Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives

Achouak, 2013, Shaping of microbial community structure and function in the rhizosphere by four diverse plant species, vol 1, 161 Afzal, 2013, Ecology of alkane degrading bacteria and their interaction with the plant, 975 Ahkami, 2017, Rhizosphere engineering: enhancing sustainable plant ecosystem productivity, Rhizos., 3, 233, 10.1016/j.rhisph.2017.04.012 Akum, 2015, The Piriformospora indica effectors PIIN 08944 promotes the mutualistic Sebacinale an symbiosis, Front. Plant Sci., 6, 906, 10.3389/fpls.2015.00906 Altieri, 2004, Linking ecologists and traditional farmers in the search for sustainable agriculture, Front. Ecol. Environ., 2, 35, 10.1890/1540-9295(2004)002[0035:LEATFI]2.0.CO;2 An, 2006, Multi vesicular compartments proliferate in susceptible and resistant MLA12-barley leaves in response to infection by the biotrophic powdery mildew fungus, New Phytol., 172, 563, 10.1111/j.1469-8137.2006.01844.x Angel, 2010, Biogeography of soil archaea and bacteria along a steep precipitation gradient, ISME J., 4, 553, 10.1038/ismej.2009.136 Ansari, 2019, Growth stimulation and alleviation of salinity stress to wheat by the biofilm forming Bacillus pumilus strain FAB10, Agric., Ecosyst. Environ., Appl. Soil Ecol., 3, 45, 10.1016/j.apsoil.2019.05.023 Arabidopsis Interactome Mapping Consortium, 2011, ) Evidence for network evolution in an Arabidopsis interactome map, Science, 333, 601, 10.1126/science.1203877 Azcón, 2013, Abiotic stress remediation by the arbuscular mycorrhizal symbiosis and rhizosphere bacteria/ yeast interactions, 991 Backer, 2018, Plant growth promoting rhizobacteria: context, mechanisms of action and roadmap to commercialization of biostimulants for sustainable agriculture, Front. Plant Sci., 9, 1473, 10.3389/fpls.2018.01473 Bainard, 2014, Spatial and temporal structuring of arbuscular mycorrhizal communities is differentially influenced by abiotic factors and host crop in a semi-arid prairie agroecosystem, FEMS Microbiol. Ecol., 88, 333, 10.1111/1574-6941.12300 Bakker, 2012, Harnessing the rhizosphere microbiome through plant breeding and agricultural management, Plant Soil, 360, 1, 10.1007/s11104-012-1361-x Bandyopadhyay, 2017, Emergence of plant and rhizospheric microbiota as stable interactomes, Protoplasma, 254, 617, 10.1007/s00709-016-1003-x Banerjee, 2018, Keystone taxa as drivers of microbiome structure and functioning, Nat. Rev. Microbiol., 16, 567, 10.1038/s41579-018-0024-1 Banerjee, 2019, Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots, ISME J., 13, 1722, 10.1038/s41396-019-0383-2 Baran, 2015, Exometabolite niche partitioning among sympatric soil bacteria, Nat. Commun., 6, 8289, 10.1038/ncomms9289 Barea, 2015, Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions, J. Soil Sci. Plant Nutr., 15, 261 Barea, 2013, Microbial interactions in the rhizosphere, 29 Barea, 2013, Arbuscular mycorrhizas and their significance in promoting soil-plant systems sustainability against environmental stresses, 353 Barret, 2013, Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere, 57 Bell, 2014, Linkage between bacterial and fungal rhizosphere communities in hydrocarbon contaminated soils is related to plant phylogeny, ISME J., 8, 331, 10.1038/ismej.2013.149 Bengtsson-Palme, 2017, Environmental factors influencing the development and spread of antibiotic resistance, FEMS Microbiol. Rev., 42, 10.1093/femsre/fux053 Berendsen, 2012, Rhizosphere microbiome and plant health, Trends Plant Sci., 17, 478, 10.1016/j.tplants.2012.04.001 Berendsen, 2015, Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417, BMC Genomics, 16, 539, 10.1186/s12864-015-1632-z Berg, 2018, Nutrient and dose-dependent microbiome mediated protection against a plant pathogen, Curr. Biol., 28, 2487, 10.1016/j.cub.2018.05.085 Berg, 2016, The plant microbiome explored:implications for experimental botany, J. Exp. Bot., 67, 995, 10.1093/jxb/erv466 Bhattacharyya, 2016, Perspective of beneficial microbes in agriculture under changing climatic scenario: a review, J. Phytol., 8, 26, 10.19071/jp.2016.v8.3022 Bhise, 2019, Mitigation of salinity stress in plants using plant growth promoting bacteria, Symbiosis., 1 Boller, 2009, A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors, Ann. Rev. Plant Biol., 60, 379, 10.1146/annurev.arplant.57.032905.105346 Bonduriansky, 2012, The implications of non-genetic inheritance for evolution in changing environments, Evol. Appl., 5, 10.1111/j.1752-4571.2011.00213.x Bonfante, 2015, Arbuscular mycorrhizas: the lives of beneficial fungi and their plant host, 235 Botero, 2018, Network analyses in plant pathogens, Front. Microbiol., 9, 10.3389/fmicb.2018.00035 Bouffaud, 2014, Root microbiome relates to plant host evolution in maize and other Poaceae, Environ. Microbiol., 16, 2804, 10.1111/1462-2920.12442 Brader, 2017, Ecology and genomic insights of plant pathogenic and nonpathogenic endophytes, Annu. Rev. Phytopathol., 55, 61, 10.1146/annurev-phyto-080516-035641 Braga, 2016, Microbial interactions: ecology in a molecular perspective, Braz. J. Microbiol., 47, 86, 10.1016/j.bjm.2016.10.005 Breredsen, 2018, Disease induced assemblage of a plant-beneficial bacterial consortium, ISME J., 12, 1496, 10.1038/s41396-018-0093-1 Bruto, 2014, Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria, Sci. Rep., 4, 6261, 10.1038/srep06261 Buendia, 2016, The LysM receptor-like kinase SlLYK10 regulates the arbuscular mycorrhizal symbiosis in tomato, New Phytol., 210, 184, 10.1111/nph.13753 