References
Amir, A., McDonald, D., Navas-Molina, J.A., Kopylova, E., Morton, J.T., Zech Xu, Z., et al. (2017) Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2 : e00191-16.
Antwis, R.E., Griffiths, S.M., Harrison, X.E., Aranega-Bou, P., Arce, A., Bettridge, A.S., et al. (2017) Fifty important research questions in microbial ecology. FEMS Microbiol Ecol 93 : fix044.
Arnold, A.E. (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev21 : 51–66.
Arnold, A.E. and Herre, E.A. (2003) Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95 : 388–398.
Arnold, A.E. and Lutzoni, F. (2007) Diversity and host range of foliar fungal endophytes: are topical leaves biodiversity hotspots?Ecology 88 : 541–549.
Barge, E.G., Leopold, D.R., Peay, K.G., Newcombe, G., and Busby, P.E. (2019) Differentiating spatial from environmental effects on foliar fungal communities of Populus trichocarpa. J Biogeogr46 : 2001–2011.
Barton, K. (2019) MuMIn: Multi-Model Inference.
Bates, D., Maechler, M., Bolker, B., and Walker, S. (2015) Fitting linear mixed-effects models using lme4. J Stat Softw 67 : 1–48.
Bernstein, M.E. and Carroll, G.C. (1977) Internal fungi in old-growth Douglas fir foliage. Can J Bot 55 : 644–653.
Blaalid, R., Carlsen, T., Kumar, S., Halvorsen, R., Ugland, K.I., Fontana, G., and Kauserud, H. (2012) Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Mol Ecol 21 : 1897–1908.
Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., et al. (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol37 : 852–857.
Borcard, D. and Legendre, P. (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices.Ecol Modell 153 : 51–68.
Ter Braak, C.J.F. (1986) Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis.Ecology 67 : 1167–1179.
Brown, S.P. and Jumpponen, A. (2014) Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils.Mol Ecol 23 : 481–497.
Buffelskloof Nature Reserve (2019) Buffelskloof private nature reserve.
Burnham, K.P. and Anderson, D.R. (2002) Model selection and multimodel inference: a practical information-theoretic approach, 2nd ed. New York: Springer-Verlag.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods7 : 335–336.
Carney, K.M. and Matson, P.A. (2006) The influence of tropical plant diversity and composition on soil microbial communities. Microb Ecol 52 : 226–238.
Chang, C. and HilleRisLambers, J. (2016) Integrating succession and community assembly perspectives. F1000Research 5 : F1000 Faculty Rev-2294.
Chang, C.C. and Turner, B.L. (2019) Ecological succession in a changing world. J Ecol 107 : 503–509.
Christian, N., Sullivan, C., Visser, N.D., and Clay, K. (2016) Plant host and geographic location drive endophyte community composition in the face of perturbation. Microb Ecol 72 : 621–632.
Compant, S., Van Der Heijden, M.G.A., and Sessitsch, A. (2010) Climate change effects on benefcial plant-microorganism interactions. FEMS Microbiol Ecol 73 : 197–214.
Compant, S., Samad, A., Faist, H., and Sessitsch, A. (2019) A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. J Adv Res 19 : 29–37.
Cordier, T., Robin, C., Capdevielle, X., Desprez-Loustau, M.L., and Vacher, C. (2012) Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecol 5 : 509–520.
Cordovez, V., Dini-Andreote, F., Carrión, V.J., and Raaijmakers, J.M. (2019) Ecology and evolution of plant microbiomes. Annu Rev Microbiol 73 : 69–88.
Crowther, T.W., Maynard, D.S., Crowther, T.R., Peccia, J., Smith, J.R., and Bradford, M.A. (2014) Untangling the fungal niche: the trait-based approach. Front Microbiol 5 : 1–12.
Darlison, J., Mogren, L., Rosberg, A.K., Grudén, M., Minet, A., Liné, C., et al. (2019) Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia). Sci Total Environ 675 : 501–512.
Davey, M., Blaalid, R., Vik, U., Carlsen, T., Kauserud, H., and Eidesen, P.B. (2015) Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root-associated fungi mirrors plant succession in two glacial chronosequences. Environ Microbiol 17 : 2777–2790.
David, A.S., Seabloom, E.W., and May, G. (2016) Plant host species and geographic distance affect the structure of aboveground fungal symbiont communities, and environmental filtering affects belowground communities in a coastal dune ecosystem. Microb Ecol 71 : 912–926.
