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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 蔡怡陞 | zh_TW |
| dc.contributor.advisor | Isheng Jason Tsai | en |
| dc.contributor.author | 簡維廷 | zh_TW |
| dc.contributor.author | Wei-Ting Chien | en |
| dc.date.accessioned | 2026-08-24T16:36:22Z | - |
| dc.date.available | 2026-08-25 | - |
| dc.date.copyright | 2026-08-24 | - |
| dc.date.issued | 2026 | - |
| dc.date.submitted | 2026-08-11 23:30:23 | - |
| dc.identifier.citation | Ashton, P., & Zhu, H. (2020). The tropical-subtropical evergreen forest transition in East Asia: An exploration. Plant Divers, 42(4), 255-280. https://doi.org/10.1016/j.pld.2020.04.001
Barros, K. O., Alvarenga, F. B. M., Magni, G., Souza, G. F. L., Abegg, M. A., Palladino, F., da Silva, S. S., Rodrigues, R., Sato, T. K., Hittinger, C. T., & Rosa, C. A. (2023). The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species. Yeast, 40(2), 84-101. https://doi.org/10.1002/yea.3837 Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting Linear Mixed-Effects Models Usinglme4. Journal of Statistical Software, 67(1). https://doi.org/10.18637/jss.v067.i01 Blazanin, M. (2024). gcplyr: an R package for microbial growth curve data analysis. BMC Bioinformatics, 25(1), 232. https://doi.org/10.1186/s12859-024-05817-3 Boonmak, C., Khunnamwong, P., & Limtong, S. (2020). Yeast communities of primary and secondary peat swamp forests in southern Thailand. Antonie Van Leeuwenhoek, 113(1), 55-69. https://doi.org/10.1007/s10482-019-01317-0 Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471-2105-10-421 Capella-Gutierrez, S., Silla-Martinez, J. M., & Gabaldon, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25(15), 1972-1973. https://doi.org/10.1093/bioinformatics/btp348 Chang, C. F., Huang, L. Y., Chen, S. F., & Lee, C. F. (2012). Kloeckera taiwanica sp. nov., an ascomycetous apiculate yeast species isolated from mushroom fruiting bodies. Int J Syst Evol Microbiol, 62(Pt 6), 1434-1437. https://doi.org/10.1099/ijs.0.034231-0 Chen, X., Kohyama, T. S., & Cannon, C. H. (2018). Associated morphometric and geospatial differentiation among 98 species of stone oaks (Lithocarpus). PLoS One, 13(6), e0199538. https://doi.org/10.1371/journal.pone.0199538 David, K. T., Harrison, M. C., Opulente, D. A., LaBella, A. L., Wolters, J. F., Zhou, X., Shen, X. X., Groenewald, M., Pennell, M., Hittinger, C. T., & Rokas, A. (2024). Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci U S A, 121(10), e2316031121. https://doi.org/10.1073/pnas.2316031121 De Caceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566-3574. https://doi.org/10.1890/08-1823.1 Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460-2461. https://doi.org/10.1093/bioinformatics/btq461 Ferrier, S., Manion, G., Elith, J., & Richardson, K. (2007). Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Diversity and Distributions, 13(3), 252-264. https://doi.org/10.1111/j.1472-4642.2007.00341.x Gassler, T., Sauer, M., Gasser, B., Egermeier, M., Troyer, C., Causon, T., Hann, S., Mattanovich, D., & Steiger, M. G. (2020). The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO(2). Nat Biotechnol, 38(2), 210-216. https://doi.org/10.1038/s41587-019-0363-0 Hittinger, C. T. (2013). Saccharomyces diversity and evolution: a budding model genus. Trends Genet, 29(5), 309-317. https://doi.org/10.1016/j.tig.2013.01.002 Hsieh, T. C., Ma, K. H., Chao, A., & McInerny, G. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution, 7(12), 1451-1456. https://doi.org/10.1111/2041-210x.12613 Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., Kusel, K., Rillig, M. C., Rivett, D. W., Salles, J. F., van der Heijden, M. G., Youssef, N. H., Zhang, X., Wei, Z., & Hol, W. H. (2017). Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J, 11(4), 853-862. https://doi.org/10.1038/ismej.2016.174 Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Haeseler, A. v., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods, 14, 587–589. https://doi.org/10.1038/nmeth.4285 Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30(4), 772- 780. https://doi.org/10.1093/molbev/mst010 Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. (2017). lmerTest Package: Tests in Linear Mixed Effects Models. Journal of Statistical Software, 82(13). https://doi.org/10.18637/jss.v082.i13 Lee, C. F., Yao, C. H., Liu, Y. R., Young, S. S., & Chang, K. S. (2009). Kazachstania wufongensis sp. nov., an ascosporogenous yeast isolated from soil in Taiwan. Antonie Van Leeuwenhoek, 95(4), 335-341. https://doi.org/10.1007/s10482-009-9319-6 Lee, T. J., Liu, Y. C., Liu, W. A., Lin, Y. F., Lee, H. H., Ke, H. M., Huang, J. P., Lu, M. J., Hsieh, C. L., Chung, K. F., Liti, G., & Tsai, I. J. (2022). Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Res, 32(5), 864-877. https://doi.org/10.1101/gr.276286.121 Lin, C. P., Geroldi, A., Selem, N., Liti, G., & Tsai, I. J. (2026). A Global Synthesis of Yeast in Microbiomes. Yeast. https://doi.org/10.1002/yea.70039 Lin, C. P., Lin, Y. F., Liu, Y. C., Lu, M. J., Ke, H. M., & Tsai, I. J. (2025). Spatiotemporal dynamics reveal high turnover and contrasting assembly processes in fungal communities across contiguous habitats of tropical forests. Environ Microbiome, 20(1), 23. https://doi.org/10.1186/s40793-025-00683-9 Lin, J.-C., Chiou, C.-R., Chan, W.-H., & Wu, M.-S. (2021). Valuation of Forest Ecosystem Services in Taiwan. Forests, 12(12). https://doi.org/10.3390/f12121694 Masinova, T., Bahnmann, B. D., Vetrovsky, T., Tomsovsky, M., Merunkova, K., & Baldrian, P. (2017). Drivers of yeast community composition in the litter and soil of a temperate forest. FEMS Microbiol Ecol, 93(2). https://doi.org/10.1093/femsec/fiw223 Molinet, J., & Stelkens, R. (2025). The evolution of thermal performance curves in response to rising temperatures across the model genus yeast. Proc Natl Acad Sci U S A, 122(21), e2423262122. https://doi.org/10.1073/pnas.2423262122 Mozzachiodi, S., Bai, F. Y., Baldrian, P., Bell, G., Boundy-Mills, K., Buzzini, P., Cadez, N., Cubillos, F. A., Dashko, S., Dimitrov, R., Fisher, K. J., Gibson, B., Gouliamova, D., Greig, D., Heistinger, L., Hittinger, C. T., Jecmenica, M., Koufopanou, V., Landry, C. R.,...Boynton, P. (2022). Yeasts from temperate forests. Yeast, 39(1-2), 4-24. https://doi.org/10.1002/yea.3699 Peris, D., Ubbelohde, E. J., Kuang, M. C., Kominek, J., Langdon, Q. K., Adams, M., Koshalek, J. A., Hulfachor, A. B., Opulente, D. A., Hall, D. J., Hyma, K., Fay, J. C., Leducq, J. B., Charron, G., Landry, C. R., Libkind, D., Goncalves, C., Goncalves, P., Sampaio, J. P.,...Hittinger, C. T. (2023). Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun, 14(1), 690. https://doi.org/10.1038/s41467-023-36139-2 Qiu, Y. J., Zhu, H. Y., Zhu, Q. Y., Yang, L. X., Mao, Y. C., Wen, Z., Chen, S. X., Qiu, J. Z., Bai, F. Y., & Han, P. J. (2025). High yeast diversity in primeval forest of Shennongjia, including 21 new species characterized by morphological, phylogenetic, and genomic analyses. Mycosphere, 16(1), 4723-4782. https://doi.org/10.5943/mycosphere/16/1/35 Que, Z., Wang, S., Wei, M., Fang, Y., Ma, T., Wang, X., & Sun, X. (2024). The powerful function of Saccharomyces cerevisiae in food science and other fields: a critical review. Food Innovation and Advances, 3(2), 167-180. https://doi.org/10.48130/fia-0024-0016 Robinson, H. A., Pinharanda, A., & Bensasson, D. (2016). Summer temperature can predict the distribution of wild yeast populations. Ecol Evol, 6(4), 1236-1250. https://doi.org/10.1002/ece3.1919 Rosa, C. A., Lachance, M. A., Limtong, S., Santos, A. R. O., Landell, M. F., Gombert, A. K., Morais, P. B., Sampaio, J. P., Goncalves, C., Goncalves, P., Goes-Neto, A., Santa-Brigida, R., Martins, M. B., Janzen, D. H., & Hallwachs, W. (2023). Yeasts from tropical forests: Biodiversity, ecological interactions, and as sources of bioinnovation. Yeast, 40(11), 511-539. https://doi.org/10.1002/yea.3903 Solieri, L. (2021). The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology. World J Microbiol Biotechnol, 37(6), 96. https://doi. org/10.1007/s11274-021-03066-7 Spagnuolo, M., Yaguchi, A., & Blenner, M. (2019). Oleaginous yeast for biofuel and oleochemical production. Curr Opin Biotechnol, 57, 73-81. https://doi.org/10.1016/j.copbio.2019.02.011 Spurley, W. J., Fisher, K. J., Langdon, Q. K., Buh, K. V., Jarzyna, M., Haase, M. A. B., Sylvester, K., Moriarty, R. V., Rodriguez, D., Sheddan, A., Wright, S., Sorlie, L., Hulfachor, A. B., Opulente, D. A., & Hittinger, C. T. (2022). Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates. Yeast, 39(1-2), 55-68. https://doi.org/10.1002/yea.3679 Su, S.-H., Chang-Yang, C.-H., Lu, C.-L., Tsui, C.-C., Lin, T.-T., Lin, C.-L., Chiou, W.-L., Kuan, L.-H., Chen, Z.-S., & Hsieh, C.-F. (2007). Fushan Subtropical Forest Dynamics Plot: Tree Species Characteristics and Distribution Patterns. Taiwan Forestry Research Institute. Sylvester, K., Wang, Q. M., James, B., Mendez, R., Hulfachor, A. B., & Hittinger, C. T. (2015). Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. FEMS Yeast Res, 15(3). https://doi.org/10.1093/femsyr/fov002 Tagawa, H. (1995). Distribution of Lucidophyll Oak-Laurel Forest Formation in Asia and Other Areas. TROPICS, 5, 1-40. https://doi.org/10.3759/tropics.5.1 Tedersoo, L., Mikryukov, V., Zizka, A., Bahram, M., Hagh-Doust, N., Anslan, S., Prylutskyi, O., Delgado-Baquerizo, M., Maestre, F. T., Parn, J., Opik, M., Moora, M., Zobel, M., Espenberg, M., Mander, U., Khalid, A. N., Corrales, A., Agan, A., Vasco-Palacios, A. M.,...Abarenkov, K. (2022). Global patterns in endemicity and vulnerability of soil fungi. Glob Chang Biol, 28(22), 6696-6710. https://doi.org/10.1111/gcb.16398 Treseder, K. K., & Lennon, J. T. (2015). Fungal traits that drive ecosystem dynamics on land. Microbiol Mol Biol Rev, 79(2), 243-262. https://doi.org/10.1128/MMBR.00001-15 Wang, Q. M., Liu, W. Q., Liti, G., Wang, S. A., & Bai, F. Y. (2012). Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol, 21(22), 5404-5417. https://doi.org/10.1111/j.1365-294X.2012.05732.x Wickham, H. (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1–20. https://doi.org/10.18637/jss.v021.i12 Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T., Miller, E., Bache, S., Müller, K., Ooms, J., Robinson, D., Seidel, D., Spinu, V.,...Yutani, H. (2019). Welcome to the Tidyverse. Journal of Open Source Software, 4(43). https://doi.org/10.21105/joss.01686 Wong, T. K. F., Ly-Trong, N., Ren, H., Demotte, P., Banos, H., Roger, A. J., Susko, E., Bielow, C., De Maio, N., Goldman, N., Hahn, M. W., Dos Reis, M., Vinh, L. S., Huttley, G., Lanfear, R., & Minh, B. Q. (2026). IQ-TREE 3: phylogenomic inference software using complex evolutionary models. Mol Biol Evol, 43(5). https://doi.org/10.1093/molbev/msag117 Yang, C.-J., Yeh, Y.-C., Hsiao, C., Liu, Y.-H., Lu, M. R., Liu, Y.-C., Liti, G., Tsai, I. J., & Ke, H.-M. (2026). A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae. bioRxiv. https://doi.org/10.64898/2026.02.13.705822 Yurkov, A. M., Rohl, O., Pontes, A., Carvalho, C., Maldonado, C., & Sampaio, J. P. (2016). Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome. FEMS Yeast Res, 16(1), fov103. https://doi.org/10.1093/femsyr/fov103 Zhu, H., & Tan, Y. (2024). The Origin of Evergreen Broad-Leaved Forests in East Asia from the Evidence of Floristic Elements. Plants (Basel), 13(8). https://doi.org/10.3390/plants13081106 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/104218 | - |
| dc.description.abstract | 酵母亞門(Saccharomycotina)酵母是森林微生物群落中的重要成員,但其多樣性和生態分佈仍缺乏充分瞭解,因許多類群豐富度低且不易偵測。本研究以台灣北部福山森林動態樣區連續47週採集的落葉樣本為核心,並結合越南與沖繩北部的探索性調查,探討亞洲闊葉林中的可培養Saccharomycotina酵母。酵母分離株經乙醇–糖富集培養(ethanol–sugar enrichment)取得,並以核糖體DNA內轉錄間隔區(ITS)序列進行分子鑑定。福山樣區共獲得687株分離株,其中613株經鑑定屬於Saccharomycotina,包含56個已描述物種及多個以ITS序列界定的操作分類單元(OTUs),顯示當地落葉環境具有高度酵母多樣性與許多潛在的新穎類群。越南與沖繩樣本亦呈現多樣的酵母組成。福山樣區內的酵母豐富度與群聚組成呈現明顯季節性動態,在溫暖潮濕時期多樣性較高,冬季則降低。溫度相關變數與此季節性模式密切相關,而細尺度空間結構對群聚組成的影響較弱。熱生長表現分析進一步支持此結果,於較溫暖時期的菌株通常具有較高的最適生長溫度,而與較低溫時期相關的菌株則具有較低的熱偏好。綜合而言,本研究顯示亞洲闊葉林落葉中蘊含豐富且尚未充分調查的可培養Saccharomycotina酵母,並支持福山森林中經富集培養回收之森林酵母受到季節性氣候篩選。 | zh_TW |
| dc.description.abstract | Although Saccharomycotina yeasts are widespread in forests, their diversity and ecology remain poorly characterised because many taxa occur at low abundance and are difficult to detect. We investigated culturable Saccharomycotina in Asian broadleaf forests using a 47-week leaf-litter time series at the Fushan Forest Dynamics Plot in northern Taiwan, supplemented by exploratory inventories from Vietnam and northern Okinawa. Yeasts were recovered by ethanol–sugar enrichment and identified by ITS sequencing. At Fushan, we recovered 687 isolates, including 613 Saccharomycotina strains representing 56 described species and numerous ITS-defined OTUs, revealing high local diversity and many putatively novel lineages. The Vietnam and Okinawa surveys also yielded diverse assemblages. At Fushan, yeast richness and composition varied strongly over time, with higher diversity during warm, wet periods and lower diversity in winter. Temperature-related variables were associated with these seasonal patterns, whereas fine-scale spatial structure was comparatively weak. Thermal performance assays supported this association: strains recovered during warmer periods tended to have higher thermal optima than those associated with cooler periods. Together, these results show that Asian broadleaf-forest litter harbours diverse, and incompletely sampled culturable Saccharomycotina, and support seasonal climatic filtering of enrichment-recovered forest yeasts at Fushan. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2026-08-24T16:36:22Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2026-08-24T16:36:22Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員審定書 i