Bulgarelli, 2013, Structure and functions of the bacterial microbiota of plants, Annu. Rev. Plant Biol., 64, 807, 10.1146/annurev-arplant-050312-120106 Bulgarelli, 2015, Structure and function of the bacterial root microbiota in wild and domesticated barley, Cell Host Microb., 17, 392, 10.1016/j.chom.2015.01.011 Cai, 2017, The nutrient preference of plants influences their rhizosphere microbiome, Agric., Ecosyst. Environ., Appl. Soil Ecol., 110, 146, 10.1016/j.apsoil.2016.11.006 Carrión, 2018, Involvement of Burkholderiaceae and sulfurous volatiles in disease suppressive soils, ISME J., 12, 2307, 10.1038/s41396-018-0186-x Carvalhais, 2013, Rhizosphere metatranscriptomics: challenges and opportunities, vol 2, 1137 Castello, 2018, NPR1 paralogs of Arabidopsis and their role in salicylic acid perception, PLoS One, 13, 10.1371/journal.pone.0209835 Castrillo, 2017, Root microbiota drive direct integration of phosphate stress and immunity, Nature, 543, 513, 10.1038/nature21417 Chandra, 2019, Evaluation of ACC-deaminase producing rhizobacteria to alleviate water-stress impacts in wheat (Triticum aestivum L.) plants, Can. J. Microbiol., 65, 387, 10.1139/cjm-2018-0636 Chauhan, 2013, Unraveling the shed of unexplored rhizosphere microbial diversity, vol 1, 105 Chinchilla, 2006, The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception, Plant Cell, 18, 465, 10.1105/tpc.105.036574 Chowdhury, 2015, Bio-control mechanism by root-associated Bacillus amyloliquefaciens FZB42, Front. Microbiol., 6, 780, 10.3389/fmicb.2015.00780 Ciancio, 2016, Harnessing useful rhizosphere microorganisms for pathogen and pest biocontrol, Front. Microbiol., 7, 1620, 10.3389/fmicb.2016.01620 Clua, 2018, Compatibility between legumes and rhizobia for the establishment of a successful nitrogen-fixing symbiosis, Genes (Basel), 9, 10.3390/genes9030125 Compant, 2019, A review on the plant microbiome: ecology, functions and emerging trends in microbial application, J. Adv. Res., 19, 29, 10.1016/j.jare.2019.03.004 Craven, 2019, More than serendipity: the potential to manage soil carbon and emissions while promoting low-input agriculture with serendipitoid mycorrhizae, Phytobio. J., 3, 161, 10.1094/PBIOMES-12-18-0058-P Cycon, 2019, Antibiotics in the soil environment degradation and their impact on microbial activity and diversity, Front. Microbiol., 10, 338, 10.3389/fmicb.2019.00338 Danchin, 2011, Beyond DNA: integrating inclusive inheritance into an extended theory of evolution, Nat. Rev. Genet., 12, 475, 10.1038/nrg3028 Dastogeer, 2020, Plant microbiome an account of the factors that shape community composition and diversity, Curr. Plant Biol., 23 De Vries, 2012, Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities, Ecol. Lett., 15, 1230, 10.1111/j.1461-0248.2012.01844.x De-la-Pena, 2014, Biotic interactions in the rhizosphere: a diverse cooperative enterprise for plant productivity, Plant Physiol., 166, 701, 10.1104/pp.114.241810 Donley, 2019, The USA lags behind other agricultural nations in banning harmful pesticides, Environ. Health, 18, 44, 10.1186/s12940-019-0488-0 Donn, 2015, Evolution of bacterial communities in the wheat crop rhizosphere, Environ. Microbiol., 17, 610, 10.1111/1462-2920.12452 Doornbos, 2012, Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere, Agron. Sustain. Dev., 32, 227, 10.1007/s13593-011-0028-y Dou, 2012, Phytopathogen effectors subverting host immunity: different foes, similar battleground, Cell Host Microb., 12, 484, 10.1016/j.chom.2012.09.003 Dries, 2021, Rhizosphere engineering: leading towards a sustainable viticulture?, Oeno One, 55 Drogue, 2013, Control of the cooperation between plant growth promoting rhizobacteria and crops by rhizosphere signals, 281 Duran, 2018, Microbial inter kingdom interactions in roots promote Arabidopsis survival, Cell, 175, 973, 10.1016/j.cell.2018.10.020 Edwards, 2015, Structure, variation, and assembly of the root-associated microbiomes of rice, Proc. Natl. Acad. Sci. U.S.A., 112, 911, 10.1073/pnas.1414592112 Egamberdieva, 2019, Salt tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils, Front. Microbiol., 10, 10.3389/fmicb.2019.02791 El-Esawi, 2018, Bacillus firmus (SW5) augments salt tolerance in soybean (Glycine max L.) by modulating root system architecture, antioxidant defense systems and stress responsive genes expression, Plant Physiol. Biochem., 132, 375, 10.1016/j.plaphy.2018.09.026 El-Esawi, 2019, Azospirillum lipoferum FK1 confers improved salt tolerance in chickpea (Cicer arietinum L.) by modulating osmolytes, antioxidant machinery and stress related genes expression, Environ. Exp. Bot., 159, 55, 10.1016/j.envexpbot.2018.12.001 Esse, 2020, Genetic modifcation to improve disease resistance in crops, N. Phytol, 225, 70, 10.1111/nph.15967 Estendorfer, 2017, The influence of land use intensity on the plant-associated microbiome of Dactylis glomerata L, Front. Plant Sci., 8, 930, 10.3389/fpls.2017.00930 Fellbaum, 2014, Fungal nutrient allocation in common mycorrhizal networks is regulated by the carbon source strength of individual host plants, New Phytol., 203, 646, 10.1111/nph.12827 Fierer, 2017, Embracing the unknown: disentangling the complexities of the soil microbiome, Nat. Rev. Microbiol., 15, 579, 10.1038/nrmicro.2017.87 Fierer, 2007, Toward an ecological classification of soil bacteria, Ecolo., 88, 1354, 10.1890/05-1839 Finkel, 2017, Understanding and exploiting plant beneficial microbes, Curr. Opin. Plant Biol., 38, 155, 10.1016/j.pbi.2017.04.018 Fiorilli, 