References
Allison, S. D., & Martiny, J. B. H. (2008). Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 105 , 11512-11519. doi:10.1073/pnas.0801925105
Allred, D. M., & Beck, D. E. (1963). Ecological distribution of some rodents at Nevada atomic test site. Ecology, 44 (1), 211-214. doi:10.2307/1933209
Arnold, A. E., Mejía, L. C., Kyllo, D., Rojas, E. I., Maynard, Z., Robbins, N., & Herre, E. A. (2003). Fungal endophytes limit pathogen damage in a tropical tree. Proceedings of the National Academy of Sciences of the United States of America, 100 (26), 15649-15654. doi:10.1073/pnas.2533483100
Auguie, B. (2017). gridExtra: Miscellaneous Functions for ”Grid” Graphics. Retrieved from https://CRAN.R-project.org/package=gridExtra
Babjeva, I. P., & Reshetova, I. S. (1975). New yeast species from soil - candida podzolica sp n. Mikrobiologiia, 44 (2), 333-338
Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., . . . Bork, P. (2018). Structure and function of the global topsoil microbiome. Nature, 560 , 233-237. doi:10.1038/s41586-018-0386-6
Beatley, J. C. (1964). Vascular flora of Nevada Test Site Nye county Nevada. American Journal of Botany, 51 (6P2), 687
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing.Journal of the Royal Statistical Society Series B-Methodological, 57 (1), 289-300
Bodenhausen, N., Horton, M. W., & Bergelson, J. (2013). Bacterial communities associated with the leaves and the roots ofArabidopsis thaliana . Plos One, 8 (2), e56329. doi:10.1371/journal.pone.0056329
Callahan, B. J., Sankaran, K., Fukuyama, J. A., McMurdie, P. J., & Holmesa, S. P. (2016). Bioconductor workflow for microbiome data analysis: From raw reads to community analyses. . F1000Research, 5 , 1492. doi:10.12688/f1000research.8986.2
Cannon, P., & Kirk, P. (2007). Fungal Families of the World . Wallingford, UK: CABI
Chelius, M. K., & Triplett, E. W. (2001). The diversity of archaea and bacteria in association with the roots of Zea mays L.Microbial Ecology, 41 , 252-263. doi:10.1007/s002480000087
Compant, S., Heijden, M. G. A. V. D., & Sessitsch, A. (2010). Climate change effects on beneficial plant–microorganism interactionsFEMS Microbiology Ecology, 73 (2), 197-214. doi:10.1111/j.1574-6941.2010.00900.x
Csardi, G., & Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems , 1695
Delgado-Baquerizo, M., Reich, P. B., Trivedi, C., Eldridge, D. J., Abades, S., Alfaro, F. D., . . . Singh, B. K. (2020). Multiple elements of soil biodiversity drive ecosystem functions across biomes.Nature Ecology & Evolution, 4 , 210-220. doi:10.1038/s41559-019-1084-y
Dormann, C. F., Fründ, J., Blüthgen, N., & Gruber, B. (2009). Indices, graphs and null models: Analyzing bipartite ecological networks.The Open Ecology Journal, 2 , 7-24. doi:10.2174/1874213000902010007
Durrell, L. W., & Shields, L. M. (1960). Fungi isolated in culture from soils of the Nevada Test Site. Mycologia, 52 (4), 636-641. doi:10.2307/3756096
Faith, D. P., Minchin, P. R., & Belbin, L. (1987). Compositional dissimilarity as a robust measure of ecological distanceVegetatio, 69 , 57-68
Fan, K., Weisenhorn, P., Gilbert, J. A., Shi, Y., Bai, Y., & Chu, H. (2018). Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biology and Biochemistry, 121 , 185-192. doi:10.1016/j.soilbio.2018.03.017
Fang, K., Miao, Y.-F., Chen, L., Zhou, J., Yang, Z.-P., Dong, X.-F., & Zhang, H.-B. (2019). Tissue-specific and geographical variation in endophytic fungi of Ageratina adenophora and fungal associations with the environment. Frontiers in Microbiology, 10 , 2919. doi:10.3389/fmicb.2019.02919
Gange, A. C., Eschen, R., Wearn, J. A., Thawer, A., & Sutton, B. C. (2012). Differential effects of foliar endophytic fungi on insect herbivores attacking a herbaceous plant. Oecologia, 168 , 1023-1031. doi:10.1007/s00442-011-2151-5
