Do foliar fungal communities of Norway spruce shift along a tree species diversity gradient in mature European forests?

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143, 10.1128/mr.59.1.143-169.1995 Amend, 2010, Quantifying microbial communities with 454 pyrosequencing: does read abundance count?, Mol. Ecol., 19, 5555, 10.1111/j.1365-294X.2010.04898.x Anderson, 2001, A new method for non-parametric multivariate analysis of variance, Austral Ecol., 26, 32 Arnold, 2007, Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?, Ecology, 88, 541, 10.1890/05-1459 Arnold, 2000, Are tropical fungal endophytes hyperdiverse?, Ecol. Lett., 3, 267, 10.1046/j.1461-0248.2000.00159.x Arnold, 2003, Fungal endophytes limit pathogen damage in a tropical tree, Proc. Natl. Acad. Sci. U. S. A., 100, 15649, 10.1073/pnas.2533483100 Asiegbu, 2005, Conifer root and butt rot caused by Heterobasidion annosum (Fr.) Bref. s.l, Mol. Plant Pathol., 6, 395, 10.1111/j.1364-3703.2005.00295.x Baeten, 2013, A novel comparative research platform designed to determine the functional significance of tree species diversity in European forests, Perspect. Plant Ecol. Evol. Syst., 15, 281, 10.1016/j.ppees.2013.07.002 Bailey, 2005, Host plant genetics affect hidden ecological players: links among Populus, condensed tannins, and fungal endophyte infection, Can. J. Bot., 83, 356, 10.1139/b05-008 Baldrian, 2012, Active and total microbial communities in forest soil are largely different and highly stratified during decomposition, Isme J., 6, 248, 10.1038/ismej.2011.95 Bálint, 2013, Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera), PLoS One, 8, e53987, 10.1371/journal.pone.0053987 Bálint, 2015, Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars, Mol. Ecol., 24, 235, 10.1111/mec.13018 Barbosa, 2009, Associational resistance and associational susceptibility: having right or wrong neighbors, Annu. Rev. Ecol. Evol. Syst., 40, 1, 10.1146/annurev.ecolsys.110308.120242 Barklund, 1987, Occurrence and pathogenicity of Lophodermium piceae appearing as an endophyte in needles of Picea abies, Trans. Br. Mycol. Soc., 89, 307, 10.1016/S0007-1536(87)80111-0 Bates, 2015, Fitting linear mixed-effects models using lme4, J. Stat. Softw., 67, 1 Boehm, 2009, On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes, Mycol. Res., 113, 461, 10.1016/j.mycres.2008.12.001 Boonmee, 2014, Tubeufiales, ord. nov., integrating sexual and asexual generic names, Fungal Divers., 68, 239, 10.1007/s13225-014-0304-7 Breslow, 1987, vol. 2 Cardinale, 2012, Biodiversity loss and its impact on humanity, Nature, 486, 59, 10.1038/nature11148 Carnol, 2014, Ecosystem services of mixed species forest stands and monocultures: comparing practitioners' and scientists' perceptions with formal scientific knowledge, Forestry, 87, 639, 10.1093/forestry/cpu024 Carroll, 1988, Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont, Ecology, 69, 2, 10.2307/1943154 Carroll, 1978, Studies on the incidence of coniferous needle endophytes in the Pacific Northwest, Can. J. Bot., 56, 3034, 10.1139/b78-367 Castagneyrol, 2013, Plant apparency, an overlooked driver of associational resistance to insect herbivory, J. Ecol., 101, 418 Chang, 1993, A simple and efficient method for isolating RNA from pine trees, Plant Mol. Biol. Report., 11, 113, 10.1007/BF02670468 Chen, 2015, Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order – Phaeomoniellales, Mol. Phylogenet Evol., 85, 117, 10.1016/j.ympev.2015.01.008 Clemmensen, 2015, Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests, New Phytol., 205, 1525, 10.1111/nph.13208 Colwell, 2013 Cordier, 