2018, Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat, Sci. Rep., 8, 9625, 10.1038/s41598-018-27622-8 Fitzpatrick, 2018, Assembly and ecological function of the root microbiome across angiosperm plant species, Proc. Natl. Acad. Sci. U.S.A., 115, 1157, 10.1073/pnas.1717617115 Fliegmann, 2016, Immunity: flagellin seen from all sides, Nat. Plants, 2, 16136, 10.1038/nplants.2016.136 Francius, 2011, Bacterial surface appendages strongly impact nano-mechanical and electrokinetic properties of Escherichia coli cells subjected to osmotic stress, Plosone, 6, 1, 10.1371/annotation/2d1cbf5c-d0f0-40c6-8f32-eb034182538c Freilich, 2011, Competitive and cooperative metabolic interactions in bacterial communities, Nat. Commun., 2, 589, 10.1038/ncomms1597 French, 2020, Tomato genotype modulates selection and responses to root microbiota, Phytobiomes J., 4, 314, 10.1094/PBIOMES-02-20-0020-R French, 2021, Emerging strategies for precision microbiome management in diverse agroecosystems, Nat. Plants, 7, 256, 10.1038/s41477-020-00830-9 Fukami, 2018, Azospirillum: benefits that go far beyond biological nitrogen fixation, AMB Express, 8, 10.1186/s13568-018-0608-1 GAP Report, 2018 Garcia, 2018, Microbial group dynamics in plant rhizospheres and their implications on nutrient cycling, Front. Microbiol., 11, 1516, 10.3389/fmicb.2018.01516 Garrido-Oter, 2018, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia, Cell Host Microb., 24, 155, 10.1016/j.chom.2018.06.006 Germaine, 2013, Improving phytoremediation through plant-associated bacteria, 963 Glazebrook, 2005, Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens, Annu. Rev. Phytopathol., 43, 205, 10.1146/annurev.phyto.43.040204.135923 Glick, 2014, Bacteria with ACC deaminase can promote plant growth and help to feed the world, Microbiol. Res., 169, 30, 10.1016/j.micres.2013.09.009 Gopal, 2016, Microbiome selection could spur next-generation plant breeding strategies, Front. Microbiol., 7, 1971, 10.3389/fmicb.2016.01971 Goswami, 2020, Plant growth-promoting rhizobacteria alleviators of abiotic stresses in soil: a review, Pedosphere, 30, 40, 10.1016/S1002-0160(19)60839-8 Gouda, 2018, Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture, Microbiol. Res., 206, 131, 10.1016/j.micres.2017.08.016 Gough, 2011, Lipo-chitooligosaccharide signaling in endosymbiotic plant-microbe interactions, Mol. Plant Microb. Interact., 24, 867, 10.1094/MPMI-01-11-0019 Gourion, 2015, Rhizobium legume symbioses: the crucial role of plant immunity, Trends Plant Sci., 20, 186, 10.1016/j.tplants.2014.11.008 Grady, 2016, Current knowledge and perspectives of Paenibacillus: a review, Microb. Cell Fact., 15, 203, 10.1186/s12934-016-0603-7 Gu, 2020, Competition for iron drives phyto-pathogen control by natural rhizosphere microbiomes, Nat. Microbiol., 5, 1002, 10.1038/s41564-020-0719-8 Gupta, 2019, ACC deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in French bean (Phaseolus vulgaris) plants, Front. Microbiol., 10, 1506, 10.3389/fmicb.2019.01506 Gutjahr, 2014, Phytohormone signaling in arbuscular mycorhiza development, Curr. Opin. Plant Biol., 20, 26, 10.1016/j.pbi.2014.04.003 Hacquard, 2016, Disentangling the factors shaping microbiota composition across the plant holobiont, New Phytol., 209, 454, 10.1111/nph.13760 Hacquard, 2017, Interplay between innate immunity and the plant microbiota, Annu. Rev. Phytopathol., 55, 565, 10.1146/annurev-phyto-080516-035623 Han, 2016, Systemic responses of barley to the 3-hydroxy-decanoyl-homoserine lactone producing plant beneficial endophyte Acidovorax radicis N35, Front. Plant Sci., 7, 1868, 10.3389/fpls.2016.01868 Haney, 2015, Associations with rhizosphere bacteria can confer an adaptive advantage to plants, Nat. Plants, 1, 15051, 10.1038/nplants.2015.51 Hardoim, 2012, Dynamics of seed borne rice endophytes on early plant growth stages, PLoS One, 7, 10.1371/journal.pone.0030438 Hartmann, 2019, Assessment of the structural and functional diversities of plant microbiota: achievements and challenges – a review, J. Adv. Res., 10.1016/j.jare.2019.04.007 Hassan, 2012, The role of flavonoids in root-rhizosphere signaling: opportunities and challenges for improving plant microbe interactions, J. Exp. Bot., 63, 3429, 10.1093/jxb/err430 Hassani, 2018, Microbial interactions within the plant holobiont, Microbiom., 6, 10.1186/s40168-018-0445-0 Heavner, 2015, Comparative analysis of yeast metabolic network models highlights progress, opportunities for metabolic reconstruction, PLoS Comput. Biol., 11, 10.1371/journal.pcbi.1004530 Hennessy, 2017, A microplate readerbased system for visualizing transcriptional activity during in vivo microbial interactions in space and time, Sci. Rep., 7 Hillmer, 2017, The highly buffered Arabidopsis immune signaling network conceals the functions of its components, PLoS Genet., 13, 10.1371/journal.pgen.1006639 Hirsch, 2012, Who’s who in the plant root microbiome?, Nature Biotechnol., 30, 961, 10.1038/nbt.2387 Hirsch, 2013, Culture-independent molecular approaches to microbial ecology in soil and the rhizosphere, 45 Hirsch, 2013, Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits?, Vol 1, 229 Hol, 2015, Context dependency and saturating effects of loss of rare soil microbes on plant productivity, Front. Plant Sci., 6, 485, 10.3389/fpls.2015.00485 Hol, 2015, Non-random species loss in bacterial communities reduces antifungal volatile production, Ecol., 96, 2042, 10.1890/14-2359.1 Hopkins, 2017, Defensive symbionts mediate host-parasite interactions at multiple scales, Trends Parasitol., 33, 