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    Small-scale alpine topography at low latitudes and high altitudes: refuge areas of the genus Chrysanthemum and its allies

    1.
    Hirakawa, H. et al. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res. 26, 195–203 (2019).
    CAS  PubMed  Article  PubMed Central  Google Scholar 
    2.
    Stevenson, T. Chrysanthemums. Nature 90, 248 (1912).
    Google Scholar 

    3.
    Ministry of Agriculture and Fisheries UK. Control of the Chrysanthemum midge. Nature 144, 280 (1939).

    4.
    Cockshull, K. E. & Hughes, A. P. Distribution of dry matter to flowers in Chrysanthemum morifolium. Nature 215, 780–781 (1976).
    Article  Google Scholar 

    5.
    Courtney-Gutterson, N. et al. Modification of flower color in florist’s Chrysanthemum: production of a white–flowering variety through molecular genetics. Nat. Biotechnol. 12, 268–271 (1994).
    CAS  Article  Google Scholar 

    6.
    Gamalero, E. Effects of Pseudomonas putida S1Pf1Rif against Chrysanthemum yellows phytoplasma infection. Phytopathology 100, 805–813 (2010).
    PubMed  Article  PubMed Central  Google Scholar 

    7.
    Wei, Q. et al. Control of chrysanthemum flowering through integration with an aging pathway. Nat. Commun. 8, 829 (2017).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    8.
    Yang, L., Wen, X., Fu, J. & Dai, S. ClCRY2 facilitates floral transition in Chrysanthemum lavandulifolium by affecting the transcription of circadian clock-related genes under short-day photoperiods. Hortic. Res. 5, 58 (2018).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    9.
    Su, J. et al. Current achievements and future prospects in the genetic breeding of chrysanthemum: a review. Hortic. Res. 6, 109 (2019).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    10.
    Kubitzki, K. The families and genera of vascular plants, Vol. VIII Flowering Plants・Eudicots (eds Kadereit, J. W. & Jeffrey, C.) Compositae (eds. Anderberg, A. A. et al.) (Springer-Verlag Berlin Heidelberg, 2007).

    11.
    Poljakov, P. P. Duo genere novae fam. Compositae. Not. Syst. Herb. Inst. Bot. Akad. Sci. URSS 17, 418–431 (1955).
    Google Scholar 

    12.
    Muldashev, A. A. A new genus Phaeostigma (Asteraceae) from the East Asia. Botanischeskii Zh . 66, 584–588 (1981).
    Google Scholar 

    13.
    Muldashev, A. A. A critical review of the genus Ajania (Asteraceae-Anthemideae). Botanischeskii Zh . 68, 207–214 (1983).
    Google Scholar 

    14.
    Bremer, K. & Humphries, C. J. The generic monograph of the Asteraceae-Anthemideae. Bull. Nat. Hist. Mus. Lond. 23, 71–177 (1993).
    Google Scholar 

    15.
    Huang, Y., An, Y. M., Meng, S. Y., Guo, Y. P. & Rao, G. Y. Taxonomic status and phylogenetic position of Phaeostigma in the subtribe Artemisiinae (Asteraceae). J. Syst. Evol. 55, 426–436 (2017).
    Article  Google Scholar 

    16.
    Zhao, H. B., Chen, F. D., Chen, S. M., Wu, G. S. & Guo, W. M. Molecular phylogeny of Chrysanthemum, Ajania and its allies (Anthemideae, Asteraceae) as inferred from nuclear ribosomal ITS and chloroplast trnL-F IGS sequences. Plant Syst. Evol. 284, 153–169 (2010).
    CAS  Article  Google Scholar 

    17.
    Liu, P. L., Wan, Q., Guo, Y. P., Yang, J. & Rao, G. Y. Phylogeny of the Genus Chrysanthemum L.: evidence from single-copy nuclear gene and chloroplast DNA sequences. PLoS ONE 7, e48970 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    18.
    Ohashi, H. & Yonekura, K. New combinations in Chrysanthemum (Compositae-Anthemideae) of Asia with a list of Japanese Specie. J. Jpn. Bot. 79, 186–195 (2004).
    Google Scholar 

    19.
    Sanz, M. et al. Molecular phylogeny and evolution of floral characters of Artemisia and allies (Anthemideae, Asteraceae): evidence from nrDNA ETS and ITS sequences. Taxon 57, 1–13 (2008).
    Google Scholar 

    20.
    An, Y. M. Studies on the Phylogeny and Biogeography of the Genus Ajania and Its Allies. Master’s thesis. Peking University (2012).

