https://doi.org/10.1371/journal.pone.00849131
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., … Bai, Y. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nature biotechnology , 37 (8), 852-857.https://doi.org/10.1038/s41587-019-0209-9
Bonan, G. B. (2008). Forests and climate change: forcings, feedbacks, and the climate benefits of forests. science , 320 (5882), 1444-1449. https://doi.org/10.1126/science.1155121
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC bioinformatics , 10 (1), 421.https://doi.org/10.1186/1471-2105-10-421
Carey, A. B., & Wilson, S. M. (2001). Induced spatial heterogeneity in forest canopies: responses of small mammals. The Journal of wildlife management , 65(4), 1014-1027.https://doi.org/10.2307/3803050
Carrias, J. F., Cussac, M. E., & Corbara, B. (2001). A preliminary study of freshwater protozoa in tank bromeliads. Journal of Tropical Ecology , 17 (4), 611-617.https://doi.org/10.1017/S0266467401001456
Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., & Ellison, A. M. (2014). Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological monographs , 84 (1), 45-67.https://doi.org/10.1890/13-0133.1
Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., & Schadt, C. W. (2018). The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.Microbiome , 6 (1), 31.https://doi.org/10.1186/s40168-018-0413-8
Crowther, T. W., Glick, H. B., Covey, K. R., Bettigole, C., Maynard, D. S., Thomas, S. M., … & Tuanmu, M. N. (2015). Mapping tree density at a global scale. Nature , 525 (7568), 201-205.https://doi.org/10.1038/nature14967
Dumack, K., Flues, S., Hermanns, K., & Bonkowski, M. (2017). Rhogostomidae (Cercozoa) from soils, roots and plant leaves (Arabidopsis thaliana): Description of Rhogostoma epiphylla sp. nov. andR. cylindrica sp. nov. European journal of protistology ,60 , 76-86.https://doi.org/10.1016/j.ejop.2017.06.001
Dumack, K., Feng, K., Flues, S., Sapp, M., Schreiter, S., Grosch, R., … Bonkowski, M. (2020). What drives the assembly of plant-associated protist microbiomes? bioRxiv .https://doi.org/10.1101/2020.02.16.951384
Dunthorn, M., Stoeck, T., Wolf, K., Breiner, H. W., & Foissner, W. (2012). Diversity and endemism of ciliates inhabiting Neotropical phytotelmata. Systematics and Biodiversity , 10 (2), 195-205.https://doi.org/10.1080/14772000.2012.685195
Ellwood, M. D., & Foster, W. A. (2004). Doubling the estimate of invertebrate biomass in a rainforest canopy. Nature ,429 (6991), 549-551.https://doi.org/10.1038/nature02560
Fenchel, T. O. M., & Finlay, B. J. (2004). The ubiquity of small species: patterns of local and global diversity. Bioscience ,54 (8), 777-784.https://doi.org/10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2
Fiore‐Donno, A. M., Rixen, C., Rippin, M., Glaser, K., Samolov, E., Karsten, U., … Bonkowski, M. (2018). New barcoded primers for efficient retrieval of cercozoan sequences in high‐throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Molecular ecology resources , 18 (2), 229-239.https://doi.org/10.1111/1755-0998.12729
Fiore-Donno, A. M., Richter-Heitmann, T., & Bonkowski, M. (2020). Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties. bioRxiv .https://doi.org/10.1101/2020.03.22.001768
Fiore-Donno, AM & Bonkowski, M. (2020). Distinct responses of oomycete plant parasites according to their lifestyle in a landscape-scale metabarcoding survey. bioRxiv .https://doi.org/10.1101/2020.04.05.026096
Flues, S., Bass, D., & Bonkowski, M. (2017). Grazing of leaf‐associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function. Environmental microbiology ,19 (8), 3297-3309.https://doi.org/10.1111/1462-2920.13824
Gehlenborg, N. (2019) UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets. Available at: https://cran.r-project.org/package=UpSetR.
Gilbert, G. S., Reynolds, D. R., & Bethancourt, A. (2007). The patchiness of epifoliar fungi in tropical forests: host range, host abundance, and environment. Ecology , 88 (3), 575-581.https://doi.org/10.1890/05-1170
Goetz, S., Steinberg, D., Dubayah, R., & Blair, B. (2007). Laser remote sensing of canopy habitat heterogeneity as a predictor of bird species richness in an eastern temperate forest, USA. Remote Sensing of Environment , 108 (3), 254-263.https://doi.org/10.1016/j.rse.2006.11.016
Guerreiro, M. A., Brachmann, A., Begerow, D., & Peršoh, D. (2018). Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter. Fungal diversity , 89 (1), 237-251.https://doi.org/10.1007/s13225-017-0390-4
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., … del Campo, J. (2012). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic acids research , 41 (D1), D597-D604.https://doi.org/10.1093/nar/gks1160
Hijii, N., Umeda, Y., & Mizutani, M. (2001). Estimating density and biomass of canopy arthropods in coniferous plantations: an approach based on a tree-dimensional parameter. Forest Ecology and Management , 144 (1-3), 147-157.https://doi.org/10.1016/S0378-1127(00)00367-4
Hsieh, T. C., Ma, K. H. and Chao, A. (2019) ‘iNEXT: Interpolation and Extrapolation for Species Diversity’. Available at: http://chao.stat.nthu.edu.tw/blog/software-download/.