53, 10.1016/j.pt.2016.10.003 Hu, 2018, Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota, Nature Commun., 9, 2738, 10.1038/s41467-018-05122-7 Huang, 2020, Natural variation at OsCERK1 regulates arbuscular mycorrhizal symbiosis in rice, N. Phytol, 225, 1762, 10.1111/nph.16158 Hunter, 2014, Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica, Front. Plant Sci., 5, 27, 10.3389/fpls.2014.00027 Innes, 2018, The positives and negatives of NPR: a unifying model for salicylic acid signaling in plants, Cell, 173, 1314, 10.1016/j.cell.2018.05.034 Jablonka, 2009, Trans-generational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution, Q. Rev. Biol., 84, 131, 10.1086/598822 Jacob, 2013, Evolution and conservation of plant NLR functions, Front. Immunol., 4, 297, 10.3389/fimmu.2013.00297 Jacoby, 2017, The role of soil microorganisms in plant mineral nutrition current knowledge and future directions, Front. Plant Sci., 8, 10.3389/fpls.2017.01617 Jayaraman, 2012, Leveraging proteomics to understand plant-microbe interactions, Front. Plant Sci., 3, 44, 10.3389/fpls.2012.00044 Jha, 2018, Mechanistic insights on plant root colonization by bacterial endophytes: a symbiotic relationship for sustainable agriculture, Environ. Sustain., 1, 25, 10.1007/s42398-018-0011-5 Johnston-Monje, 2011, Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology, PLoS One, 6, 10.1371/journal.pone.0020396 Jones, 2014, Border controls a membrane-linked interactome of Arabidopsis, Science, 344, 711, 10.1126/science.1251358 Jones, 2019, Plant host-associated mechanisms for microbial selection, Front. Plant Sci., 10, 862, 10.3389/fpls.2019.00862 Jourdan, 2009, Insights into the defense related events occurring in plant cells following perception of surfactin type lipopeptide from Bacillus subtilis, Mol. Plant Microb. Interact., 22, 456, 10.1094/MPMI-22-4-0456 Jousset, 2017, Where less may be more: how the rare biosphere pulls ecosystems strings, ISME J., 11, 853, 10.1038/ismej.2016.174 Jung, 2012, Mycorrhiza-induced resistance and priming of plant defences, J. Chem. Ecol., 38, 651, 10.1007/s10886-012-0134-6 Kadmiri, 2018, Phosphate solubilizing and auxin producing rhizobacteria promote plant growth under saline conditions, Arab. J. Sci. Eng., 43, 3403, 10.1007/s13369-017-3042-9 Kaiser, 2015, Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation, New Phytol., 205, 1537, 10.1111/nph.13138 Kandel, 2017, Bacterial endophyte colonization and distribution within plants, Microorganisms, 5, 77, 10.3390/microorganisms5040077 Katsir, 2008, COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine, Proc. Natl. Acad. Sci. U.S.A., 105, 7100, 10.1073/pnas.0802332105 Katsuragi, 2015, CD2-1, the C-terminal region of flagellin, modulates the induction of immune responses in rice, Mol. Plant Microb. Interact., 28, 648, 10.1094/MPMI-11-14-0372-R Kawasaki, 2016, Microbiome and exudates of the root and rhizosphere of Brachypodium distachyon, a model for wheat, PLoS One, 11, 10.1371/journal.pone.0164533 Kazan, 2014, Intervention of phytohormone pathways by pathogen effectors, Plant Cell, 26, 2285, 10.1105/tpc.114.125419 Kazan, 2016, The link between flowering time and stress tolerance, J. Exp. Bot., 67, 47, 10.1093/jxb/erv441 Kiers, 2011, Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis, Science, 333, 880, 10.1126/science.1208473 Kour, 2019, Agriculturally and industrially importantfungi: current developments and potential biotechnological applications, 1 Kuai, 2015, Integrating data on the Arabidopsis NPR1/NPR3/NPR4 salicylic acid receptors; a differentiating argument, Front. Plant Sci., 6, 235, 10.3389/fpls.2015.00235 Kudjordiie, 2019, Maize synthesized benzoxazinoids affect the host associated microbiome, Microbiom., 7, 59, 10.1186/s40168-019-0677-7 Kumar, 2020, Rhizosphere microbiome: engineering bacterial competitiveness for enhancing crop production, J. Adv. Res., 24, 337, 10.1016/j.jare.2020.04.014 Kumar, 2015, Interaction of Piriformospora indica with Azotobacter chroococcum, Sci. Rep., 5, 13911, 10.1038/srep13911 Kumawat, 2019, Synergism of Pseudomonas aeruginosa (LSE-2) nodule endophyte with Bradyrhizobium sp. (LSBR-3) for improving plant growth, nutrient acquisition and soil health in soybean, World J. Microbiol. Biotechnol., 35, 1, 10.1007/s11274-019-2622-0 Kumawat, 2019, Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production, World J. Microbiol. Biotechnol., 35, 1, 10.1007/s11274-019-2752-4 Kumawat, 2021, Dual microbial inoculation, a game changer? – bacterial biostimulants with multifunctional growth promoting traits to mitigate salinity stress in spring mungbean, Front. Microbiol., 11, 10.3389/fmicb.2020.600576 Lakshmanan, 2014, Functional soil microbiome: belowground solutions to an aboveground problem, Plant Physiol., 166, 689, 10.1104/pp.114.245811 Lareen, 2016, Plant root-microbe communication in shaping root microbiomes, Plant Mol. Biol., 90, 575, 10.1007/s11103-015-0417-8 Lebeis, 2015, Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa, Science, 349, 860, 10.1126/science.aaa8764 Lemanceau, 2017, Let the core microbiota be functional, Trends Plant Sci., 22, 583, 10.1016/j.tplants.2017.04.008 Lemmon, 2018, Rapid improvement of domestication traits in an orphan crop by genome editing, Nat. Plants, 4, 766, 10.1038/s41477-018-0259-x Li, 2004, The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense, Plant Cell, 16, 319, 10.1105/tpc.016980 Li, 2015, Bio-control agent Bacillus amyloliquefaciens LJ02 induces systemic resistance against cucurbits powdery