsinger C, Swenie R, Loucks JJ, Perry BA, Hererra M, Osmundson T, Duhon-Delong S, Beker HJ, Mueller GM. (2023). Does one size fit all? Variation in the DNA barcode gap of macrofungal genera. Journal of Fungi, 9, 788. doi: 10.3390/jof9080788
Ke Y-H, Branco S, Bazzicalupo AL, Nguyen NH, Liao HL, Kennedy P, Bruns TD, Kuo A, LaButti K, Barry K, Grigoriev I, Vilgalys R. (2023). Genomic determination of breeding systems in basidiomycete fungi: direct evidence for balancing selection and trans-specific evolution of HD MAT genes between sister genera of suilloid fungi. Genetics, Apr 18:iyad069. doi: 10.1093/genetics/iyad069
Nguyen NH. (2023). Fungal hyphosphere microbiomes are distinct from surrounding substrates and show consistent association patterns. Microbiology Spectrum, 11:2, e04708-22. doi: 10.1128/spectrum.04708-22
Shemesh H, Bruns TD, Peay KG, Kennedy PG, Nguyen NH. (2023). Changing balance between dormancy and mortality determines trajectory of ectomycorrhizal fungal spore longevity over a 15 year burial experiment. New Phytologist, 238:11–15. doi: 10.1111/nph.18677
Dhungana I, Kantar MB, Nguyen NH. (2023). Root exudate quality from different plant species influences the growth of rhizosphere bacteria. Rhizosphere, 25:100645. doi: 10.1016/j.rhisph.2022.100645
2022
McGrath CR, Hicks Pries CE, Nguyen NH, Glazer B, Lio S, Crow SE. (2022). Minerals limit the deep soil respiration response to warming in a tropical Andisol. Biogeochemistry. In press. https://doi.org/10.1007/s10533-022-00965-1. Paper
Amend AS, et al. (2022). A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes. Proceedings of the National Academy of Sciences, 119:e2204146119. DOI: 10.1073/pnas.2204146119. Paper
Plakidas JD, Nguyen NH, Ferro ML (2022). A new species of Neostenoptera Meunier (Diptera: Cecidomyiidae: Winnertziinae) from Hawai‘i. Insecta Mundi 941: 1–12. Paper
Heisey S, Ryals R, Maaz MT, Nguyen NH (2022). A single application of compost can leave lasting impacts on soil microbial community structure and alter cross-domain interaction networks. Frontiers in Soil Science, 2:749212. DOI: 10.3389/fsoil.2022.749212. Paper
Erlandson S, Margis R, Ramirez A, Nguyen NH, Lofgren L, Liao H-L, Vilgalys R, Kennedy P, Peay K. (2022). Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens. New Phytologist, 234:1910–1913. DOI: 10.1111/nph.17816. Paper
Maaz MT, Nguyen NH, Del Valle Echevarria A, Kantar M, Mileyko Y, Muszynski M. (2022). Design and implementation of a cohort-based undergraduate research experience in the agricultural sciences. Natural Sciences Education, 51, e20076. DOI: 10.1002/nse2.20076. Paper
2021
Nuccio EE, Nguyen NH, Nunes da Rocha U, Mayali X, Weber P, Brodie E, Firestone M. 2021. Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil. ISME Communications, doi:10.1038/s43705-021-00059-3. Paper
Bazzicalupo AL, Erlandson S, Branine M, Ratz M, Ruffing L, Nguyen NH, Branco S. 2021. Fungal community shift along steep environmental gradients from geothermal soils in Yellowstone National Park. Microbial Ecology, DOI:10.1007/s00248-021-01848-y. Paper
Perez-Pazos E, Certano A, Gagne J, Lebeuf R, Siegel N, Nguyen NH, Peter Kennedy. 2021. The slippery nature of ectomycorrhizal host specificity: Suillus fungi associated with novel pinoid (Picea) and abietoid (Abies) hosts. Mycologia, DOI: 10.1080/00275514.2021.1921525. Paper