Ishii, H. T., Tanabe, S. I., & Hiura, T. (2004). Exploring the relationships among canopy structure, stand productivity, and biodiversity of temperate forest ecosystems. Forest Science ,50 (3), 342-355.https://doi.org/10.1093/forestscience/50.3.342
Jonsson, M., Kardol, P., Gundale, M. J., Bansal, S., Nilsson, M. C., Metcalfe, D. B., & Wardle, D. A. (2015). Direct and indirect drivers of moss community structure, function, and associated microfauna across a successional gradient. Ecosystems , 18 (1), 154-169.https://doi.org/10.1007/s10021-014-9819-8
Lambais, M. R., Crowley, D. E., Cury, J. C., Büll, R. C., & Rodrigues, R. R. (2006). Bacterial diversity in tree canopies of the Atlantic forest. Science , 312 (5782), 1917-1917.https://doi.org/10.1126/science.1124696
Lara, E., Roussel‐Delif, L., Fournier, B., Wilkinson, D. M., & Mitchell, E. A. (2016). Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae. Journal of biogeography , 43 (3), 520-532. https://doi.org/10.1111/jbi.12660
Leff, J. W., Del Tredici, P., Friedman, W. E., & Fierer, N. (2015). Spatial structuring of bacterial communities within individual Ginkgo biloba trees. Environmental Microbiology , 17 (7), 2352-2361.https://doi.org/10.1111/1462-2920.12695
Lehtijärvi, A., Aday Kaya, A. G., Woodward, S., Jung, T., & Doğmuş Lehtijärvi, H. T. (2017). Oomycota species associated with deciduous and coniferous seedlings in forest tree nurseries of Western Turkey.Forest Pathology , 47 (5), e12363.https://doi.org/10.1111/efp.12363
Lentendu, G., Wubet, T., Chatzinotas, A., Wilhelm, C., Buscot, F., & Schlegel, M. (2014). Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach. Molecular Ecology , 23 (13), 3341-3355.https://doi.org/10.1111/jbi.12660
Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R., & Pfister, H. (2014). UpSet: visualization of intersecting sets. IEEE transactions on visualization and computer graphics , 20 (12), 1983-1992.https://doi.org/10.1109/TVCG.2014.2346248
Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., … Edgar, R. C. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature , 488 (7409), 86-90.https://doi.org/10.1038/nature11237
Lyons, B., Nadkarni, N. M., & North, M. P. (2000). Spatial distribution and succession of epiphytes on Tsuga heterophylla (western hemlock) in an old-growth Douglas-fir forest. Canadian Journal of botany ,78 (7), 957-968.https://doi.org/10.1139/b00-064
MacArthur, R. H., & MacArthur, J. W. (1961). On bird species diversity.Ecology , 42 (3), 594-598.https://doi.org/10.2307/1932254
Mahé, F., Rognes, T., Quince, C., de Vargas, C., & Dunthorn, M. (2015). Swarm v2: highly-scalable and high-resolution amplicon clustering.PeerJ , 3 , e1420.https://doi.org/10.7717/peerj.1420
Mahé, F., de Vargas, C., Bass, D., Czech, L., Stamatakis, A., Lara, E., … Siemensmeyer, T. (2017). Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology & Evolution , 1 (4), 0091.https://doi.org/10.1038/s41559-017-0091
Marmor, L., Torra, T., Lauri, S. A. A. G., Leppik, E., & Randlane, T. (2013). Lichens on Picea abies and Pinus sylvestris–from tree bottom to the top. The Lichenologist , 45 (1), 51-63.https://doi.org/10.1017/S0024282912000564
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal , 17 (1), 10-12.https://doi.org/10.14806/ej.17.1.200
Mazei, Y., Belyakova, O., Coppellotti, O., & Payne, R. J. (2016). Testate amoeba communities of epilithic mosses and lichens: new data from Russia, Switzerland and Italy. Acta Protozoologica ,55 (1).https://doi.org/10.4467/16890027AP.16.006.4047
Mieczan, T., & Tarkowska, M. (2014). Ecology of moss dwelling ciliates from King George Island, Antarctic: the effect of environmental parameters. Polish Polar Research , 35 (4), 609-625.https://doi.org/10.2478/popore-2014-0026
Mitchell, E. A., Bragazza, L., & Gerdol, R. (2004). Testate amoebae (Protista) communities in Hylocomium splendens (Hedw.) BSG (Bryophyta): relationships with altitude, and moss elemental chemistry.Protist , 155 (4), 423-436.https://doi.org/10.1078/1434461042650334
Nadkarni, N. M. (2001). Enhancement of forest canopy research, education, and conservation in the new millennium. Plant Ecology ,153 (1-2), 361-367.https://doi.org/10.1007/978-94-017-3606-0_29
Nadkarni, N. M., Schaefer, D., Matelson, T. J., & Solano, R. (2002). Comparison of arboreal and terrestrial soil characteristics in a lower montane forest, Monteverde, Costa Rica. Pedobiologia ,46 (1), 24-33.https://doi.org/10.1078/0031-4056-00110
Ofek-Lalzar, M., Sela, N., Goldman-Voronov, M., Green, S. J., Hadar, Y., & Minz, D. (2014). Niche and host-associated functional signatures of the root surface microbiome. Nature communications , 5 (1), 1-9.https://doi.org/10.1038/ncomms5950
Oksanen, J. et al. (2019) ‘vegan: Community Ecology Package’. Available at: https://cran.r-project.org/package=vegan.