mildew, Front. Microbiol., 6, 883, 10.3389/fmicb.2015.00883 Li, 2018, The interactomic analysis reveals pathogenic protein networks in Phomopsis longicolla underlying seed decay of soybean, Front. Genet., 9, 104, 10.3389/fgene.2018.00104 Li, 2018, Domestication of wild tomato is accelerated by genome editing, Nat. Biotechnol., 36, 1160, 10.1038/nbt.4273 Libault, 2010, Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection, Plant Physiol., 152, 541, 10.1104/pp.109.148379 Lidbury, 2016, Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria, Environ. Microbiol., 18, 3535, 10.1111/1462-2920.13390 Lu, 2014, Transgenic plants that express the phytoplasma effector SAP11 show altered phosphate starvation and defense responses, Plant Physiol., 164, 1456, 10.1104/pp.113.229740 Macho, 2014, Plant PRRs and the activation of innate immune signaling, Mol. Cell, 54, 263, 10.1016/j.molcel.2014.03.028 Magne, 2018, Lotus japonicus noot-bopcoch-like1 is essential for nodule, nectar, leaf and flower development, Plant J., 94, 880, 10.1111/tpj.13905 Magurran, 2003, Explaining the excess of rare species in natural species abundance distributions, Nature, 422, 714, 10.1038/nature01547 Maillet, 2011, Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza, Nature, 469, 58, 10.1038/nature09622 Mallon, 2015, Resource pulses can alleviate the biodiversity invasion relationship in soil microbial communities, Ecol, 96, 915, 10.1890/14-1001.1 Marin-de la Rosa, 2015, Primer on protein-protein interaction maps, eLS, 10.1002/9780470015902.a0006205.pub2 Martino, 2018, Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists, New Phytol., 217, 1213, 10.1111/nph.14974 Mendes, 2013, The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol. Rev., 37, 634, 10.1111/1574-6976.12028 Mhlongo, 2018, The chemistry of plant-microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and induced systemic resistance, Front. Plant Sci., 9, 10.3389/fpls.2018.00112 Miedes, 2014, The role of the secondary cell wall in plant resistance to pathogens, Front. Plant Sci., 5, 358, 10.3389/fpls.2014.00358 Millet, 2010, Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns, Plant Cell, 22, 973, 10.1105/tpc.109.069658 Miotto-Vilanova, 2016, Burkholderia phytofirmans PsJN confers grapevine resistance against Botrytis cinerea via a direct antimicrobial effect combined with a better resource mobilization, Front. Plant Sci., 7, 1236, 10.3389/fpls.2016.01236 Miransari, 2014, Plant hormones as signals in arbuscular mycorrhizal symbiosis, Crit. Rev. Biotechnol., 34, 123, 10.3109/07388551.2012.731684 Mithani, 2011, Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in Pseudomonas, Mol. Biol. Evol., 28, 483, 10.1093/molbev/msq213 Miwa, 2017, How effectors promote beneficial interactions, Curr. Opin. Plant Biol., 38, 148, 10.1016/j.pbi.2017.05.011 Miyata, 2014, The bi-functional plant receptor, OsCERK1, regulates both chitin triggered immunity and arbuscular mycorrhizal symbiosis in rice, Plant Cell Physiol., 55, 1864, 10.1093/pcp/pcu129 Mohanram, 2019, Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions, Annal. Microbiol., 69, 307, 10.1007/s13213-019-01448-9 Molina-Romero, 2017, Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth, PLoS One, 12, 10.1371/journal.pone.0187913 Morella, 2020, Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection, Proc. Natl. Acad. Sci., 117, 1148, 10.1073/pnas.1908600116 Morgan, 2017, The grapevine and wine microbiome: insights from high throughput amplicon sequencing, Front. Microbiol., 11, 820, 10.3389/fmicb.2017.00820 Mueller, 2015, Engineering microbiomes to improve plant and animal health, Trends Microbiol., 23, 606, 10.1016/j.tim.2015.07.009 Mukhtar, 2011, Independently evolved virulence effectors converge onto hubs in a plant immune system network, Science, 333, 596, 10.1126/science.1203659 Nagpal, 2020, Coordination of Mesorhizobium sp. and endophytic bacteria as elicitor of bio-control against Fusarium wilt in chickpea, Eur. J. Plant Pathol., 10.1007/s10658-020-02062-1 Nam, 2002, BRI1/BAK1, a receptor kinase pair mediating brassino-steroid signaling, Cell, 110, 203, 10.1016/S0092-8674(02)00814-0 Navarrete, 2010, A molecular survey of the diversity of microbial communities in diff ;erent Amazonian agricultural model systems, Diversity, 2, 787, 10.3390/d2050787 Naylor, 2018, Drought stress and root-associated bacterial communities, Front. Plant Sci., 8, 2223, 10.3389/fpls.2017.02223 Netzker, 2015, Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters, Front. Microbiol., 6, 299, 10.3389/fmicb.2015.00299 Nguyen, 2016, How plants handle multiple stresses: hormonal interactions underlying responses to abiotic stress and insect herbivory, Plant Mol. Biol., 91, 727, 10.1007/s11103-016-0481-8 Niu, 2016, Induced growth promotion and higher salt tolerance in the halophyte grass Puccinellia tenuiflora by beneficial rhizobacteria, Plant Soil, 407, 217, 10.1007/s11104-015-2767-z Okazaki, 2013, Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system, Proc. Natl. Acad. Sci. U.S.A., 110, 17131, 10.1073/pnas.1302360110 Olanrewaju, 2017, Mechanisms of action of plant growth promoting bacteria, World J. Microbiol. Biotechnol., 33, 197, 10.1007/s11274-017-2364-9 Oldroyd, 2014, Biotechnological solutions to the nitrogen problem, Curr. Opin. Biotechnol., 26, 19, 10.1016/j.copbio.2013.08.006 Olenska, 2020, Beneficial features of plant growth promoting rhizobacteria for improving plant growth and health in challenging conditions: a methodical review, Sci. Tot. Environ., 