    21.
    Barreda, V. D. et al. Eocene Patagonia fossils of the daisy family. Science 329, 1621–1621 (2010).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    22.
    Wefferling, K. M. & Hoot, S. B. Dated phylogeography of western North American subalpine marshmarigolds (Caltha spp. Ranunculaceae): Miocene-Pliocene divergence of hexaploids, multiple origins of allododecaploids during the Pleistocene, and repeated recolonization of Last Glacial Maxim. J. Biogeogr. 45, 1077–1089 (2018).
    Article  Google Scholar 

    23.
    Wiens, J. J. Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution 58, 193–197 (2004).
    PubMed  Article  PubMed Central  Google Scholar 

    24.
    Ricklefs, R. E. Evolutionary diversification and the origin of the diversity-environment relationship. Ecology 87, S3–S13 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    25.
    Li, J., Wan, Q., Guo, Y. P., Abbott, R. J. & Rao, G. Y. Should I stay or should I go: biogeographic and evolutionary history of a polyploid complex (Chrysanthemum indicum complex) in response to Pleistocene climate change in China. N. Phytol. 201, 1031–1044 (2014).
    CAS  Article  Google Scholar 

    26.
    Rahbek, C. et al. Humboldt’s enigma: What causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    27.
    Rahbek, C. et al. Building mountain biodiversity: Geological and evolutionary processes. Science 365, 1114–1119 (2019).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    28.
    Cosacov, A., Sérsic, A. N., Sosa, V., Johnson, L. A. & Cocucci, A. A. Multiple periglacial refugia in the Patagonian steppe and post-glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza. J. Biogeogr. 37, 1463–1477 (2010).
    Google Scholar 

    29.
    García-Aloy, S. et al. North-west Africa as a source and refuge area of plant biodiversity: a case study on Campanula kremeri and Campanula occidentalis. J. Biogeogr. 44, 2057–2068 (2017).
    Article  Google Scholar 

    30.
    Pérez-Escobar, O. A. et al. Recent origin and rapid speciation of Neotropical orchids in the world’s richest plant biodiversity hotspot. N. Phytol. 215, 891–905 (2017).
    Article  Google Scholar 

    31.
    Zhao, Y. P. et al. Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat. Commun. 10, 4201 (2019).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    32.
    Xing, Y. & Ree, R. H. Uplift-driven diversification in the Hengduan mountains, a temperate biodiversity hotspot. Proc. Natl Acad. Sci. USA 114, E3444 (2017).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    33.
    Sun, H. 2002. Evolution of arctic-tertiary flora in Himalayan-Hengduan mountains. Acta Bot. Yunnanica. 24, 671–688 (2002).
    Google Scholar 

    34.
    Sun, H. & Li, Z. M. Qinghai-Tibet Plateau uplift and its impact on Tethys flora. Adv. Earth. Sci. 18, 852–862 (2003).
    Google Scholar 

    35.
    Zhang, D. C., Zhang, Y. H., Boufford, D. E. & Sun, H. Elevational patterns of species richness and endemism for some important taxa in the Hengduan mountains, southwestern China. Biodivers. Conserv. 18, 699–716 (2009).
    Article  Google Scholar 

    36.
    Royer, D. L., McElwain, J. C., Adams, J. M. & Wilf, P. Sensitivity of leaf size and shape to climate within Acer rubrum and Quercus kelloggii. N. Phytol. 179, 808–817 (2008).
    Article  Google Scholar 

    37.
    Opedal, Ø. H., Armbruster, W. S. & Graae, B. J. Linking small-scale topography with microclimate, plant species diversity and intra-specific trait variation in an alpine landscape. Plant Ecol. Divers. 8, 305–315 (2015).
    Article  Google Scholar 

    38.
    Tölgyesi, C. Tree-herb co-existence and community assembly in natural forest-steppe transitions. Plant Ecol. Divers. 11, 465–477 (2018).
    Article  Google Scholar 

    39.
    Rumpf, S. B. Range dynamics of mountain plants decrease with elevation. Proc. Natl Acad. Sci. USA 115, 1848–1853 (2018).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    40.
    Camarero, J. J., Gutiérrez, E. & Fortin, M. J. Spatial patterns of plant richness across treeline ecotones in the Pyrenees reveal different locations for richness and tree cover boundaries. Glob. Ecol. Biogeogr. 15, 182–191 (2006).
    Article  Google Scholar 

