Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A. & Dufresne, A. The importance of the microbiome of the plant holobiont. New Phytol. 206, 1196–1206 (2015).
Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012). This is one of the first studies to use high-throughput sequencing to profile the plant-associated microbiota, suggesting compartment-specific assembly of microbial communities.
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).
Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl Acad. Sci. USA 110, 6548–6553 (2013).
Ofek-Lalzar, M. et al. Niche and host-associated functional signatures of the root surface microbiome. Nat. Commun. 5, 4950 (2014).
Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015). In this study, shotgun metagenome analysis was used to elucidate the microbial traits involved in the bacterium–bacteriophage, interbacterial and host–bacterium interactions that govern plant colonization.
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA 112, E911–E920 (2015).
Zarraonaindia, I. et al. The soil microbiome influences grapevine-associated microbiota. mBio 6, e02527–14 (2015).
Coleman-Derr, D. et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811 (2016).
De Souza, R. S. C. et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci. Rep. 6, 28774 (2016).
Fonseca-García, C. et al. The cacti microbiome: interplay between habitat-filtering and host-specificity. Front. Microbiol. 7, 150 (2016).
Fitzpatrick, C. R. et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl Acad. Sci. USA 115, E1157–E1165 (2018).
Hamonts, K. et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. 20, 124–140 (2018).
Niu, B., Paulson, J. N., Zheng, X. & Kolter, R. Simplified and representative bacterial community of maize roots. Proc. Natl Acad. Sci. USA 114, E2450–E2459 (2017).
Xu, J. et al. The structure and function of the global citrus rhizosphere microbiome. Nat. Commun. 9, 4894 (2018). This study presents one of the most comprehensive investigations on the structure and functional features of the microbiome associated with a particular plant species, identifying the core microbiota and functions that are persistently present at a global scale.
Bergelson, J., Mittelstrass, J. & Horton, M. W. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Sci. Rep. 9, 24 (2019).
Wagner, M. R. et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7, 12151 (2016).
Roman-Reyn, V. et al. The rice leaf microbiome has a conserved community structure controlled by complex host-microbe. Preprint at bioRxiv https://doi.org/10.1101/615278 (2019).
Cregger, M. A. et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6, 31 (2018).
Lemanceau, P., Blouin, M., Muller, D. & Moënne-Loccoz, Y. Let the core microbiota be functional. Trends Plant Sci. 22, 583–595 (2017).
Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663 (2013).
Leach, J. E., Triplett, L. R., Argueso, C. T. & Trivedi, P. Communication in the phytobiome. Cell 169, 587–596 (2018).
Levy, A. et al. Genomic features of bacterial adaptation to plants. Nat. Genet. 50, 138–150 (2018). In this study, comparative genomics is used to identify the genes involved in bacterial adaptation to plants, including genes associated with plant colonization, microorganism–microorganism competition and host–microorganism interactions.
Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl Acad. Sci. USA 106, 16428–16433 (2009).
Liu, Z. et al. A genome-wide screen identifies genes in rhizosphere-associated Pseudomonas required to evade plant defenses. mBio 9, e00433-–18 (2018).
Cole, B. J. et al. Genome-wide identification of bacterial plant colonization genes. PLoS Biol. 15, e2002860 (2018).
Richardson, A. E. & Simpson, R. J. Soil microorganisms mediating phosphorus availability update on microbial phosphorus. Plant Physiol. 156, 989–996 (2011).
Pieterse, C. M. et al. Induced systemic resistance by beneficial microbes. Ann. Rev. Phytopathol. 52, 347–375 (2014).
Trivedi, P., Trivedi, C., Grinyer, J., Anderson, I. C. & Singh, B. K. Harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria. Front. Plant Sci. 7, 1423 (2016).
Backer, R. et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front. Plant Sci. 9, 1473 (2018).
Gouda, S. et al. Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol. Res. 206, 131–140 (2018).
Mendes, R. et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100 (2011). This study identifies vital bacterial groups and functional traits that are involved in building disease-suppressive soils, thus demonstrating that selective enrichment of microbial groups in response to pathogen attack protects plants against infections.
Santhanam, R., Weinhold, A., Goldberg, J., Oh, Y. & Baldwin, I. T. Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc. Natl Acad. Sci. USA 112, E5013–E5020 (2015).
Trivedi, P. et al. Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Soil. Biol. Biochem. 111, 10–14 (2017).
Ravanbakhsh, M., Kowalchuk, G. A. & Jousset, A. Root-associated microorganisms reprogram plant life history along the growth–stress resistance tradeoff. ISME J. 13, 3093–3101 (2019).
Xue, C. et al. Manipulating the banana rhizosphere microbiome for biological control of Panama disease. Sci. Rep. 5, 11124 (2015).