32, 429 OrtizCastro, 2013, Small molecules involved in trans-kingdom communication between plants and rhizobacteria, 295 Pangesti, 2013, Two way plant-mediated interactions between root-associated microbes and insects: from ecology to mechanisms, Front. Plant Sci., 4 Panke-Buisse, 2015, Selection on soil microbiomes reveals reproducible impacts on plant function, ISME J., 9, 980, 10.1038/ismej.2014.196 Parnell, 2016, From the lab to the farm: an industrial perspective of plant beneficial microorganisms, Front. Plant Sci., 7, 1110, 10.3389/fpls.2016.01110 Penselin, 2016, Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses, BMC Genom., 17, 953, 10.1186/s12864-016-3299-5 Pérez-Jaramillo, 2015, Impact of domestication on rhizosphere microbiome assembly and functions, Plant Mol. Biol., 90, 635, 10.1007/s11103-015-0337-7 Pérez-Jaramillo, 2017, Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits, ISME J., 11, 2244, 10.1038/ismej.2017.85 Pfeiffer, 2017, Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development, FEMS Microbiol. Ecol., 93, 10.1093/femsec/fiw242 Phillipot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nat. Rev. Microbiol., 11, 789, 10.1038/nrmicro3109 Pieterse, 2014, Induced systemic resistance by beneficial microbes, Annu. Rev. Phytopathol., 52, 347, 10.1146/annurev-phyto-082712-102340 Pineda, 2010, Helping plants to deal with insects: the role of beneficial soil-borne microbes, Trends Plant Sci., 15, 507, 10.1016/j.tplants.2010.05.007 Pineda, 2017, Steering soil microbiomes to suppress aboveground insect pests, Trends Plant Sci., 22, 770, 10.1016/j.tplants.2017.07.002 Pinedo, 2015, Burkholderia phytofirmans PsJN induces long term metabolic and transcriptional changes involved in Arabidopsis thaliana salt tolerance, Front. Plant Sci., 6, 1, 10.3389/fpls.2015.00466 Pongrac, 2013, Arbuscular mycorrhiza in glucosinolate-containing plants: the story of the metal hyperaccumulator Noccaea (Thlaspi) praecox (brassicaceae), 1023 Ponomarova, 2017, Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow, Cell Syst., 5, 345, 10.1016/j.cels.2017.09.002 Porter, 2020, Agriculture and the disruption of plant–microbial symbiosis, Trends Ecol. Evol. (Amst.), 35, 426, 10.1016/j.tree.2020.01.006 Poudel, 2016, Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management, Phytopathol., 106, 1083, 10.1094/PHYTO-02-16-0058-FI Pozo, 2013, Root allies: arbuscular mycorrhizal fungi help plants to cope with biotic stresses, 289 Pozo, 2015, Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses, New Phytol., 205, 1431, 10.1111/nph.13252 Prithiviraj, 2003, A host-specific bacteria-to-plant signal molecule (Nod factor) enhances germination and early growth of diverse crop plants, Planta, 216, 437, 10.1007/s00425-002-0928-9 Raaijmakers, 2015, The minimal rhizosphere microbiome, 411 Rascovan, 2016, Integrated analysis of root microbiomes of soybean and wheat from agricultural fields, Sci. Rep., 6, 28084, 10.1038/srep28084 Rashid, 2016, Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils, Microbiol. Res., 183, 26, 10.1016/j.micres.2015.11.007 Ray, 2016, Sebacina vermifera: a unique root symbiont with vast agronomic potential, World J. Microbiol. Biotechnol., 32, 1, 10.1007/s11274-015-1970-7 Ray, 2020, Microbe to microbiome: a paradigm shift in the application of microorganisms for sustainable agriculture, Front. Microbiol., 11, 10.3389/fmicb.2020.622926 Reinhold-Hurek, 2015, Roots shaping their microbiome: global hotspots for microbial activity, Ann. Rev. Phytopathol., 53, 403, 10.1146/annurev-phyto-082712-102342 Rich, 2017, Diet of arbuscular mycorrhizal fungi: bread and butter?, Trends Plant Sci., 22, 652, 10.1016/j.tplants.2017.05.008 Richard, 2019, Metabolic niches in the rhizosphere microbiome: new tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange, J. Exper. Bot., 70, 1087, 10.1093/jxb/ery438 Robertson, 2017, Cellulosic biofuel contributions to a sustainable energy future: choices and outcomes, Science, 356, 2324, 10.1126/science.aal2324 Rodenburg, 2018, Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach, Mol. Plant Pathol., 19, 1403, 10.1111/mpp.12623 Rodriguez, 2019, Systems biology of plant-microbiome interactions, Mol. Plant, 12, 804, 10.1016/j.molp.2019.05.006 Rogers, 2014, Synthetic biology approaches to engineering the nitrogen symbiosis in cereals, J. Exp. Bot., 65, 1939, 10.1093/jxb/eru098 Rosenberg, 2018, The hologenome concept of evolution after 10 years, Microbiom., 6, 78, 10.1186/s40168-018-0457-9 Ryan, 2009, Rhizosphere engineering and management for sustainable agriculture, Plant Soil, 321, 363, 10.1007/s11104-009-0001-6 Ryu, 2020, Control of nitrogen fixation in bacteria that associate with cereals, Nat. Microbiol., 5, 314, 10.1038/s41564-019-0631-2 Samad, 2017, Comparative genome analysis of the vineyard weeds endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity, Sci. Rep., 7, 17336, 10.1038/s41598-017-16495-y Samad, 2017, Shared and host specific microbiome diversity and functioning of grapevine and accompanying weed plants, Environ. Microbiol., 19, 1407, 10.1111/1462-2920.13618 Santhanam, 2015, Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping, Proc. Natl. Acad. Sci. U.S.A., 112, 5013, 10.1073/pnas.1505765112 Santoyo, 2017, The role of abiotic factors modulating the plant-microbe-soil interactions: toward sustainable agriculture. A review, Span. J. Agric. Res., 15, 1, 10.5424/sjar/2017151-9990 Sapre, 2018, Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa), Microbiol. Res., 206, 25, 