    41.
    Liang, E. et al. Species interactions slow warming-induced upward shifts of treelines on the Tibetan Plateau. Proc. Natl Acad. Sci. USA 113, 4380–4385 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    42.
    Li, P. et al. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.). Mol. Genet. Genomics. 291, 1117–1125 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    43.
    Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321–4325 (1980).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    44.
    Zhang, F. et al. SRAP-based mapping and QTL detection for inflorescence-related traits in chrysanthemum (Dendranthema morifolium). Mol. Breed. 27, 11–23 (2011).
    CAS  Article  Google Scholar 

    45.
    Li, G. & Quiros, C. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103, 455–461 (2001).
    CAS  Article  Google Scholar 

    46.
    Shen, J. et al. Lake sediment records on climate change and human activities since the Holocene in Erhai catchment, Yunnan Province, China. Sci. China Ser. D. Earth Sci. 48, 353–363 (2005).
    CAS  Article  Google Scholar 

    47.
    Hoorn, C. et al. Eocene palynological record of climate change and Tibetan Plateau uplift (Xining Basin, China). Palaeogeogr. Palaeoclimatol. Palaeoecol. 344–345, 16–38 (2012).
    Article  Google Scholar 

    48.
    Cao, X., Ni, J., Herzschuh, U., Wang, Y. & Zhao, Y. A late Quaternary pollen dataset from eastern continental Asia for vegetation and climate reconstructions: Set up and evaluation. Rev. Palaeobot. Palyno. 194, 21–37 (2013).
    Article  Google Scholar 

    49.
    Li, S. et al. Magnetostratigraphy of the Dali Basin in Yunnan and implications for late Neogene rotation of the southeast margin of the Tibetan Plateau. J. Geophys. Res-Sol. Ea. 118, 791–807 (2013).
    Article  Google Scholar 

    50.
    Gourbet, L. et al. Reappraisal of the Jianchuan Cenozoic basin stratigraphy and its implications on the SE Tibetan plateau evolution. Tectonophysics 700–701, 162–179 (2017).
    Article  CAS  Google Scholar 

    51.
    Wu, J. et al. Paleoelevations in the Jianchuan Basin of the southeastern Tibetan Plateau based on stable isotope and pollen grain analyses. Palaeogeogr. Palaeoclimatol. Palaeoecol. 510, 93–108 (2018).
    Article  Google Scholar 

    52.
    Li, Q., Wu, H., Yu, Y., Sun, A. & Luo, Y. Large-scale vegetation history in China and its response to climate change since the Last Glacial Maximum. Quat. Int. 500, 108–119 (2019).
    Article  Google Scholar 

    53.
    Mutanga, O. et al. Explaining grass-nutrient patterns in a savanna rangeland of southern Africa. J. Biogeogr. 31, 819–829 (2004).
    Article  Google Scholar 

    54.
    Rowe, R. J. Elevational gradient analyses and the use of historical museum specimens:a cautionary tale. J. Biogeogr. 32, 1883–1897 (2005).
    Article  Google Scholar 

    55.
    Barbo, D. N., Chappelka, A. H., Somers, G. L., Miller-Goodman, M. S. & Stolte, K. Diversity of an early successional plant community as influenced by ozone. N. Phytol. 138, 653–662 (1998).
    CAS  Article  Google Scholar 

    56.
    Liang, J. et al. Positive biodiversity-productivity relationship predominant in global forests. Science 354, aaf8957 (2016).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    57.
    Vermeer, J. & Peterson, R. L. Glandular trichomes on the inflorescence of Chrysanthemum morifolium cv. Dramatic (Compositae). II. Ultrastruct. Histochem. Can. J. Bot. 57, 705–713 (1979).
    Google Scholar 

    58.
    Ren, J. B. & Guo, Y. P. Behind the diversity: Ontogenies of radiate, disciform, and discoid capitula of Chrysanthemum and its allies. J. Syst. Evol. 53, 520–528 (2015).
    Article  Google Scholar 

    59.
    Li, J., Guo, Y. & Romane, F. Environmental heterogeneity and population variability of Sclerophyllous Oaks (Quercus Sec. suber) in East Himalayan region. Forestry Stud. China 2, 1–15 (2000).
    CAS  Google Scholar 

    60.
    Wright, A. J. et al. Plants are less negatively affected by flooding when growing in species-rich plant communities. N. Phytol. 213, 645–656 (2017).
    Article  Google Scholar 

    61.
    Hughes, C. E. & Atchison, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan mountains. N. Phytol. 207, 275–282 (2015).
    Article  Google Scholar 