Dini-Andreote, F., Pylro, V.S., Baldrian, P., Van Elsas, J.D., and Salles, J.F. (2016) Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities.ISME J 10 : 1984–1997.
Dini-Andreote, F., Stegen, James, C., van Elsas, Jan, D., and Salles, Joana, F. (2015) Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.Proc Natl Acad Sci U S A 112 : E1326–E1332.
Dong, K., Tripathi, B., Moroenyane, I., Kim, W., Li, N., Chu, H., and Adams, J. (2016) Soil fungal community development in a high Arctic glacier foreland follows a directional replacement model, with a mid-successional diversity maximum. Sci Rep 6 : 1–9.
Elston, D.A., Moss, R., Boulinier, T., Arrowsmith, C., and Lambin, X. (2001) Analysis of aggregation, a worked example: Numbers of ticks on red grouse chicks. Parasitology 122 : 563–569.
Ferrier, S., Manion, G., Elith, J., and Richardson, K. (2007) Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers Distrib 13 : 252–264.
Fitzpatrick, M.C., Mokany, K., Manion, G., Lisk, M., Ferrier, S., and Neito-Lugilde, D. (2021) gdm: Generalized Dissimilarity Modeling. R package version 1.4.2.2.
Fitzpatrick, M.C., Sanders, N.J., Normand, S., Svenning, J.-C., Ferrier, S., Gove, A.D., and Dunn, R.R. (2013) Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients. Proc R Soc B Biol Sci 280 :.
Fox, J. (2003) Effect displays in R for generalised linear models.J Stat Softw 8 : 1–27.
Fox, J. and Weisberg, S. (2019) An {R} Companion to Applied Regression, Third. Thousand Oaks, California: Sage.
Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Purdom, E., et al. (2019) Strong succession in arbuscular mycorrhizal fungal communities. ISME J 13 : 214–226.
Gardes, M. and Bruns, T.D. (1993) ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts. Mol Ecol 2 : 113–118.
Glassman, S.I., Wang, I.J., and Bruns, T.D. (2017) Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. Mol Ecol 26 : 6960–6973.
Gotelli, N.J. (2000) Null model analysis of species co-occurrence patters. Ecology 81 : 2606–2621.
Gotelli, N.J. and Graves, G.R. (1996) Co-occurrence. In Null Models in Ecology . Washington: Smithsonian Institution Press, pp. 153–205.
Greve, M., Gaston, K.J., van Rensburg, B.J., and Chown, S.L. (2008) Environmental factors, regional body size distributions and spatial variation in body size of local avian assemblages. Glob Ecol Biogeogr 17 : 514–523.
Griffin, E. and Carson, W.P. (2018) Tropical tree endophytes: cryptic drivers of forest diversity, species composition, and ecosystem function., pp. 1–52.
Griffin, E.A., Harrison, J.G., McCormick, M.K., Burghardt, K.T., and Parker, J.D. (2019) Tree diversity reduces fungal endophyte richness and diversity in a large-scale temperate forest experiment. Diversity11 : 1–20.
Harrison, J.G. and Griffin, E.A. (2020) The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol22 : 2107–2123.
Hausmann, N.T. and Hawkes, C. V. (2009) Plant neighborhood control of arbuscular mycorrhizal community composition. New Phytol183 : 1188–1200.
Hoch, J.M.K., Rhodes, M.E., Shek, K.L., Dinwiddie, D., Hiebert, T.C., Gill, A.S., et al. (2019) Soil microbial assemblages are linked to plant community composition and contribute to ecosystem services on urban green roofs. Front Ecol Evol 7 :.
Hu, Y., Veresoglou, S.D., Tedersoo, L., Xu, T., Ge, T., Liu, L., et al. (2019) Contrasting latitudinal diversity and co-occurrence patterns of soil fungi and plants in forest ecosystems. Soil Biol Biochem131 : 100–110.
Hubbell, S.P. (2001) Unified neutral theory of biodiversity, 1st ed. Princeton: (Princeton University Press.
Jamison-Daniels, S.-L., Kissling, W.D., Botha, M., Harris, M.A., Gordon, C.E., and Greve, M. (2021) The role of deterministic succession during forest development within a southern African savanna. Biotropica53 : 466–476.
Johnson, A.E. (1979) Succession an unfinished revolution. Ecology60 : 240–241.
Kembel, S.W. and Mueller, R.C. (2014) Plant traits and taxonomy drive host associations in tropical Phyllosphere fungal communities1.Botany 92 : 303–311.