Castrillo, G. et al. Root microbiota drive direct integration of phosphate stress and immunity. Nature 543, 513–518 (2017). In this study, a synthetic microbial community is used to define the molecular interactions that activate a microbiome-mediated response under nutrient-deficient conditions while repressing host immune output, allowing selective microbial colonization.
Zhang, J. et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat. Biotechnol. 37, 676–684 (2019). This study demonstrates that slight variation in single plant genes can result in differential recruitment and enrichment of selected microbial groups and functions that correlate with higher nitrogen use efficiency of indica than of japonica varieties of rice.
Durán, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983 (2018). This study demonstrates that biocontrol traits of root-associated bacteria modulate interkingdom interactions between bacterial and filamentous eukaryotic microorganisms, resulting in a balanced plant–microbiome interaction that favours plant growth and survival against root-derived fungi and/or oomycetes.
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M. & Simmons, S. L. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. mBio 5, e00682-13 (2014).
Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015). This study demonstrates a significant overlap between bacterial isolates from plant environments and their representation in culture-independent surveys, suggesting that a substantial proportion of the plant-associated microbiota is culturable.
Edwards, J. A. et al. Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. PLoS Biol. 16, e2003862 (2018).
Morella, N. M. et al. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc. Natl Acad. Sci. USA 117, 1148–1159 (2019).
Moissl-Eichinger, C. et al. Archaea are interactive components of complex microbiomes. Trends Microbiol. 26, 70–85 (2018).
Taffner, J. et al. What is the role of Archaea in plants? New insights from the vegetation of alpine bogs. MSphere 3, e00122-–18 (2018).
Taffner, J., Cernava, T., Erlacher, A. & Berg, G. Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.). J. Adv. Res. 19, 39–48 (2019).
Pratama, A. A. & van Elsas, J. D. The ‘neglected’ soil virome — potential role and impact. Trends Microbiol. 26, 649–662 (2018).
Trubl, G. et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 3, e00076-18 (2018).
Morella, N. M., Gomez, A. L., Wang, G., Leung, M. S. & Koskella, B. The impact of bacteriophages on phyllosphere bacterial abundance and composition. Mol. Ecol. 27, 2025–2038 (2018).
Castillo, J. D., Vivanco, J. M. & Manter, D. K. Bacterial microbiome and nematode occurrence in different potato agricultural soils. Microb. Ecol. 74, 888–900 (2017).
Elhady, A. et al. Microbiomes associated with infective stages of root-knot and lesion nematodes in soil. PLoS ONE 12, e0177145 (2017).
Treonis, A. M. et al. Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches. Sci. Rep. 8, 2004 (2018).
Gao, Z., Karlsson, I., Geisen, S., Kowalchuk, G. & Jousset, A. Protists: puppet masters of the rhizosphere microbiome. Trends Plant Sci. 24, 165–176 (2018).
Larousse, M. & Galiana, E. Microbial partnerships of pathogenic oomycetes. PLoS Pathog. 13, e1006028 (2017).
Ploch, S. & Thines, M. Obligate biotrophic pathogens of the genus Albugo are widespread as asymptomatic endophytes in natural populations of Brassicaceae. Mol. Ecol. 20, 3692–3699 (2015).
Benhamou, N. et al. Pythium oligandrum: an example of opportunistic success. Microbiol 158, 2679–2694 (2012).
Sapp, M., Ploch, S., Fiore-Donno, A. M., Bonkowski, M. & Rose, L. E. Protists are an integral part of the Arabidopsis thaliana microbiome. Environ. Microbiol. 20, 30–43 (2018).
Astudillo-García, C. et al. Evaluating the core microbiota in complex communities: a systematic investigation. Environ. Microbiol. 19, 1450–1462 (2017).
Yeoh, Y. K. et al. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nat. Commun. 8, 215 (2017).
Garrido-Oter, R. et al. Modular traits of the rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host Microbe 24, 155–167 (2018).
Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, e1002352 (2016). This study demonstrates the presence of highly interconnected ‘hub species’ in microbial networks that act as mediators between a host and its associated microbiome.
Muller, E. E. et al. Using metabolic networks to resolve ecological properties of microbiomes. Curr. Opin. Sys. Biol. 8, 73–80 (2018).
Röttjers, L. & Faust, K. From hairballs to hypotheses — biological insights from microbial networks. FEMS Microbiol. Rev. 42, 761–780 (2018).
Shade, A., Jacques, M. A. & Barret, M. Ecological patterns of seed microbiome diversity, transmission, and assembly. Curr. Opin. Microbiol. 37, 15–22 (2017).