    62.
    Pfister, C. A. & Hay, M. E. Associational plant refuges: convergent patterns in marine and terrestrial communities result from differing mechanisms. Oecologia 77, I18–I129 (1988).
    Article  Google Scholar 

    63.
    Zhang, Y. C., Shi, G. R. & Shen, S. Z. A review of Permian stratigraphy, palaeobiogeography and palaeogeography of the Qinghai–Tibet plateau. Gondwana Res. 24, 55–76 (2013).
    CAS  Article  Google Scholar 

    64.
    Zhou, X. et al. Vegetation change and evolutionary response of large mammal fauna during the mid-Pleistocene transition in temperate northern East Asia. Palaeogeogr. Palaeoclimatol. Palaeoecol. 505, 287–294 (2018).
    Article  Google Scholar 

    65.
    Barreda, V. D. et al. Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica. Proc. Natl Acad. Sci. USA 112, 10989–10994 (2105).
    Article  CAS  Google Scholar 

    66.
    Huang, C. H. et al. Multiple polyploidization events across asteraceae with two nested events in the early history revealed by nuclear phylogenomics. Mol. Biol. Evol. 33, 2820–2835 (2016).

    67.
    Credner, W. Geography Investigation Report in 1931. In: Report Collecton of Department of Geography, Vol. 1, 1–35 (National Sun Yat-sen University, 1931).

    68.
    Credner, W. Observation on geology and morphology of Yunnan. Geol. Surv. Kwangtung Kwangshi, Spec. Publ. No. X, 51 (1932).
    Google Scholar 

    69.
    Yang, J. Q., Cui, Z. J., Yi, C. L., Sun, J. M. & Yang, L. R. “Tali Glaciation” on Massif Diancang. Sci. China Ser. D 50, 1685–1692 (2007).
    Article  Google Scholar 

    70.
    Hoke, G. D., Zeng, J. L., Hren, M. T., Wissink, G. K. & Garzione, C. N. Stable isotopes reveal high southeast Tibetan Plateau margin since the Paleogene. Earth Planet. Sc. Lett. 394, 270–278 (2014).
    CAS  Article  Google Scholar 

    71.
    Li, S., Currie, B. S., Rowley, D. B. & Ingalls, M. Cenozoic paleoaltimetry of the SE margin of the Tibetan Plateau: constraints on the tectonic evolution of the region. Earth Planet. Sc. Lett. 432, 415–424 (2015).
    CAS  Article  Google Scholar 

    72.
    Kuang, M. et al. Study on the Palaeovegation and Palaeoclimate Since Late Pleistocene in the Dianchang Mountain Area in Dali of YunNan Province. J. Southwest China Norm. Univ 27, 759–765 (2002).
    Google Scholar 

    73.
    Xiao, X. et al. Latest Pleistocene and Holocene vegetation and climate history inferred from an alpine lacustrine record, northwestern Yunnan Province, southwestern China. Quat. Sci. Rev. 86, 35–48 (2014).
    Article  Google Scholar 

    74.
    Mandela, J. R. et al. A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proc. Natl Acad. Sci. USA 116, 14083–14088 (2019).
    Article  CAS  Google Scholar 

    75.
    Sheldon, N. D. Quaternary glacial-interglacial climate cycles in Hawaii. J. Geol. 114, 367–376 (2006).
    Article  Google Scholar 

    76.
    Milbau, A., Shevtsova, A., Osler, N., Mooshammer, M. & Graae, B. J. Plant community type and small-scale disturbances, but not altitude, influence the invasibility in subarctic ecosystems. N. Phytol. 197, 1002–1011 (2013).
    Article  Google Scholar 

    77.
    Wang, W. M. On the origin and development of Artemisia (Asteraceae) in the geological past. Bot. J. Linn. Soc. 145, 331–336 (2004).
    Article  Google Scholar 

    78.
    Pellicer, J. et al. Palynological study of Ajania and related genera (Asteraceae, Anthemideae). Bot. J. Linn. Soc. 161, 171–189 (2009).
    Article  Google Scholar 

    79.
    Friedman, J. & Barrett, S. C. H. Wind of change: new insights on the ecology and evolution of pollination and mating in wind-pollinated plants. Ann. Bot.-Lond. 103, 1515–1527 (2009).
    Article  Google Scholar 