Koide, R.T., Ricks, K.D., and Davis, E.R. (2017) Climate and dispersal influence the structure of leaf fungal endophyte communities of Quercus gambelii in the eastern Great Basin, USA. Fungal Ecol30 : 19–28.
Laforest-Lapointe, I., Paquette, A., Messier, C., and Kembel, S.W. (2017) Leaf bacterial diversity mediates plant diversity and ecosystem function relationships. Nature 546 : 145–147.
Lau, M.K., Arnold, A.E., and Johnson, N.C. (2013) Factors influencing communities of foliar fungal endophytes in riparian woody plants.Fungal Ecol 6 : 365–378.
Lawson, A., Biggeri, A., Böhnng, D., Lasaffre, E., Viel, J.-E., and Bertollini, R. (eds). (1999) Disease mapping and risk assessment for public health, 1st ed. Chichester, UK: John Wiley.
Legendre, P. and Borcard, D. (2008) Analyzing or Explaining Beta Diversity? Comment. Ecology 89 : 3238–3244.
Legendre, P. and Legendre, L. (2012) Numerical Ecology, 3rd ed. Elsevier.
Liu, J., Zhao, J., Wang, G., and Chen, J. (2019) Host identity and phylogeny shape the foliar endophytic fungal assemblages of Ficus.Ecol Evol 9 : 10472–10482.
McCulloch, C.E. (1997) An Introduction to Generalized Linear Mixed Models.
McMurdie, P.J. and Holmes, S. (2014) Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLOS Comput Biol 10 : e1003531.
Morisita, M. (1962) Iẟ-Index, a measure of dispersion of individuals.Popul Ecol 4 : 1–7.
Mucina, L. and Rutherford, M.C. (2011) The vegetation of South Africa, Lesotho and Swaziland., Reprint. Pretoria: Strelitzia 19. South African National Biodiversity Institute.
Nakagawa, S., Johnson, P.D.C., and Schielzeth, H. (2017) The coefficient of determination R2 and intra-class correlation coefficient from generalized linear-mixed effects models revisited and expanded. J R Soc Interface 14 :.
Nekola, J.C. and White, P.S. (1999) The distance decay of similarity in biogeography and ecology. J Biogeogr 26 : 867–878.
Nemergut, D.R., Schmidt, S.K., Fukami, T., O’Neill, S.P., Bilinski, T.M., Stanish, L.F., et al. (2013) Patterns and Processes of Microbial Community Assembly. Microbiol Mol Biol Rev 77 : 342–356.
Oksanen, J.F., Blanchet, G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al. (2019) vegan: Community Ecology Package.
Oono, R., Lefèvre, E., Simha, A., and Lutzoni, F. (2015) A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda). Fungal Biol 119 : 917–928.
Oono, R., Rasmussen, A., and Lefèvre, E. (2017) Distance decay relationships in foliar fungal endophytes are driven by rare taxa.Environ Microbiol 19 : 2794–2805.
Peay, K.G., Kennedy, P.G., and Talbot, J.M. (2016) Dimensions of biodiversity in the Earth mycobiome. Nat Rev Microbiol14 : 434–447.
Põlme, S., Bahram, M., Jacquemyn, H., Kennedy, P., Kohout, P., Moora, M., et al. (2018) Host preference and network properties in biotrophic plant–fungal associations. New Phytol 217 : 1230–1239.
R Core Team (2019) R: A language and environment for statistical computing.
Raup, D.M. and Crick, R.E. (1979) Measurement of faunal similarity in paleontology. J Paleontol 53 : 1213–1227.
Reich, P.B., Ellsworth, D.S., Walters, M.B., Vose, J.M., Gresham, C., Volin, J.C., and Bowman, W.D. (1999) Generality of leaf trait relationships: A test across six biomes. Ecology 80 : 1955–1969.
Salles, J.F., Poly, F., Schmid, B., and Roux, X. Le (2009) Community niche predicts the functioning of denitrifying bacterial assemblages.Ecology 90 : 3324–3332.
Santoyo, G., Hernández-Pacheco, C., Hernández-Salmerón, J., and Hernández-León, R. (2017) The role of abiotic factors modulating the plant-microbe-soil interactions: Toward sustainable agriculture. A review. Spanish J Agric Res 15 : 1–15.
Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9 : 671–675.
Scholtysik, A., Unterseher, M., Otto, P., and Wirth, C. (2013) Spatio-temporal dynamics of endophyte diversity in the canopy of European ash (Fraxinus excelsior). Mycol Prog 12 : 291–304.