Gardes, M., & Bruns, T. D. (1993). ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology, 2 (2), 113-118. doi:10.1111/j.1365-294X.1993.tb00005.x
Guo, L. D., Hyde, K. D., & Liew, E. C. Y. (2000). Identification of endophytic fungi from Livistona chinensis based on morphology and rDNA sequences. New Phytologist, 147 , 617-630
Lande, R., & Shannon, S. (1996). The role of genetic variation in adaptation and population persistence in a changing environmentEvolution, 50 (1), 434-437. doi:10.2307/2410812
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology, 75 (15), 5111–5120. doi:10.1128/AEM.00335-09
Lavrinienko, A., Tukalenko, E., Mappes, T., & Watts, P. C. (2018). Skin and gut microbiomes of a wild mammal respond to different environmental cues. Microbiome, 6 , 209. doi:10.1186/s40168-018-0595-0
Liu, X. Z., Wang, Q. M., Goeker, M., Groenewald, M., Kachalkin, A. V., Lumbsch, H. T., . . . Bai, F. Y. (2015). Towards an integrated phylogenetic classification of the Tremellomycetes. Studies in Mycology, 81 , 85-147. doi:10.1016/j.simyco.2015.12.001
Ma, B., Lv, X. F., Warren, A., & Gong, J. (2013). Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China.Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 104 (5), 759-768. doi:10.1007/s10482-013-9984-3
Markert, J. A., Champlin, D. M., Gutjahr-Gobell, R., Grear, J. S., Kuhn, A., Jr, T. J. M., . . . Nacci, D. E. (2010). Population genetic diversity and fitness in multiple environments. Bmc Evolutionary Biology, 10 , 205. doi:10.1186/1471-2148-10-205
Mendiburu, F. d. (2019). agricolae: Statistical Procedures for Agricultural Research. R package version 1.3-1. Retrieved from https://CRAN.R-project.org/package=agricolae
Murrell, P. (2005). R Graphics . London, UK: Chapman & Hall/CRC Press
Nevo, E. (2001). Evolution of genome-phenome diversity under environmental stress. Proceedings of the National Academy of Sciences of the United States of America, 98 (11), 6233-6240. doi:10.1073/pnas.101109298
Nilsson, R., Larsson, K.-H., Taylor, A., Bengtsson-Palme, J., Jeppesen, T., Schigel, D., . . . Abarenkov, K. (2019). The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47 (D1), D259-D264. doi:10.1093/nar/gky1022
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., . . . Wagner, H. (2016). Package ’vegan’: Community ecology package. Retrieved from https://cran.r-project.org
Paradis, E., & Schliep, K. (2018). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R Bioinformatics, 35 (3), 526-528. doi:10.1093/bioinformatics/bty633
Porras-Alfaro, A., & Bayman, P. (2011). Hidden fungi, emergent properties: Endophytes and microbiomes. Annual Review of Phytopathology, 49 , 291-315. doi:10.1146/annurev-phyto-080508-081831
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., . . . Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41 (D1), D590-D596. doi:10.1093/nar/gks1219
R Development Core Team. (2016). R: A language and environment for statistical computing. Retrieved from http://www.R-project.org
Rickard, W. H., & Beatley, J. C. (1965). Canopy-coverage of the desert shrub vegetation mosaic of the Nevada Test Site. Ecology, 46 (4), 524-529. doi:10.2307/1934886
Rodriguez, R. J., Henson, J., Volkenburgh, E. V., Hoy, M., Wright, L., Beckwith, F., . . . Redman, R. S. (2008). Stress tolerance in plants via habitat-adapted symbiosis. Isme Journal, 2 , 404-416. doi:10.1038/ismej.2007.106
Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., . . . Fierer, N. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal, 4 , 1340-1351. doi:10.1038/ismej.2010.58