10.1016/j.micres.2017.09.009 Sarkar, 2018, A halotolerant Enterobacter sp. displaying ACC deaminase activity promotes rice seedling growth under salt stress, Microbiol. Res., 169, 20, 10.1016/j.resmic.2017.08.005 Savka, 2013, The “biased rhizosphere” concept and advances in the omics era to study bacterial competitiveness and persistence in the phytosphere, 1147 Schikora, 2016, Beneficial effects of bacteria-plant communication based on quorum sensing molecules of the N-acyl homoserine lactone group, Plant Mol. Biol., 90, 605, 10.1007/s11103-016-0457-8 Schlaeppi, 2015, The plant microbiome at work, Mol. Plant Microbe Interact., 28, 212, 10.1094/MPMI-10-14-0334-FI Schreiter, 2015, Microbial communities in the rhizosphere analyzed by cultivation independent DNA-based methods, 289 Schulze, 2010, Rapid heteromerization and phosphorylation of ligand activated plant transmembrane receptors and their associated kinase BAK1, J. Biol. Chem., 285, 9444, 10.1074/jbc.M109.096842 Schumacher, 2014, Differential secretome analysis of Pseudomonas syringae pv tomato using gel-free MS proteomics, Front. Plant Sci., 5, 242, 10.3389/fpls.2014.00242 Schwessinger, 2011, Phosphorylation dependent differential regulation of plant growth, cell death and innate immunity by the regulatory receptor like kinase BAK1, PLoS Genet.7, 10.1371/journal.pgen.1002046 Selosse, 2014, Microbial priming of plant and animal immunity: symbionts as developmental signals, Trends Microbiol., 22, 607, 10.1016/j.tim.2014.07.003 Sergaki, 2018, Challenges and approaches in microbiome research: from fundamental to applied, Front. Plant Sci., 9, 1205, 10.3389/fpls.2018.01205 Seyfferth, 2014, Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming, Front. Plant Sci., 5, 697, 10.3389/fpls.2014.00697 Shah, 2003, The salicylic acid loop in plant defense, Curr. Opin. Plant Biol., 6, 365, 10.1016/S1369-5266(03)00058-X Shahzad, 2018, What is there in seeds? Vertically transmitted endophytic resources for sustainable improvement in plant growth, Front. Plant Sci., 9, 10.3389/fpls.2018.00024 Sharifi, 2018, Revisiting bacterial volatile-mediated plant growth promotion: lessons from the past and objectives for the future, Ann. Bot., 122, 349, 10.1093/aob/mcy108 Shrivastava, 2015, Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation, Saudi J. Biol. Sci., 22, 123, 10.1016/j.sjbs.2014.12.001 Singh, 2012, Activation of calcium and calmodulin dependent protein kinase (CCaMK), the central regulator of plant root endosymbiosis, Curr. Opin. Plant Biol., 15, 444, 10.1016/j.pbi.2012.04.002 Singh, 2003, Effect of plant growth promoting Rhizobacteria and culture filtrate of Sclerotium rolfsii on phenolic and salicylic acid contents in chickpea (Cicer arietinum), Curr. Microbiol., 46, 131, 10.1007/s00284-002-3834-2 Singh, 2013, Bacterial diversity in the mountains of South-West China: climate dominates over soil parameters, J. Microbiol., 51, 439, 10.1007/s12275-013-2446-9 Singh, 2020, Global scenario of plant microbiome for sustainable agriculture: current advancements and future challenges Smakowska-Luzan, 2018, An extracellular network of Arabidopsis leucine-rich repeat receptor kinases, Nature, 553, 342, 10.1038/nature25184 Smigielski, 2019, Nodulation induces systemic resistance of Medicago truncatula and Pisum sativum against Erysiphe pisi and primes for powdery mildewtriggered salicylic acid accumulation, Mol. Plant Microb. Interact, 10.1094/MPMI-11-18-0304-R Smith, 1999, Genetic basis in plants for interactions with disease-suppressive bacteria, Proc. Natl. Acad. Sci. U.S.A., 96, 4786, 10.1073/pnas.96.9.4786 Song, 2010, Interplant communication of tomato plants through underground common mycorrhizal networks, PLoS One, 5, 1, 10.1371/journal.pone.0013324 Souza, 2015, Plant growth-promoting bacteria as inoculants in agricultural soils, Genet. Mol. Biol., 38, 401, 10.1590/S1415-475738420150053 Srivastava, 2012, Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium, Plant Signal. Behav., 7, 235, 10.4161/psb.18957 Stedtfeld, 2018, Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements, FEMS Microbiol. Ecol., 94, 10.1093/femsec/fiy130 Su, 2015, Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana, Front. Plant Sci., 6, 810, 10.3389/fpls.2015.00810 Sultana, 2018, Salinity intrusion and coastal agriculture: adaptation strategies using salt tolerant plant growth promoting rhizobacteria for sustainable food security, Reg. Probl., 21, 58 Tamayo, 2014, Genome wide analysis of copper, iron and zinc transporters in the arbuscular mycorrhizal fungus Rhizophagus irregularis, Front. Plant Sci., 5, 547, 10.3389/fpls.2014.00547 Tanaka, 2015, Effect of lipochitooligosaccharide on early growth of C4 grass seedlings, J. Exp. Bot., 66, 5727, 10.1093/jxb/erv260 Tardif, 2016, The willow microbiome is influenced by soil petroleum-hydrocarbon concentration with plant compartment-specific eff ;ects, Front. Microbiol., 7, 1363 Terrazas, 2016, Plant-microbiota interactions as a driver of the mineral turnover in the rhizosphere, Adv. Appl. Microbiol., 95, 1, 10.1016/bs.aambs.2016.03.001 Timm, 2015, Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment, Front. Microbiol., 6, 1118, 10.3389/fmicb.2015.01118 Timmermann, 2017, Paraburkholderia phytofirmans PsJN protects Arabidopsis thaliana against a virulent strain of Pseudomonas syringae through the activation of induced resistance, Mol. Plant Microb. Interact., 30, 215, 10.1094/MPMI-09-16-0192-R Tiwari, 2017, Bacillus amyloliquefaciens confers tolerance to various abiotic stresses