Soil Microbial Ecology | Nguyen Lab @ UH Mānoa

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) faculty

Courses

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.