2012, Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica), Fungal Ecol., 5, 509, 10.1016/j.funeco.2011.12.004 Cordier, 2012, The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient, New Phytol., 196, 510, 10.1111/j.1469-8137.2012.04284.x De Deyn, 2004, Plant species identity and diversity effects on different trophic levels of nematodes in the soil food web, Oikos, 106, 576, 10.1111/j.0030-1299.2004.13265.x Deckert, 2000, Distribution of foliar fungal endophytes of Pinus strobus between and within host trees, Can. J Res., 30, 1436, 10.1139/x00-078 Delhomme, 2015, Serendipitous meta-transcriptomics: the fungal community of Norway spruce (Picea abies), PLoS One, 10, e0139080, 10.1371/journal.pone.0139080 Demanèche, 2001, Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA, Appl. Environ. Microbiol., 67, 293, 10.1128/AEM.67.1.293-299.2001 England, 1997, Persistence of Pseudomonas aureofaciens strains and DNA in soil, Soil Biol. Biochem., 29, 1521, 10.1016/S0038-0717(97)00013-8 Ertz, 2014, Molecular data resolve a new order of Arthoniomycetes sister to the primarily lichenized Arthoniales and composed of black yeasts, lichenicolous and rock-inhabiting species, Fungal divers.., 66, 113, 10.1007/s13225-013-0250-9 Espinosa-Garcia, 1990, The endophytic fungal community in leaves of a coastal redwood population - diversity and spatial patterns, New Phytol., 116, 89, 10.1111/j.1469-8137.1990.tb00513.x Felton, 2016, Replacing monocultures with mixed-species stands: ecosystem service implications of two production forest alternatives in Sweden, Ambio, 45, 124, 10.1007/s13280-015-0749-2 Gadgil, 1974, Effect of temperature and leaf wetness period on infection of Pinus radiata by Dothistroma pini, N. Z. J. For. Sci., 4, 495 Gamfeldt, 2015, Marine biodiversity and ecosystem functioning: what's known and what's next?, Oikos, 124, 252, 10.1111/oik.01549 Gamfeldt, 2013, Higher levels of multiple ecosystem services are found in forests with more tree species, Nat. Commun., 4, 1, 10.1038/ncomms2328 Haegeman, 2013, Robust estimation of microbial diversity in theory and in practice, Isme J., 7, 1092, 10.1038/ismej.2013.10 Hantsch, 2013, Species richness and species identity effects on occurrence of foliar fungal pathogens in a tree diversity experiment, Ecosphere, 4, 10.1890/ES13-00103.1 Hantsch, 2014, Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation, J. Ecol., 102, 1673 Heiniger, 1986, Schweiz. Z. Forstwes. J. For. Suisse, 2, 157 Helander, 1995, Responses of pine needle endophytes to air pollution, New Phytol., 131, 223, 10.1111/j.1469-8137.1995.tb05723.x Hibbett, 2007, A higher-level phylogenetic classification of the Fungi, Mycol. Res., 111, 509, 10.1016/j.mycres.2007.03.004 Higgins, 2007, Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages, Mol. Phylogenet Evol., 42, 543, 10.1016/j.ympev.2006.07.012 Hodkinson, 2011, The orders of ostropomycetidae (lecanoromycetes, Ascomycota): recognition of sarrameanales and trapeliales with a request to retain pertusariales over agyriales, Phytologia, 93, 407 Hoffman, 2008, Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees, Mycol. Res., 112, 331, 10.1016/j.mycres.2007.10.014 Hosmer, 1989 Huntley, 1983 Ihrmark, 2012, New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities, Fems Microbiol. Ecol., 82, 666, 10.1111/j.1574-6941.2012.01437.x Jangid, 2011, Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties, Soil Biol. Biochem., 43, 2184, 10.1016/j.soilbio.2011.06.022 Jost, 2006, Entropy and diversity, Oikos, 113, 363, 10.1111/j.2006.0030-1299.14714.x Jumpponen, 2009, Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere, New Phytol., 184, 438, 