    80.
    Watson, L. E., Bates, P. L., Evans, T. M., Unwin, M. M. & Estes, R. J. Molecular phylogeny of Subtribe Artemisiinae (Asteraceae), including Artemisia and its allied and segregate genera. BMC Evol. Biol. 2, 17–28 (2002).
    PubMed  Article  PubMed Central  Google Scholar  More

  • in

    Characterising the effect of crop species and fertilisation treatment on root fungal communities

    1.
    Ramankutty, N. et al. Trends in global agricultural land use: Implications for environmental health and food security. Annu. Rev. Plant Biol. 69, 789–815 (2018).
    CAS  PubMed  Article  PubMed Central  Google Scholar 
    2.
    Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl. Acad. Sci. USA 108, 20260–20264 (2011).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    3.
    Bender, S. F., Wagg, C. & van der Heijden, M. G. A. An underground revolution: Biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol. Evol. 31, 440–452 (2016).
    PubMed  Article  PubMed Central  Google Scholar 

    4.
    Schröder, P. et al. Discussion paper: Sustainable increase of crop production through improved technical strategies, breeding and adapted management—A European perspective. Sci. Total Environ. 678, 146–161 (2019).
    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

    5.
    Bardgett, R. D., Mommer, L. & De Vries, F. T. Going underground: Root traits as drivers of ecosystem processes. Trends Ecol. Evol. 29, 692–699 (2014).
    PubMed  Article  PubMed Central  Google Scholar 

    6.
    Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    7.
    Wissuwa, M., Mazzola, M. & Picard, C. Novel approaches in plant breeding for rhizosphere-related traits. Plant Soil 321, 409–430 (2009).
    CAS  Article  Google Scholar 

    8.
    Backer, R. et al. Plant growth-promoting rhizobacteria: Context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front. Plant Sci. 871, 1–17 (2018).
    Google Scholar 

    9.
    Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    10.
    Chaparro, J. M., Badri, D. V. & Vivanco, J. M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790–803 (2014).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    11.
    Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA 112, E911–E920 (2015).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    12.
    Food and Agriculture Organization of United Nations. World Food and Agriculture Statistical Workbook 2018 https://www.fao.org/3/ca1796en/ca1796en.pdf (2018).

    13.
    International Potato Centre. Annual Report 2017 https://cipotato.org/annualreport2017/ (2017).

    14.
    Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, 1–14 (2017).
    Article  CAS  Google Scholar 

    15.
    Lareen, A., Burton, F. & Schäfer, P. Plant root-microbe communication in shaping root microbiomes. Plant Mol. Biol. 90, 575–587 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    16.
    Adair, K. L. & Douglas, A. E. Making a microbiome: The many determinants of host-associated microbial community composition. Curr. Opin. Microbiol. 35, 23–29 (2017).
    PubMed  Article  PubMed Central  Google Scholar 

    17.
    Donn, S., Kirkegaard, J. A., Perera, G., Richardson, A. E. & Watt, M. Evolution of bacterial communities in the wheat crop rhizosphere. Environ. Microbiol. 17, 610–621 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    18.
    Grayston, S. J., Wang, S., Campbell, C. D. & Edwards, A. C. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol. Biochem. 30, 369–378 (1998).
    CAS  Article  Google Scholar 

    19.
    Esperschütz, J., Gattinger, A., Mäder, P., Schloter, M. & Fließbach, A. Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations. FEMS Microbiol. Ecol. 61, 26–37 (2007).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    20.
    Francioli, D. et al. Mineral vs. organic amendments: Microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. 7, 1–16 (2016).
    Article  Google Scholar 

    21.
    Lupatini, M., Korthals, G. W., de Hollander, M., Janssens, T. K. S. & Kuramae, E. E. Soil microbiome is more heterogeneous in organic than in conventional farming system. Front. Microbiol. 7, 1–13 (2017).
    Article  Google Scholar 

    22.
    Kätterer, T., Börjesson, G. & Kirchmann, H. Changes in organic carbon in topsoil and subsoil and microbial community composition caused by repeated additions of organic amendments and N fertilisation in a long-term field experiment in Sweden. Agric. Ecosyst. Environ. 189, 110–118 (2014).
    Article  Google Scholar 

    23.
    Liu, B., Tu, C., Hu, S., Gumpertz, M. & Ristaino, J. B. Effect of organic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors and the incidence of Southern blight. Appl. Soil Ecol. 37, 202–214 (2007).
    Article  Google Scholar 

