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).
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).
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).
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).
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).
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).
Wissuwa, M., Mazzola, M. & Picard, C. Novel approaches in plant breeding for rhizosphere-related traits. Plant Soil 321, 409–430 (2009).
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).
Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015).
Chaparro, J. M., Badri, D. V. & Vivanco, J. M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790–803 (2014).
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA 112, E911–E920 (2015).
Food and Agriculture Organization of United Nations. World Food and Agriculture Statistical Workbook 2018 https://www.fao.org/3/ca1796en/ca1796en.pdf (2018).
International Potato Centre. Annual Report 2017 https://cipotato.org/annualreport2017/ (2017).
Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, 1–14 (2017).
Lareen, A., Burton, F. & Schäfer, P. Plant root-microbe communication in shaping root microbiomes. Plant Mol. Biol. 90, 575–587 (2016).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Estonian Weather Service. Meteorological Yearbook of Estonia 2017 https://www.ilmateenistus.ee/wp-content/uploads/2018/03/aastaraamat_2017.pdf (2018).
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).
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).
Nikitin, B. A. Methods for soil humus determination. Agric.Chem. (Agrokhimya) 3, 156–158 (1999) in Russian
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
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
Riit, T. et al. Oomycete-specific ITS primers for identification and metabarcoding. MycoKeys 14, 17–30 (2016).
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).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 2016, 1–22 (2016).
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).
Abarenkov, K. et al. The UNITE database for molecular identification of fungi—Recent updates and future perspectives. New Phytol 186, 281–285 (2010).
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).
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).
Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinform. 10, 1–9 (2009).
Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
Agrios, G. N. In Plant Pathology 5th edn (ed. Agrios, G. N.) (Elsevier Academic Press, Amsterdam, 2005).
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).
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).
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).
Clarke, K. R. & Gorley, R. N. PRIMERv7: User Manual/Tutorial (PRIMER-E, Plymouth, 2015).
Anderson, M. J., Gorley, R. N. & Clarke, K. R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods 1–214 (PRIMER-E, Plymouth, 2008).
Anderson, M. J. & Willis, T. J. Canonical analysis of principal coordinates: A useful method of constrained ordination for ecology. Ecology 84, 511–525 (2003).
Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006).
McArdle, B. H. & Anderson, M. J. Fitting multivariate models to community data. Ecology 82, 290–297 (2001).
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).
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).
Badri, D. V. & Vivanco, J. M. Regulation and function of root exudates. Plant Cell Environ. 32, 666–681 (2009).
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).
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).
Hawes, M. C., Bengough, G., Cassab, G. & Ponce, G. Root caps and rhizosphere. J. Plant Growth Regul. 21, 352–367 (2002).
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).
Moody, S. F., Clarke, A. E. & Bacic, A. Structural analysis of secreted slime from wheat and cowpea roots. Phytochemistry 27, 2857–2861 (1988).
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).
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).
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).
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).
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).
Yamaguchi, J. Measurement of root diameter in field-grown crops under a microscope without washing. Soil Sci. Plant Nutr. 48, 625–629 (2002).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Mariotte, P. et al. Plant–soil feedback: Bridging natural and agricultural sciences. Trends Ecol. Evol. 33, 129–142 (2018).
Banerjee, S. et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 13, 1722–1736 (2019).
Paungfoo-Lonhienne, C. et al. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Sci. Rep. 5, 1–6 (2015).
Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).
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).
Strickland, M. S. & Rousk, J. Considering fungal: Bacterial dominance in soils—Methods, controls, and ecosystem implications. Soil Biol. Biochem. 42, 1385–1395 (2010).
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).
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).
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).
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).
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).
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).
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).
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).
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).
van Agtmaal, M. et al. Exploring the reservoir of potential fungal plant pathogens in agricultural soil. Appl. Soil Ecol. 121, 152–160 (2017).
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).
Source: Ecology - nature.com