Jamison J, Khanal SK, Nguyen NH, Deenik JL. 2021. Assessing the effects of digestates and combinations of digestates and fertilizer on yield and nutrient use of Brassica juncea (Kai Choy). Agronomy 11:509. DOI: 10.3390/agronomy11030509. Paper
Yuan M, Kakouridis A, Starr E, Nguyen NH, Shi S, Pett-Ridge J, Nuccio E, Zhou J, and Firestone M. 2021. Fungal-bacterial co-occurrence patterns differ between AMF and non-mycorrhizal fungi across soil niches. mBio 12:e03509-20. DOI: 10.1128/mBio.03509-20. Paper
Lofgren L, Nguyen NH, Vilgalys R, Ruytinx J, Liao H-L, Branco S, Kuo A, LaButti K, Lipzen Anna, Andreopoulos W, Pangilinan J, Riley R, Hundley H, Na H, Barry K, Grigoriev I, Stajich J, Kennedy P. 2021. Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. New Phytologist 230:774-792. DOI: 10.1111/nph.17160 Paper
Põlme, S., Abarenkov, K., Henrik Nilsson, R., Lindahl, B. D., Clemmensen, K. E., Kauserud, H., … Tedersoo, L. 2021. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105:1-16. DOI: 10.1007/s13225-020-00466-2. Paper
2020
Bazzicalupo A, Ruytinx J, Ke Y-H, Coninx L, Colpaert J, Nguyen NH, Vilgalys R, Branco S. 2020. Fungal heavy metal adaptation through single nucleotide polymorphisms and copy-number variation. Molecular Ecology 29:4157-4169. DOI:10.1111/mec.15618. Paper
Kennedy P, Gagne J*, Pérez PE, Lofgren LA, Nguyen NH. 2020. Does fungal competitive ability explain host specificity or rarity in ectomycorrhizal symbioses? PLoS ONE, 15:e0234099. DOI: 10.1371/journal.pone.0234099. Paper
2019
Bruns TD, Hale LM, Nguyen NH. 2019. Rhizopogon olivaceotinctus increases its inoculum potential in heated soil independent of competitive release from other ectomycorrhizal fungi. Mycologia 111:936-941. https://doi.org/10.1080/00275514.2019.1657354.Paper
Wehr NH, Kinney MK, Nguyen NH, Giardina CP, Litton CM. 2019. Changes in soil bacterial community diversity following the removal of invasive feral pigs from a Hawaiian tropical montane wet forest. Scientific Reports, Scientific Reports 9:14681. doi.org/10.1038/s41598-019-48922-7.Paper
2018
Lofgren L, Nguyen NH, Kennedy P. Ectomycorrhizal host specificity in a changing world: can legacy effects explain anomalous current associations? New Phytologist, 220:1273-1284. DOI: 10.1111/nph.15008. Paper
Nguyen NH. 2018. Longevity of light and dark-colored basidiospores from saprotrophic mushroom-forming fungi. Mycologia 110:131-135. DOI: 10.1111/nph.15008. Paper
Hynson NA, Frank KL, Alegado RA, Amend AS, Arif M, Bennett GM, Jani AJ, Medeiros MCI, Mileyko Y, Nelson CE, Nguyen NH, Nigro OD, Prisic S, Shin S, Takagi D, Wilson ST, Yew JY. 2018. Synergy among microbiota and their hosts: Leveraging the Hawaiian archipelago and local collaborative networks to address pressing questions in microbiome research. mSystems. 3:e00159-1, doi:10.1128/mSystems.00159-17. Paper
Kennedy P, Louis Mielke, Nguyen NH. 2018. Ecological responses to forest age, habitat, and host vary by mycorrhizal type in boreal peatlands. Mycorrhiza 28:315-328. DOI: 10.1007/s00572-018-0821-4. Paper
2017
Branco S, Bi K, Liao H-L, Gladieux P, Badouin H, Ellison CE, Nguyen NH, Vilgalys R, Peay KG, Taylor JW, Bruns TD. 2017. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Molecular Ecology. Molecular Ecology 26: 2063–2076. DOI: 10.1111/mec.13892. Paper