Saikkonen, K., Faeth, S. H., Helander, M., & Sullivan, T. J. (1998). Fungal endophytes: A continuum of interactions with host plants.Annual Review of Ecology and Systematics, 29 , 319-343. doi:doi.org/10.1146/annurev.ecolsys.29.1.319
Scrucca, L. (2004). qcc: an R package for quality control charting and statistical process control. R News, 4 (1), 11-17
Shields, L. M., & Drouet, F. (1962). Distribution of terrestrial algae within Nevada Test Site. American Journal of Botany, 49 (6), 547-554. doi:10.2307/2439709
Shields, L. M., Durrell, L. W., & Sparrow, A. H. (1961). Preliminary-observations on radiosensitivity of algae and fungi from soils of Nevada Test Site. Ecology, 42 (2), 440-441. doi:10.2307/1932103
Su, Y. Y., Guo, L. D., & Hyde, K. D. (2010). Response of endophytic fungi of Stipa grandis to experimental plant function group removal in Inner Mongolia steppe, China Fungal Diversity, 43 (1), 93-101. doi:10.1007/s13225-010-0040-6
Sun, X., Ding, Q., Hyde, K. D., & Guo, L. D. (2012). Community structure and preference of endophytic fungi of three woody plants in a mixed forest. Fungal Ecology, 5 (5), 624-632. doi:10.1016/j.funeco.2012.04.001
Sun, X., Guo, L. D., & Hyde, K. D. (2011). Community composition of endophytic fungi in Acer truncatum and their role in decomposition. Fungal Diversity, 47 (1), 85-95. doi:10.1007/s13225-010-0086-5
Tilman, D. (1996). Biodiversity: Population versus ecosystem stability. Ecology, 77 (2), 350-363. doi:10.2307/2265614
U’Ren, J. M., Lutzoni, F., Miadlikowska, J., Laetsch, A. D., & Arnold, A. E. (2012). Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany, 99 (5), 898-914. doi:10.3732/ajb.1100459
Veach, A. M., Morris, R., Yip, D. Z., Yang, Z. K., Engle, N. L., Cregger, M. A., . . . Schadt, C. W. (2019). Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin. Microbiome, 7 , 76. doi:10.1186/s40168-019-0668-8
Venables, W. N., & Ripley, B. D. (2002). Modern Applied Statistics with S (Fourth ed.). New York: Springer
Vries, F. T. D., Griffiths, R. I., Bailey, M., Craig, H., Girlanda, M., Gweon, H. S., . . . Bardgett, R. D. (2018). Soil bacterial networks are less stable under drought than fungal networks. Nature Communications, 9 , 3033. doi:10.1038/s41467-018-05516-7
Wehrden, H. V., Fischer, J., Brandt, P., Wagner, V., Kümmerer, K., Kuemmerle, T., . . . Hostert, P. (2012). Consequences of nuclear accidents for biodiversity and ecosystem services. Conservation Letters, 5 (2), 81-89. doi:10.1111/j.1755-263X.2011.00217.x
White, T., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogeneics. In M. Innis, D. Gelfand, J. Sninsky, & T. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315-322). San Diego: Academic
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis : Springer-Verlag New York.
Wilkinson, S. (2018). kmer: an R package for fast alignment-free clustering of biological sequences. R package version 1.0.0. Retrieved from https://cran.r-project.org/package=kmer
Yao, X., Chen, Z., Wei, X., Chen, S., White, J., Huang, X., . . . Nan, Z. (2020). A toxic grass Achnatherum inebrians serves as a diversity refuge for the soil fungal community in rangelands of northern China. Plant and Soil, 448 , 425-438. doi:doi.org/10.1007/s11104-020-04440-4
Zhdanova, N. N., Zakharchenko, V. A., & Haselwandter, K. (2005). Radionuclides and fungal communities. In J. Dighton, J. F. White, & P. Oudemans (Eds.), The Fungal Community - Its Organization and Role in the Ecosystem (Third Edition ed., pp. 759-768). Boca Raton, FL: CRC Press
Zhdanova, N. N., Zakharchenko, V. A., Vember, V. V., & Nakonechnaya, L. T. (2000). Fungi from Chernobyl: mycobiota of the inner regions of the containment structures of the damaged nuclear reactor. Mycological Research, 104 (12), 1421-1426. doi:10.1017/S0953756200002756