Ottesen, A. R., Peña, A. G., White, J. R., Pettengill, J. B., Li, C., Allard, S., … Strain, E. (2013). Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC microbiology , 13 (1), 114.https://doi.org/10.1186/1471-2180-13-114
Ozanne, C. M., Anhuf, D., Boulter, S. L., Keller, M., Kitching, R. L., Körner, C., … Stork, N. E. (2003). Biodiversity meets the atmosphere: a global view of forest canopies. Science , 301 (5630), 183-186.https://doi.org/10.1126/science.1084507
Peay, K. G., Kennedy, P. G., & Talbot, J. M. (2016). Dimensions of biodiversity in the Earth mycobiome. Nature Reviews Microbiology ,14 (7), 434.https://doi.org/10.1038/nrmicro.2016.59
Ploch, S., Rose, L. E., Bass, D., & Bonkowski, M. (2016). High diversity revealed in leaf‐associated protists (Rhizaria: Cercozoa) of Brassicaceae. Journal of Eukaryotic Microbiology , 63 (5), 635-641.https://doi.org/10.1111/jeu.12314
R Core Team (2019) ‘R: A Language and Environment for Statistical Computing’. Vienna, Austria. Available at: https://www.r-project.org/.
Redford, A. J., Bowers, R. M., Knight, R., Linhart, Y., & Fierer, N. (2010). The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.Environmental microbiology , 12 (11), 2885-2893.https://doi.org/10.1111/j.1462-2920.2010.02258.x
Rizzo, D. M., & Garbelotto, M. (2003). Sudden oak death: endangering California and Oregon forest ecosystems. Frontiers in Ecology and the Environment , 1 (4), 197-204.https://doi.org/10.1890/1540-9295(2003)001[0197:SODECA]2.0.CO;2
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ ,4 , e2584.https://doi.org/10.7717/peerj.2584
Sapp, M., Ploch, S., Fiore‐Donno, A. M., Bonkowski, M., & Rose, L. E. (2018). Protists are an integral part of the Arabidopsis thaliana microbiome. Environmental microbiology , 20 (1), 30-43.https://doi.org/10.1111/1462-2920.13941
Sasse, J., Martinoia, E., & Northen, T. (2018). Feed your friends: do plant exudates shape the root microbiome?. Trends in plant science , 23 (1), 25-41.https://doi.org/10.1016/j.tplants.2017.09.003
Stein, A., & Kreft, H. (2015). Terminology and quantification of environmental heterogeneity in species‐richness research.Biological Reviews , 90 (3), 815-836.https://doi.org/10.1111/brv.12135
Thapa, S., Prasanna, R., Ranjan, K., Velmourougane, K., & Ramakrishnan, B. (2017). Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice.Microbiological research , 204 , 55-64.https://doi.org/10.1016/j.micres.2017.07.007
Thompson, I.; Mackey, B.; McNulty, S.; Mosseler, A. (2009). Forest Resilience, Biodiversity, and Climate Change: a synthesis of the biodiversity/resilience/stability relationship in forest ecosystems.Secretariat of the Convention on Biological Diversity, Montreal. Technical Series no. 43, 1-67.
Turner, T. R., Ramakrishnan, K., Walshaw, J., Heavens, D., Alston, M., Swarbreck, D., … Poole, P. S. (2013). Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants.The ISME journal , 7 (12), 2248-2258.https://doi.org/10.1038/ismej.2013.119
Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont.New Phytologist , 206 (4), 1196-1206.https://doi.org/10.1111/nph.13312
Vorholt, J. A. (2012). Microbial life in the phyllosphere. Nature Reviews Microbiology , 10 (12), 828-840.https://doi.org/10.1038/nrmicro2910
Wagner, M. R., Lundberg, D. S., Tijana, G., Tringe, S. G., Dangl, J. L., & Mitchell-Olds, T. (2016). Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications , 7 (1), 1-15.https://doi.org/10.1038/ncomms12151
Wickham, H. (2016) ggplot2: Elegant Graphics for Data Analysis . Springer-Verlag New York. Available at: https://ggplot2.tidyverse.org.
Williams, C. B. (1964) Patterns in the balance of nature and related problems of quantitative ecology. London & New York., UK & USA: Academic Press.