    24.
    Liu, Y. et al. Direct and indirect influences of 8 year of nitrogen and phosphorus fertilisation on glomeromycota in an alpine meadow ecosystem. New Phytol. 194, 523–535 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    25.
    Liu, W. et al. Arbuscular mycorrhizal fungi in soil and roots respond differently to phosphorus inputs in an intensively managed calcareous agricultural soil. Sci. Rep. 6, 1–11 (2016).
    Article  CAS  Google Scholar 

    26.
    Beauregard, M. S. et al. Various forms of organic and inorganic P fertilizers did not negatively affect soil- and root-inhabiting AM fungi in a maize–soybean rotation system. Mycorrhiza 23, 143–154 (2013).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    27.
    Wemheuer, B., Thomas, T. & Wemheuer, F. Fungal endophyte communities of three agricultural important grass species differ in their response towards management regimes. Microorganisms 7, 37 (2019).
    CAS  Article  Google Scholar 

    28.
    Hartman, K. et al. Erratum: Correction to: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (Microbiome (2018) 6 1 (14)). Microbiome 6, 74 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    29.
    Estonian Weather Service. Meteorological Yearbook of Estonia 2017 https://www.ilmateenistus.ee/wp-content/uploads/2018/03/aastaraamat_2017.pdf (2018).

    30.
    De Leon, D. G. et al. Different wheat cultivars exhibit variable responses to inoculation with arbuscular mycorrhizal fungi from organic and conventional farms. PLoS ONE 15, 1–17 (2020).
    Google Scholar 

    31.
    Van Reeuwijk, L. P. Nitrogen in Procedures for soil analysis 6th edn (ed. Van Reeuwijk L. P.) (International Soil Reference and Information Centre, Wageningen, 2002).
    Google Scholar 

    32.
    Nikitin, B. A. Methods for soil humus determination. Agric.Chem. (Agrokhimya) 3, 156–158 (1999) in Russian
    Google Scholar 

    33.
    Egnér, H., Riehm, H. & Domingo, W. R. Untersuchungen über die chemische Bodenanalyse als Grundlage für die Beurteilung des Nährstoffzustandes der Böden. II. Chemische Extraktionsmethoden zur Phosphor- und Kaliumbestimmung 199–215 (The Annals of the Royal Agricultural College of Sweden, 1960) in German

    34.
    Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    35.
    Riit, T. et al. Oomycete-specific ITS primers for identification and metabarcoding. MycoKeys 14, 17–30 (2016).
    Article  Google Scholar 

    36.
    Anslan, S., Bahram, M., Hiiesalu, I. & Tedersoo, L. PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.12692 (2017).
    Article  PubMed  Google Scholar 

    37.
    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 2016, 1–22 (2016).
    Google Scholar 

    38.
    Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    39.
    Abarenkov, K. et al. The UNITE database for molecular identification of fungi—Recent updates and future perspectives. New Phytol 186, 281–285 (2010).
    PubMed  Article  PubMed Central  Google Scholar 

    40.
    Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).
    Google Scholar 

    41.
    Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    42.
    Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinform. 10, 1–9 (2009).
    Article  CAS  Google Scholar 

    43.
    Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
    Article  Google Scholar 

    44.
    Agrios, G. N. In Plant Pathology 5th edn (ed. Agrios, G. N.) (Elsevier Academic Press, Amsterdam, 2005).

    45.
    Jensen, B., Lübeck, P. S. & Jørgensen, H. J. L. Clonostachys rosea reduces spot blotch in barley by inhibiting prepenetration growth and sporulation of Bipolaris sorokiniana without inducing resistance. Pest Manag. Sci. 72, 2231–2239 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    46.
    Knudsen, I. M. B., Hockehull, J. & Jensen, D. N. Biocontrol of seedling diseases of barley and wheat caused by Fusarium culmorum and Bipolaris sorokiniana: Effects of selected fungal antagonists on growth and yield components. Plant Pathol 44, 467–477 (1995).
    Article  Google Scholar 

    47.
    Bálint, M. et al. Millions of reads, thousands of taxa: Microbial community structure and associations analyzed via marker genesa. FEMS Microbiol. Rev. 40, 686–700 (2016).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    48.
    Clarke, K. R. & Gorley, R. N. PRIMERv7: User Manual/Tutorial (PRIMER-E, Plymouth, 2015).
    Google Scholar 

    49.
    Anderson, M. J., Gorley, R. N. & Clarke, K. R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods 1–214 (PRIMER-E, Plymouth, 2008).
    Google Scholar 

    50.
    Anderson, M. J. & Willis, T. J. Canonical analysis of principal coordinates: A useful method of constrained ordination for ecology. Ecology 84, 511–525 (2003).
    Article  Google Scholar 