Fernandez C, Nguyen NH, Stefanski A, Han Y, Hobbie S, Montgomery R, Reich PB, Kennedy P. 2017. Reduced boreal tree host photosynthetic performance in response to warming selectively alters ectomycorrhizal fungal community structure. Global Change Biology 23:1598–1609. DOI: 10.1111/gcb.13510. Paper
2016
Ferro ML, Nguyen NH. 2016. Survey of twig-inhabiting Coleoptera in Louisiana, USA. The Coleopterists Bulletin 70: 551–558. Paper
Nguyen NH, Williams L, Stefanski A, Vincent J, Cavender-Bares J, Messier C, Paquette A, Gravel, D, Reich P, Kennedy PG. 2016. Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment. Molecular Ecology 25:4032–4046. doi: 10.1111/mec.13719. Paper
Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling J, Kennedy P. 2016. FUNGuild: an open annotation tool for parsing high-throughput fungal community datasets by ecological guilds. Fungal Ecology 20:241–248. doi:10.1016/j.funeco.2015.06.006. Paper
Marshall DL, Dickson JS, Nguyen NH. 2016. Ensuring food safety in insect based foods: Mitigating microbiological and other foodborne hazards. In: A.T. Dossey, J.A. Morales-Ramos, and M.G. Rojas, eds. Insects as Sustainable Food Ingredients: Production, Processing and Food Applications. Academic Press. p. 385. doi:10.1016/B978-0-12-802856-8.00008-9
Rineau F, Stas J, Nguyen NH, Kuyper TW, Carleer R, Vangronsveld J, Colpaert J V, Kennedy PG. 2016. Soil organic nitrogen availability predicts ectomycorrhizal fungal protein degradation ability. Applied Environmental Microbiology 82:1391–1400, doi:10.1128/AEM.03191-15. Paper
2015
Song Z, Schlatter D, Kennedy P, Kinkel, Kistler HC, Nguyen NH; Bates S. 2015. Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils. PLOS ONE 10: e0127234. DOI: 10.1371/journal.pone.0127234. Paper
Nguyen NH, Bruns TD. 2015. The microbiome of Pinus muricata ectomycorrhizae: community assemblages, fungal species effects, and Burkholderia as important bacteria in multi-partnered symbioses. Microbial Ecology 69:914-921. DOI: 10.1007/s00248-015-0574-y. Paper
Nguyen NH, Smith D, Peay KP, Kennedy P. 2015. Parsing ecological signal from noise in next generation amplicon sequencing. New Phytologist 205:1389–1393. DOI: 10.1111/nph.12923. Paper
Siegel N, Nguyen NH, Vellinga EC. 2015. Pholiota olivaceophylla, a forgotten name for a common snowbank fungus, and notes on Pholiota nubigena. Mycotaxon 130:517–532, doi:10.5248/130.517. Paper
2014
Arora D, Nguyen NH 2014. A new species of Russula, subgenus Compactae from California. North American Fungi 9:1-7. 10.2509/naf2014.009.008. Paper
Kennedy P, Nguyen NH, Cohen H, Peay KG. 2014. Missing checkerboards: an absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities. PeerJ 2:e686 https://dx.doi.org/10.7717/peerj.686. Paper
Justo A, Malysheva E, Bulyonkova T, Vellinga EC, Cobian G, Nguyen NH, Minnis AM, Hibbett DS. 2014. Molecular phylogeny and phylogeography of Holarctic species of Pluteus section Pluteus (Agaricales: Pluteaceae), with description of twelve new species. Phytotaxa 180:1-85. DOI: 10.11646/phytotaxa.180.1.1 Paper
Ceja-Navarro JA, Nguyen NH*, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL. 2014. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. The ISME Journal 8:6–18. DOI:10.1038/ismej.2013.13. *1st and 2nd author contributed equally to this work. Paper
2013