Acknowledgements 誌謝 ii 中文摘要 iv Abstract v Contents vi List of figures viii List of tables x CHAPTER 1. Introduction 1 CHAPTER 2. Materials and Methods 7 2.1 Study sites and sample collection 7 2.1.1 Taiwan 7 2.1.2 Vietnam 9 2.1.3 Okinawa 11 2.2 Yeast enrichment workflow 13 2.3 Sequence classification and OTU clustering 17 2.4 ITS alignment and phylogeny construction of novel OTUs in lineage-rich genera 19 2.5 Thermal phenotyping of Fushan yeast isolates 20 2.6 Ecological data preparation and statistical analyses 22 2.6.1 Data curation and incidence transformation 22 2.6.2 Sampling completeness and alpha-diversity estimation 23 2.6.3 Environmental associations of richness at Fushan 24 2.6.4 Environmental associations of community composition and taxon occurrence at Fushan 25 2.6.5 Spatial community turnover at Fushan 27 2.6.6 Exploratory regional comparisons 28 CHAPTER 3. Results 30 3.1 Sampling effort and yeast recovery across forest sites 30 3.2 Dominant taxa across different forests 34 3.3 Family- and genus-level composition of known and novel lineages 36 3.4 Phylogenetic placement and regional distribution of novel OTUs in lineage-rich genera 41 3.5 Seasonal dynamics of yeast diversity at Fushan 47 3.6 Temporal shifts in yeast community composition at Fushan 50 3.7 Thermal phenotyping of Fushan yeast isolates 54 3.8 Spatial heterogeneity in yeast richness at Fushan 57 3.9 Spatial structuring of yeast community composition at Fushan 59 3.10 Diversity and community composition across Fushan, Vietnam, and Okinawa 65 CHAPTER 4. Discussion 71 References 87 | - |
| dc.language.iso | en | - |
| dc.subject | 酵母亞門 | - |
| dc.subject | 森林酵母 | - |
| dc.subject | 落葉 | - |
| dc.subject | 福山森林動態樣區 | - |
| dc.subject | 乙醇–糖富集培養 | - |
| dc.subject | 季節性動態 | - |
| dc.subject | 熱生長表現 | - |
| dc.subject | Saccharomycotina | - |
| dc.subject | forest yeasts | - |
| dc.subject | leaf-litter | - |
| dc.subject | Fushan Forest Dynamics Plot | - |
| dc.subject | ethanol–sugar enrichment | - |
| dc.subject | seasonal dynamics | - |
| dc.subject | thermal performance | - |
| dc.title | 亞洲闊葉林中酵母亞門落葉酵母的時空動態與多樣性 | zh_TW |
| dc.title | Spatiotemporal dynamics and diversity of Saccharomycotina litter yeasts in Asian broadleaf forests | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 114-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.coadvisor | 丁照棣 | zh_TW |
| dc.contributor.coadvisor | Chau-Ti Ting | en |
| dc.contributor.oralexamcommittee | 柯柏如;張楊家豪 | zh_TW |
| dc.contributor.oralexamcommittee | Po-Ju Ke;Chia-Hao Chang-Yang | en |
| dc.subject.keyword | 酵母亞門; 森林酵母; 落葉; 福山森林動態樣區; 乙醇–糖富集培養; 季節性動態; 熱生長表現 | zh_TW |
| dc.subject.keyword | Saccharomycotina; forest yeasts; leaf-litter; Fushan Forest Dynamics Plot; ethanol–sugar enrichment; seasonal dynamics; thermal performance | en |
| dc.relation.page | 94 | - |
| dc.identifier.doi | 10.6342/NTU202604234 | - |
| dc.rights.note | 同意授權(全球公開) | - |
| dc.date.accepted | 2026-08-14 | - |
| dc.contributor.author-college | 生命科學院 | - |
| dc.contributor.author-dept | 生態學與演化生物學研究所 | - |
| dc.date.embargo-lift | 2026-08-25 | - |
| 顯示於系所單位: | 生態學與演化生物學研究所 | |
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