Gloria, T. C. et al. Functional microbial features driving community assembly during seed germination and emergence. Front. Plant Sci. 9, 902 (2018).
Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, eaaw0759 (2019).
Tian, B. et al. Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome. Agric. Ecosys. Env. 247, 149–156 (2017).
Lau, J. A. & Lennon, J. T. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl Acad. Sci. USA. 109, 14058–14062 (2012).
Gehring, C. A., Sthultz, C. M., Flores-Rentería, L., Whipple, A. V. & Whitham, T. G. Tree genetics defines fungal partner communities that may confer drought tolerance. Proc. Natl Acad. Sci. USA 114, 11169–11174 (2017).
Zhang, Y. et al. Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome. Microbiome 5, 97 (2017).
Knief, C. et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6, 1378–1390 (2012).
Jiménez Bremont, J. F. et al. Physiological and molecular implications of plant polyamine metabolism during biotic interactions. Front. Plant Sci. 5, 95 (2014).
Busk, P. K. & Lange, L. Classification of fungal and bacterial lytic polysaccharide monooxygenases. BMC Genomics 16, 368 (2015).
Trivedi, P., Anderson, I. C. & Singh, B. K. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol. 21, 641–651 (2013).
Jiang, X. et al. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME J. 12, 1443–1456 (2018).
Blair, P. M. et al. Exploration of the biosynthetic potential of the Populus microbiome. mSystems 3, e00045–18 (2018).
Sessitsch, A. et al. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant Microbe Interact. 25, 28–36 (2012).
Han, G. Z. Origin and evolution of the plant immune system. New Phytol. 222, 70–83 (2019).
Eitas, T. K. & Dangl, J. L. NB-LRR proteins: pairs, pieces, perception, partners, and pathways. Curr. Opin. Plant Biol. 13, 472–477 (2010).
Hardoim, P. R. et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).
McCann, H. C. et al. Origin and evolution of the kiwifruit canker pandemic. Genome Biol. Evol. 9, 932–944 (2017).
Berendsen, R. L. et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 12, 1496–1507 (2018).
Kwak, M. J. et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100–1109 (2018). This study demonstrates that the disease resistance traits of plant varieties are conferred by selective assembly of a native microbiota to rescue a plant from fungal invasion.
Mendes, L. W., Raaijmakers, J. M., de Hollander, M., Mendes, R. & Tsai, S. M. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME J. 12, 212–224 (2019).
Carrión, V. J. et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366, 606–612 (2019). This study demonstrates a microbiome-mediated, multitiered defence system against fungal pathogens, in which the first defence layer is formed by the rhizosphere microbiota; any subsequent attempt to colonize the plant root activates a second layer of defence through plant endophytes that produce antifungal compounds, including effectors, enzymes and antibiotics.
Helfrich, E. J. et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat. Microbiol. 3, 909–919 (2018).
Rutherford, S. T. & Bassler, B. L. Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb. Perspect. Med. 2, a012427 (2012).
Hartmann, A. & Schikora, A. Plant responses to bacterial quorum sensing molecules. Front. Plant Sci. 6, 643 (2015).
Mousa, W. K. et al. Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nat. Microbiol. 1, 16167 (2016).
Trivedi, P., Spann, T. & Wang, N. Isolation and characterization of beneficial bacteria associated with citrus roots in Florida. Microb. Ecol. 62, 324–336 (2011).
Chagas, F. O. et al. Chemical signaling involved in plant–microbe interactions. Chem. Soc. Rev. 47, 1652–1704 (2018).
Schmidt, R. et al. Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Sci. Rep. 7, 862 (2017).
Korenblum, E. et al. Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling. Proc. Natl Acad. Sci. USA 117, 3874–3883 (2020).
Russell, A. B., Peterson, S. B. & Mougous, J. D. Type VI secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol. 12, 137–148 (2014).
Bernal, P., Llamas, M. A., Filloux, A. & Type, V. I. Secretion systems in plant-associated bacteria. Environ. Microbiol. 201, 15–72 (2018).
Speare, L. et al. Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host. Proc. Natl Acad. Sci. USA 115, E8528–E8537 (2018).
Vorholt, J. A., Vogel, C., Carlström, C. I. & Mueller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155 (2019).
Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Ann. Rev. Microbiol. 73, 69–88 (2019).
Hestrin, R., Hammer, E. C., Mueller, C. W. & Lehmann, J. Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition. Commun. Biol. 2, 233 (2019).
Averill, C., Bhatnagar, J. M., Pearse, W. D. & Kivlin, S. N. Global imprint of mycorrhizal fungi on whole-plant nutrient economics. Proc. Natl Acad. Sci. USA 116, 23163–23168 (2019).