and modulates plant response to phyto-hormones through osmoprotection and gene expression regulation in rice, Front. Plant Sci., 8, 1510, 10.3389/fpls.2017.01510 Toju, 2018, Core microbiomes for sustainable agro-ecosystems, Nat. Plants, 4, 247, 10.1038/s41477-018-0139-4 Topfer, 2015, Integration of metabolomics data into metabolic networks, Front. Plant Sci., 6, 49 Trivedi, 2017, Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems, Soil Biol. Biochem., 111, 10, 10.1016/j.soilbio.2017.03.013 Tsuda, 2009, Network properties of robust immunity in plants, PLoS Genet., 5, 10.1371/journal.pgen.1000772 Van Dam, 2016, Metabolomics in the rhizosphere: tapping into belowground chemical communication, Trends Plant Sci., 21, 256, 10.1016/j.tplants.2016.01.008 Van der Heijden, 2015, Root surface as a frontier for plant microbiome research, Proc. Natl. Acad. Sci., 112, 2299, 10.1073/pnas.1500709112 Van Loon, 1998, Systemic resistance induced by rhizosphere bacteria, Annu. Rev. Phytopathol., 36, 453, 10.1146/annurev.phyto.36.1.453 Vandenkoornhuyse, 2015, The importance of the microbiome of the plant holobiont, New Phytol., 206, 1196, 10.1111/nph.13312 Vella, 2017, From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data, EURASIP J. Bioinform. Syst. Biol., 6, 10.1186/s13637-017-0059-z Venkateshwaran, 2015, Exploring the feasibility of transferring nitrogen fixation to cereal crops, 403 Vives-Peris, 2018, Salt stress alleviation in citrus plants by plant growth promoting rhizobacteria Pseudomonas putida and Novosphingobium sp, Plant Cell Rep., 37, 1557, 10.1007/s00299-018-2328-z Vogel, 2016, The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health, New Phytol., 212, 192, 10.1111/nph.14036 Voort, 2016, Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression, Ecol. Lett., 19, 375, 10.1111/ele.12567 Vorholt, 2012, Microbial life in the phyllosphere, Nat. Rev., 10, 828 Vos, 2015, Impact of hormonal crosstalk on plant resistance and fitness under multiattacker conditions, Front. Plant Sci., 6, 639, 10.3389/fpls.2015.00639 Vrancken, 2013, Pathogenicity and infection strategies of the fire blight pathogen Erwinia amylovora in Rosaceae: state of the art, Microbiol., 159, 823, 10.1099/mic.0.064881-0 Wagner, 2014, Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative, Ecol. Lett., 17, 717, 10.1111/ele.12276 Wallace, 2018, Quantitative genetics of the maize leaf microbiome, Phytobiomes J., 10.1094/PBIOMES-02-18-0008-R Walsh, 2013, The culturable soil antibiotic resistome: a community of multi-drug resistant bacteria, PLoS One, 8, 10.1371/journal.pone.0065567 Walters, 2018, Large-scale replicated field study of maize rhizosphere identifes heritable microbes, Proc. Natl. Acad. Sci. U.S.A., 115, 7368, 10.1073/pnas.1800918115 Wasternack, 2013, Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development, Ann. Bot., 111, 1021, 10.1093/aob/mct067 Wei, 2019, Initial soil microbiome composition and functioning predetermine future plant health, Sci. Adv., 5, 10.1126/sciadv.aaw0759 Werner, 2014, Evolution of microbial markets, Proc. Natl. Acad. Sci. U.S.A., 111, 1237, 10.1073/pnas.1315980111 Wessling, 2014, Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life, Cell Host Microb., 16, 364, 10.1016/j.chom.2014.08.004 Wintermans, 2016, Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria, Plant Mol. Biol., 90, 623, 10.1007/s11103-016-0442-2 Yadav, 2018, Stress adaptive microbes for plant growth promotion and alleviation of drought stress in plants, Acta. Sci. Agric., 2, 85 Yadav, 2017, Plant growth promoting bacteria: biodiversity and multifunctional attributes for sustainable agriculture, Adv. Biotechnol. Microbiol., 5, 1 Yeats, 2013, The formation and function of plant cuticles, Plant Physiol., 163, 5, 10.1104/pp.113.222737 Yoneyama, 2012, How do nitrogen and phosphorus deficiencies affect strigolactone production and exudation, Planta, 235, 1197, 10.1007/s00425-011-1568-8 Zancarini, 2013, Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities’ interactions in the rhizosphere, vol 1, 69 Zandalinas, 2018, Plant adaptations to the combination of drought and high temperatures, Physiol. Plant., 162, 2, 10.1111/ppl.12540 Zarraonaindia, 2015, The soil microbiome influences grapevine associated microbiota, mBio, 6, 2527, 10.1128/mBio.02527-14 Zavala-Gonzalez, 2017, Arabidopsis thaliana root colonization by the nematophagous fungus Pochonia chlamydosporia is modulated by jasmonate signaling and leads to accelerated flowering and improved yield, New Phytol., 213, 351, 10.1111/nph.14106 Zelezniak, 2015, Metabolic dependencies drive species co-occurrence in diverse microbial communities, Proc. Natl. Acad. Sci. U.S.A., 112, 6454 Zhalnina, 2014, Soil pH determines microbial diversity and composition in the park grass experiment, Microb. Ecol., 69, 395, 10.1007/s00248-014-0530-2 Zhalnina, 2018, Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly, Nat. Microbiol., 3, 470, 10.1038/s41564-018-0129-3 Zhang, 2015, The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling, Plant J., 81, 258, 10.1111/tpj.12723 Zhang, 2018, Salt-tolerant and plant growth promoting bacteria isolated from high yield paddy soil, Can. J. Microbiol., 64, 968, 10.1139/cjm-2017-0571 Zhang, 2019, Arbuscular mycorrhizal fungi increase grain yields: a meta-analysis, N. Phytol., 222, 543, 10.1111/nph.15570 Zolla, 2013, Understanding root-microbiome interactions, vol 2, 745 Zsogon, 2018, De novo domestication of wild tomato using genome editing, Nat. Biotechnol., 36, 1211, 10.1038/nbt.4272