    51.
    Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    52.
    McArdle, B. H. & Anderson, M. J. Fitting multivariate models to community data. Ecology 82, 290–297 (2001).
    Article  Google Scholar 

    53.
    Broeckling, C. D., Broz, A. K., Bergelson, J., Manter, D. K. & Vivanco, J. M. Root exudates regulate soil fungal community composition and diversity. Appl. Environ. Microbiol. 74, 738–744 (2008).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    54.
    Hu, L. et al. Root exudate metabolites drive plant–soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Commun. 9, 1–13 (2018).
    ADS  Article  CAS  Google Scholar 

    55.
    Badri, D. V. & Vivanco, J. M. Regulation and function of root exudates. Plant Cell Environ. 32, 666–681 (2009).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    56.
    Emmett, B. D., Youngblut, N. D., Buckley, D. H. & Drinkwater, L. E. Plant phylogeny and life history shape rhizosphere bacterial microbiome of summer annuals in an agricultural field. Front. Microbiol. 8, 1–16 (2017).
    Article  Google Scholar 

    57.
    Hawes, M. C., Gunawardena, U., Miyasaka, S. & Zhao, X. The role of root border cells in plant defense. Trends Plant Sci. 5, 128–133 (2000).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    58.
    Hawes, M. C., Bengough, G., Cassab, G. & Ponce, G. Root caps and rhizosphere. J. Plant Growth Regul. 21, 352–367 (2002).
    CAS  Article  Google Scholar 

    59.
    Koroney, A. S. et al. Root exudate of Solanum tuberosum is enriched in galactose-containing molecules and impacts the growth of pectobacterium atrosepticum. Ann. Bot. 118, 797–808 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    60.
    Moody, S. F., Clarke, A. E. & Bacic, A. Structural analysis of secreted slime from wheat and cowpea roots. Phytochemistry 27, 2857–2861 (1988).
    CAS  Article  Google Scholar 

    61.
    Wang, Q., Wang, N., Wang, Y., Wang, Q. & Duan, B. Differences in root-associated bacterial communities among fine root branching orders of poplar (Populus × euramericana (Dode) Guinier.). Plant Soil 421, 123–135 (2017).
    CAS  Article  Google Scholar 

    62.
    Tedersoo, L., Mett, M., Ishida, T. A. & Bahram, M. Phylogenetic relationships among host plants explain differences in fungal species richness and community composition in ectomycorrhizal symbiosis. New Phytol. 199, 822–831 (2013).
    PubMed  Article  PubMed Central  Google Scholar 

    63.
    Rich, S. M. & Watt, M. Soil conditions and cereal root system architecture: Review and considerations for linking Darwin and Weaver. J. Exp. Bot. 64, 1193–1208 (2013).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    64.
    Watt, M., Magee, L. J. & McCully, M. E. Types, structure and potential for axial water flow in the deepest roots of field-grown cereals. New Phytol. 178, 135–146 (2008).
    PubMed  Article  PubMed Central  Google Scholar 

    65.
    Watt, M., Schneebeli, K., Dong, P. & Wilson, I. W. The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops. Funct. Plant Biol. 36, 960–969 (2009).
    PubMed  Article  PubMed Central  Google Scholar 

    66.
    Yamaguchi, J. Measurement of root diameter in field-grown crops under a microscope without washing. Soil Sci. Plant Nutr. 48, 625–629 (2002).
    Article  Google Scholar 

    67.
    Yamaguchi, J., Tanaka, A. & Tanaka, A. Quantitative observation on the root system of various crops growing in the field. Soil Sci. Plant Nutr. 36, 483–493 (1990).
    Article  Google Scholar 

    68.
    Detheridge, A. P. et al. The legacy effect of cover crops on soil fungal populations in a cereal rotation. Agric. Ecosyst. Environ. 228, 49–61 (2016).
    Article  Google Scholar 

    69.
    Tedersoo, L. et al. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. ISME J. 10, 346–362 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    70.
    Chen, M. et al. Soil eukaryotic microorganism succession as affected by continuous cropping of peanut—Pathogenic and beneficial fungi were selected. PLoS ONE 7, e40659 (2012).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    71.
    Song, X., Pan, Y., Li, L., Wu, X. & Wang, Y. Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. Continuous cropping fields. PLoS ONE 13, 1–14 (2018).
    Google Scholar 