10.1111/j.1469-8137.2009.02990.x Jumpponen, 2010, Massively parallel 454-sequencing of Quercus spp. ectomycorrhizosphere indicates differences in fungal community composition richness, and diversity among urban and rural environments, Mol. Ecol., 19, 41, 10.1111/j.1365-294X.2009.04483.x Juniper, 1991, The leaf from the inside and the outside: a microbe's perspective, 21 Kató, 1967 Keesing, 2006, Effects of species diversity on disease risk, Ecol. Lett., 9, 485, 10.1111/j.1461-0248.2006.00885.x Korhonen, 1998, Biology of Heterobasidion annosum, 43 Legault, 1989, Mycoflora of Pinus banksiana and Pinus resinosa needles. II. Epiphytic fungi, Can. J. Bot., 67, 2061, 10.1139/b89-260 Legendre, 1998 Lindahl, 2013, Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide, New Phytol., 199, 288, 10.1111/nph.12243 Livsey, 1992, Lophodermium piceae and Rhizosphaera kalkhoffii in fallen needles of Norway spruce (Picea abies), Eur. J. For. Pathol., 22, 204, 10.1111/j.1439-0329.1992.tb00785.x Lodge, 1995, Fungal communities in wet tropical forests: variation in time and space, Can. J. Bot., 73, 1391, 10.1139/b95-402 Lodge, 1996, Endophytic fungi of Manilkara bidentata leaves in Puerto Rico, Mycologia, 88, 733, 10.1080/00275514.1996.12026710 Menkis, 2015, High-throughput sequencing reveals drastic changes in fungal communities in the phyllosphere of Norway spruce (Picea abies) following invasion of the spruce bud scale (Physokermes piceae), Microb. Ecol., 1 Millberg, 2015, Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden, Fungal Ecol., 17, 126, 10.1016/j.funeco.2015.05.012 Moricca, 2011, The holomorph Apiognomonia quercina/Discula quercina as a pathogen/endophyte in oak, 47 Möykkynen, 1997, Estimation of dispersal gradients of S- and P-type basidiospores of Heterobasidion annosum, Eur. J. For. Pathol., 27, 291, 10.1111/j.1439-0329.1997.tb01083.x Müller, 1998, Diversity of Norway spruce needle endophytes in various mixed and pure Norway spruce stands, Mycol. Res., 102, 1183, 10.1017/S0953756298006285 Müller, 2000, Fungal diversity in Norway spruce: a case study, Mycol. Res., 104, 1139, 10.1017/S0953756200003105 Müller, 2001, Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers, Mol. Ecol., 10, 1801, 10.1046/j.1365-294X.2001.01304.x Nadrowski, 2010, Is forest diversity driving ecosystem function and service?, Curr. Opin. Sust., 2, 75, 10.1016/j.cosust.2010.02.003 Nguyen, 2016, Fungal disease incidence along tree diversity gradients depends on latitude in European forests, Ecol. Evol., 6, 2426, 10.1002/ece3.2056 O'Brien, 2005, Fungal community analysis by large-scale sequencing of environmental samples, Appl. Environ. Microbiol., 71, 5544, 10.1128/AEM.71.9.5544-5550.2005 Oksanen, 2013 Ottosson, 2015, Diverse ecological roles within fungal communities in decomposing logs of Picea abies, Fems Microbiol. Ecol., 91, 10.1093/femsec/fiv012 Pautasso, 2005, Susceptibility to fungal pathogens of forests differing in tree diversity, 263 Pennanen, 2004, Community-level responses of metabolically-active soil microorganisms to the quantity and quality of substrate inputs, Soil Biol. Biochem., 36, 841, 10.1016/j.soilbio.2004.01.014 Peršoh, 2010, First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and its host Pinus sylvestris, Fungal Biol-UK, 114, 585, 10.1016/j.funbio.2010.04.009 Persson, 2011, Do bark beetles facilitate the establishment of rot fungi in Norway spruce?, Fungal Ecol., 4, 262, 10.1016/j.funeco.2011.01.005 Persson, 2009, Fungi vectored by the bark beetle Ips typographus following hibernation under the bark of standing trees and in the forest litter, Microb. Ecol., 58, 651, 10.1007/s00248-009-9520-1 