Ferro ML, Nguyen NH, Tishechkin A, Park J-S, Bayless V, Carlton CE. 2013. Coleoptera collected from rotting fishhook barrel cacti (Ferocactus wislizeni (Engelm.) Britton and Rose), with a review of neartic Coleoptera associated with succulent necrosis. The Coleopterists Bulletin 67:419–443. Paper
Kõljalg U, Nilsson RH, Abarenkov K., et al. 2013 Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology 22: 5271–5277. DOI: 10.1111/mec.12481 Paper
Nguyen NH, Landeros F, Garibay-Orijel Roberto, Hansen Karen, Vellinga EC. 2013. The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites. Mycologia 105:1275-1286. DOI: 10.3852/12–391 Paper
2012
Nguyen NH, Kerekes JF, Vellinga EC, Bruns TD. 2012. Synonymy of Suillus imitatus, the imitator of two species within the S. caerulescens/ponderosus complex. Mycotaxon 122:389–398. DOI: 10.5248/122.389. Paper
Nguyen NH, Hynson NA, Bruns TD. 2012. Stayin’ Alive: survival of mycorrhizal fungal propagules from 6-yr-old forest soil. Fungal Ecology 5:741–746; DOI: 10.1016/j.funeco.2012.05.006. Paper
Peay GP, Schubert MG, Nguyen NH, Bruns TD. 2012. Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules. Molecular Ecology 21: 4122-4136; DOI: 10.1111/j.1365-294X.2012.05666.x. Paper
2011
Nguyen NH, Suh S-O & Blackwell M. 2011. Spathaspora Nguyen, Suh & Blackwell. In: The Yeasts, a taxonomic study, 5th Edition. Eds. Kurtzman, C.P., J. Fell, and T. Boekhout. Elsevier, Amsterdam. Paper
2009
Bruns TD, Peay KG, Boynton PJ, Grubisha LC, Hynson NA, Nguyen NH, Rosenstock NP. 2009. Inoculum potential of Rhizopogon spores increases with time over the first four years of a 99-year spore burial experiment. New Phytologist 181:463–470. Paper
2008
M. I. Bidartondo et al. 2008. Preserving Accuracy in GenBank. Science 319:1616. Paper
Nguyen NH, Driscoll HE, & Specht CD. 2008. A molecular phylogeny of the wild onions (Allium; Alliaceae) with a focus on the Western North American center of diversity. Molecular Phylogenetics and Evolution 47:1157–1172. Paper
Suh S-O, Nguyen NH & Blackwell M. 2008. Yeasts isolated from plant-associated beetles and other insects: seven novel Candida species near Candida albicans. FEMS Yeast Research 8:88–102. Paper
2007
Nguyen NH, Suh S-O & Blackwell M. 2007. Five novel yeast species associated with Neuroptera and other insects. Mycologia 99:842–858. Paper
2006
Suh S-O, Nguyen NH & Blackwell M. 2006. A yeast clade near Candida kruisii uncovered: nine novel Candida species associated with basidioma-feeding beetles. Mycological Research 110:1379–1394. Paper
Nguyen NH, Suh S-O, Marshall C & Blackwell M. 2006. Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. nov., sp. nov. and Candida jeffriesii sp. nov. Mycological Research 110:1232–1241. Paper
Nguyen NH, Suh SO, Erbil CK & Blackwell M. 2006. Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidae sp. nov., isolated from green lacewings, and beetles. Mycological Research 110: 346-356. Paper
Nardi JB, Bee CM, Miller LA, Nguyen NH, Suh S-O & Blackwell M. 2006. Communities of microbes that inhabit the changing hind gut landscape of a subsocial beetle. Arthropod Structure and Development 35: 57-68. Paper
2005
Suh S-O, Nguyen NH & Blackwell M. 2005. Nine new Candida species near Candida membranifaciens isolated from insects. Mycological Research 109: 261-265. Paper
2004
Suh S-O, White MM, Nguyen NH & Blackwell M. 2004. The identification of Enteroramus dimorphus: a xylose-fermenting yeast attached to the gut of beetles. Mycologia 96:756-760. Paper