Soininen, J., McDonald, R., and Hillebrand, H. (2007) The distance decay of similarity in ecological communities. Ecography (Cop)30 : 3–12.
Tellez, P.H., Woods, C.L., Formel, S., and Van Bael, S.A. (2020) Relationships between foliar fungal endophyte communities and ecophysiological traits of CAM and C3 epiphytic bromeliads in a neotropical rainforest. Diversity 12 : 1–15.
Terhonen, E., Blumenstein, K., Kovalchuk, A., and Asiegbu, F.O. (2019) Forest tree microbiomes and associated fungal endophytes: Functional roles and impact on forest health. Forests 10 : 1–32.
Tripathi, B.M., Stegen, J.C., Kim, M., Dong, K., Adams, J.M., and Lee, Y.K. (2018) Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J 12 : 1072–1083.
Turner, B.L., Zemunik, G., Laliberté, E., Drake, J.J., and Jones, F.A. (2019) Contrasting patterns of plant and microbial diversity during long-term ecosystem development. J Ecol 107 : 606–621.
U’Ren, J.M., Lutzoni, F., Miadlikowska, J., Zimmerman, N.B., Carbone, I., May, G., and Arnold, A.E. (2019) Host availability drives distributions of fungal endophytes in the imperilled boreal realm.Nat Ecol Evol 3 : 1430–1437.
Unterseher, M., Peršoh, D., and Schnittler, M. (2013) Leaf-inhabiting endophytic fungi of European Beech (Fagus sylvatica L.) co-occur in leaf litter but are rare on decaying wood of the same host. Fungal Divers 60 : 43–54.
Unterseher, M., Petzold, A., and Schnittler, M. (2012) Xerotolerant foliar endophytic fungi of Populus euphratica from the Tarim River basin, central China are conspecific to endophytic ITS phylotypes of Populus tremula from temperate Europe. Fungal Divers 54 : 133–142.
Unterseher, M., Reiher, A., Finstermeier, K., Otto, P., and Morawetz, W. (2007) Species richness and distribution patterns of leaf-inhabiting endophytic fungi in a temperate forest canopy. Mycol Prog6 : 201–212.
Unterseher, M., Siddique, A.B., Brachmann, A., and Peršoh, D. (2016) Diversity and composition of the leaf mycobiome of beech (Fagus sylvatica) are affected by local habitat conditions and leaf biochemistry. PLoS One 11 :.
Vaz, A.B.M., Fontenla, S., Rocha, F.S., Brandão, L.R., Vieira, M.L.A., de Garcia, V., et al. (2014) Fungal endophyte β-diversity associated with Myrtaceae species in an Andean Patagonian forest (Argentina) and an Atlantic forest (Brazil). Fungal Ecol 8 : 28–36.
Vellend, M. (2010) Conceptual synthesis in community ecology. Q Rev Biol 85 : 183–206.
Venables, W.N. and Ripley, B.D. (2002) Modern Applied Statistics with S, 4th ed. Springer Berlin Heidelberg.
Veteli, T.O., Kuokkanen, K., Julkunen-Tiitto, R., Roininen, H., and Tahvanainen, J. (2002) Effects of elevated CO2 and temperature on plant growth and herbivore defensive chemistry. Glob Chang Biol8 : 1240–1252.
Vincent, J.B., Weiblen, G.D., and May, G. (2016) Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Mol Ecol 25 : 825–841.
White, T.J., Bruns, T.D., Lee, S., and Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications . Innis, M., Gelfand, D., Shinsky, J., and White, T.J. (eds). San Diego, pp. 315–322.
Williams, K.J., Belbin, L., Austin, M.P., Stein, J.L., and Ferrier, S. (2012) Which environmental variables should I use in my biodiversity model? Int J Geogr Inf Sci 26 : 2009–2047.
Willis, A.D. (2019) Rarefaction, Alpha Diversity, and Statistics.Front Microbiol 0 : 2407.
Yao, H., Sun, X., He, C., Maitra, P., Li, X.-C., and Guo, L.-D. (2019) Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem. Microbiome7 : 57.
Zhou, J. and Ning, D. (2017) Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev 81 : pii: e00002-17.
Zimmerman, N.B. and Vitousek, P.M. (2012) Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape.Proc Natl Acad Sci 109 : 13022–13027.
Zuur, A., Ieno, E.N., Walker, N., Saveliev, A.A., and Smith, G.M. (2009) Mixed effects models and extensions in ecology with R, 1st ed. New York: Springe.