Lu, T. et al. Rhizosphere microorganisms can influence the timing of plant flowering. Microbiome 6, 231 (2018).
Bodenhausen, K. et al. Petunia- and Arabidopsis-specific root microbiota responses to phosphate supplementation. Phytobiomes J. 3, 112–124 (2019).
Almario, J. et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. Proc. Natl Acad. Sci. USA 114, E9403–E9412 (2017).
Hacquard, S. et al. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat. Commun. 7, 1–13 (2016).
Voges, M. J., Bai, Y., Schulze-Lefert, P. & Sattely, E. S. Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proc. Natl Acad. Sci. USA 116, 12558–12565 (2019). This study demonstrates that the production of secondary metabolites produced by plants under stress conditions acts as a signalling mechanism to sculpt the rhizosphere microbiome.
Stringlis, I. A. et al. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc. Natl Acad. Sci. USA 115, E5213–E5222 (2018).
Martínez-Medina, A., Van Wees, S. C. & Pieterse, C. M. Airborne signals from Trichoderma fungi stimulate iron uptake responses in roots resulting in priming of jasmonic acid-dependent defenses in shoots of Arabidopsis thaliana and Solanum lycopersicum. Plant Cell Env. 40, 2691–2705 (2017).
Penton, C. R. et al. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. PLoS ONE 9, e93893 (2014).
Cha, J. Y. et al. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10, 119–129 (2016).
Hol, W. G. et al. Non-random species loss in bacterial communities reduces antifungal volatile production. Ecology 96, 2042–2048 (2015).
Carrión, V. J. et al. Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. ISME J. 12, 2307–2321 (2018).
Chialva, M. et al. Native soils with their microbiotas elicit a state of alert in tomato plants. New Phytol. 220, 1296–1308 (2018).
Peralta, A. L., Sun, Y., McDaniel, M. D. & Lennon, J. T. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 9, e02235 (2018).
Kesten, C. et al. Pathogen-induced pH changes regulate the growth–defense balance of plants. EMBO J. 16, e101822550491 (2019).
Yuan, J. et al. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome 6, 56 (2018).
Hu, L. et al. Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Commun. 9, 2738 (2018).
Kong, H. G., Song, G. C. & Ryu, C. M. Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory. Environ. Microbiol. Rep. 11, 479–486 (2019).
Fitzpatrick, C. R., Mustafa, Z. & Viliunas, J. Soil microbes alter plant fitness under competition and drought. J. Evol. Biol. 32, 438–450 (2019).
Eida, A. A. et al. Desert plant bacteria reveal host influence and beneficial plant growth properties. PLoS ONE 13, e0208223 (2018).
Naylor, D. & Coleman-Derr, D. Drought stress and root-associated bacterial communities. Front. Plant Sci. 8, 2223 (2018).
Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl Acad. Sci. USA 115, E4284–E4293 (2018). Using a multi-‘omics’ approach, this study demonstrates selective enrichment of monoderms (bacteria with a thick cell wall) that possess transporters connected with specialized metabolites produced by plants under drought stress.
Timm, C. M. et al. Abiotic stresses shift belowground Populus-associated bacteria toward a core stress microbiome. mSystems 3, e00070-17 (2018).
Wagner, M. R. et al. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol. Lett. 17, 717–726 (2014).
Ravanbakhsh, M., Sasidharan, R., Voesenek, L. A., Kowalchuk, G. A. & Jousset, A. Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences. Microbiome 6, 52 (2018).
Giauque, H., Connor, E. W. & Hawkes, C. V. Endophyte traits relevant to stress tolerance, resource use and habitat of origin predict effects on host plants. New Phytol. 221, 2239–2249 (2019).
Kudjordjie, E. N., Sapkota, R., Steffensen, S. K., Fomsgaard, I. S. & Nicolaisen, M. Maize synthesized benzoxazinoids affect the host associated microbiome. Microbiome 7, 59 (2019).
Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470 (2018).
Huang, A. C. et al. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364, eaau6389 (2019).
McCann, H. C., Nahal, H., Thakur, S. & Guttman, D. S. Identification of innate immunity elicitors using molecular signatures of natural selection. Proc. Natl Acad. Sci. USA 109, 4215–4220 (2012).
Hacquard, S., Spaepen, S., Garrido-Oter, R. & Schulze-Lefert, P. Interplay between innate immunity and the plant microbiota. Ann. Rev. Phytopathol. 55, 565–589 (2017).
Chen, H. et al. One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation. PLoS ONE 14, e0211310 (2019).
Trivedi, P. et al. Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content. Environ. Microbiol. 19, 3070–3086 (2017).
Hartman, K. et al. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 6, 14 (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).
Source: Ecology - nature.com