Petrini, 1992, Fungal endophytes of tree leaves, 179 Piri, 1990, Occurrence of Heterobasidion annosum in pure and mixed spruce stands in southern Finland, Scand. J. For. Res., 5, 113, 10.1080/02827589009382598 R Core Team, 2013 Rajala, 2014, The community of needle endophytes reflects the current physiological state of Norway spruce, Fungal Biol-UK, 118, 309, 10.1016/j.funbio.2014.01.002 Rajala, 2013, Endophyte communities vary in the needles of Norway spruce clones, Fungal Biol-UK, 117, 182, 10.1016/j.funbio.2013.01.006 Rodriguez, 2009, Fungal endophytes: diversity and functional roles, New Phytol., 182, 314, 10.1111/j.1469-8137.2009.02773.x Rosling, 2011, Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi, Science, 333, 876, 10.1126/science.1206958 Saikkonen, 2007, Forest structure and fungal endophytes, Fungal Biol. Rev., 21, 67, 10.1016/j.fbr.2007.05.001 Santamaría, 2005, Fungal epiphytes and endophytes of coffee leaves (Coffea arabica), Microb. Ecol., 50, 1, 10.1007/s00248-004-0002-1 Schielzeth, 2013, Nested by design: model fitting and interpretation in a mixed model era, Methods Ecol. Evol., 4, 14, 10.1111/j.2041-210x.2012.00251.x Schoch, 2006, A multigene phylogeny of the Dothideomycetes using four nuclear loci, Mycologia, 98, 1041, 10.1080/15572536.2006.11832632 Sieber, 1988, Endophytische pilze in nadeln von gesunden und geschädigten fichten (Picea abies [L.] Karsten), Eur. J. For. Pathol., 18, 321, 10.1111/j.1439-0329.1988.tb00220.x Siepmann, 1984, Stammfäuleanteile in fichtenreinbeständen und in mischbeständen, Eur. J. For. Pathol., 14, 234, 10.1111/j.1439-0329.1984.tb00167.x Siira-Pietikäinen, 2001, Short-term responses of soil decomposer communities to forest management: clear felling versus alternative forest harvesting methods, Can. J Res., 31, 88, 10.1139/x00-148 Solheim, 1989, Fungi on spruce needles in Norway II, Eur. J. For. Pathol., 19, 189, 10.1111/j.1439-0329.1989.tb00250.x Stone, 1996, Canopy microfungi: function and diversity, Northwest Sci., 70, 37 Stone, 2008, Predicting effects of climate change on Swiss needle cast disease severity in Pacific Northwest forests, Can. J. Plant Pathol., 30, 169, 10.1080/07060661.2008.10540533 Strid, 2014, Bark beetles have a decisive impact on fungal communities in Norway spruce stem sections, Fungal Ecol., 7, 47, 10.1016/j.funeco.2013.09.003 Terhonen, 2011, The effect of latitude, season and needle-age on the mycota of Scots pine (Pinus sylvestris) in Finland, Silva Fenn., 45, 301, 10.14214/sf.104 Thor, 2005, Modelling root rot incidence in Sweden using tree, site and stand variables, Scand. J. For. Res., 20, 165, 10.1080/02827580510008347 Unterseher, 2007, Species richness and distribution patterns of leaf-inhabiting endophytic fungi in a temperate forest canopy, Mycol. Prog., 6, 201, 10.1007/s11557-007-0541-1 Vacher, 2008, Distribution of parasitic fungal species richness: influence of climate versus host species diversity, Divers. Distrib., 14, 786, 10.1111/j.1472-4642.2008.00479.x White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315 Yachi, 1999, Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis, Proc. Natl. Acad. Sci. U. S. A., 96, 1463, 10.1073/pnas.96.4.1463 Zalar, 2008, Redefinition of Aureobasidium pullulans and its varieties, Stud. Mycol., 61, 21, 10.3114/sim.2008.61.02 Zhang, 2011, A molecular, morphological and ecological re-appraisal of Venturiales―a new order of Dothideomycetes, Fungal divers.., 51, 249, 10.1007/s13225-011-0141-x Zimmerman, 2012, Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape, Proc. Natl. Acad. Sci. U. S. A., 109, 13022, 10.1073/pnas.1209872109 Zuur, 2009