    72.
    Bennett, A. J., Bending, G. D., Chandler, D., Hilton, S. & Mills, P. Meeting the demand for crop production: The challenge of yield decline in crops grown in short rotations. Biol. Rev. 87, 52–71 (2012).
    PubMed  Article  PubMed Central  Google Scholar 

    73.
    Öpik, M., Moora, M., Liira, J. & Zobel, M. Composition of root-colonizing arbuscular mycorrhizal fungal communities in different ecosystems around the globe. J. Ecol. 94, 778–790 (2006).
    Article  Google Scholar 

    74.
    Sýkorová, Z., Wiemken, A. & Redecker, D. Cooccurring Gentiana verna and Gentiana acaulis and their neighboring plants in two Swiss upper montane meadows harbor distinct arbuscular mycorrhizal fungal communities. Appl. Environ. Microbiol. 73, 5426–5434 (2007).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    75.
    Francioli, D. et al. Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant Soil https://doi.org/10.1007/s11104-020-04454-y (2020).
    Article  Google Scholar 

    76.
    Mariotte, P. et al. Plant–soil feedback: Bridging natural and agricultural sciences. Trends Ecol. Evol. 33, 129–142 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    77.
    Banerjee, S. et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 13, 1722–1736 (2019).
    PubMed  Article  PubMed Central  Google Scholar 

    78.
    Paungfoo-Lonhienne, C. et al. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Sci. Rep. 5, 1–6 (2015).
    Article  CAS  Google Scholar 

    79.
    Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).
    PubMed  Article  PubMed Central  Google Scholar 

    80.
    Rousk, J., Brookes, P. C. & Bååth, E. Fungal and bacterial growth responses to N fertilization and pH in the 150-year ‘Park Grass’ UK grassland experiment. FEMS Microbiol. Ecol. 76, 89–99 (2011).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    81.
    Strickland, M. S. & Rousk, J. Considering fungal: Bacterial dominance in soils—Methods, controls, and ecosystem implications. Soil Biol. Biochem. 42, 1385–1395 (2010).
    CAS  Article  Google Scholar 

    82.
    Marschner, P., Kandeler, E. & Marschner, B. Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol. Biochem. 35, 453–461 (2003).
    CAS  Article  Google Scholar 

    83.
    Ai, C. et al. Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation. Geoderma 319, 156–166 (2018).
    ADS  CAS  Article  Google Scholar 

    84.
    Giacometti, C. et al. Chemical and microbiological soil quality indicators and their potential to differentiate fertilization regimes in temperate agroecosystems. Appl. Soil Ecol. 64, 32–48 (2013).
    Article  Google Scholar 

    85.
    Liu, M. et al. Organic amendments with reduced chemical fertilizer promote soil microbial development and nutrient availability in a subtropical paddy field: The influence of quantity, type and application time of organic amendments. Appl. Soil. Ecol. 42, 166–175 (2009).
    Article  Google Scholar 

    86.
    Lin, X. et al. Long-term balanced fertilization decreases arbuscular mycorrhizal fungal diversity in an arable soil in north China revealed by 454 pyrosequencing. Environ. Sci. Technol. 46, 5764–5771 (2012).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    87.
    Mäder, P., Edenhofer, S., Boller, T., Wiemken, A. & Niggli, U. Arbuscular mycorrhizae in a long-term field trial comparing low-input (organic, biological) and high-input (conventional) farming systems in a crop rotation. Biol. Fertil. Soils 31, 150–156 (2000).
    Article  Google Scholar 

    88.
    Song, G. et al. Contrasting effects of long-term fertilization on the community of saprotrophic fungi and arbuscular mycorrhizal fungiin a sandy loam soil. Plant Soil Environ. 61, 127–136 (2015).
    CAS  Article  Google Scholar 

    89.
    Sun, R. et al. Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter. Environ. Microbiol. 18, 5137–5150 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    90.
    Setälä, H. & McLean, M. A. Decomposition rate of organic substrates in relation to the species diversity of soil saprophytic fungi. Oecologia 139, 98–107 (2004).
    ADS  PubMed  Article  PubMed Central  Google Scholar 

    91.
    van Agtmaal, M. et al. Exploring the reservoir of potential fungal plant pathogens in agricultural soil. Appl. Soil Ecol. 121, 152–160 (2017).
    Article  Google Scholar 

    92.
    Chung, Y. R., Hoitink, H. A. H. & Lipps, P. E. Interactions between organic-matter decomposition level and soilborne disease severity. Agric. Ecosyst. Environ. 24, 183–193 (1988).
    Article  Google Scholar  More