Boyd, L. A., Ridout, C., O’Sullivan, D. M., Leach, J. E. & Leung, H. Plant–pathogen interactions: disease resistance in modern agriculture. Trends Genet. 29, 233–240 (2013).
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA 112, E911–E920 (2015).
Bebber, D. P., Ramotowski, M. A. T. & Gurr, S. J. Crop pests and pathogens move polewards in a warming world. Nat. Clim. Change 3, 985–988 (2013).
Ham, J. H., Melanson, R. A. & Rush, M. C. Burkholderia glumae: next major pathogen of rice? Mol. Plant Pathol. 12, 329–339 (2011).
Naughton, L. M. et al. Functional and genomic insights into the pathogenesis of Burkholderia species to rice. Environ. Microbiol. 18, 780–790 (2016).
Liu, X. et al. Biotoxin tropolone contamination associated with nationwide occurrence of pathogen Burkholderia plantarii in agricultural environments in China. Environ. Sci. Technol. 52, 5105–5114 (2018).
Hautier, Y. et al. Anthropogenic environmental changes affect ecosystem stability via biodiversity. Science 348, 336–340 (2015).
Jung, B. et al. Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice. Nat. Commun. 9, 31 (2018).
Miyagawa, H., Ozaki, K. & Kimura, T. Pathogenicity of Pseudomonas glumae and P. plantarii to the ears and leaves of graminaceous plants. Bull. Chugoku Natl Agric. Exp. Stn 3, 31–43 (1988).
Wang, M., Hashimoto, M. & Hashidoko, Y. Carot-4-en-9,10-diol, a conidiation-inducing sesquiterpene diol produced by Trichoderma virens PS1-7 upon exposure to chemical stress from highly active iron chelators. Appl. Environ. Microbiol. 79, 1906–1914 (2013).
Wang, M., Hashimoto, M. & Hashidoko, Y. Repression of tropolone production and induction of a Burkholderia plantarii pseudo-biofilm by carot-4-en-9,10-diol, a cell-to-cell signaling disrupter produced by Trichoderma virens. PLoS ONE 8, e78024 (2013).
Leach, J. E., Triplett, L. R., Argueso, C. T. & Trivedi, P. Communication in the phytobiome. Cell 169, 587–596 (2017).
Wu, Y. et al. Policy distortions, farm size, and the overuse of agricultural chemicals in China. Proc. Natl Acad. Sci. USA 115, 7010–7015 (2018).
Chaparro, J. M., Badri, D. V. & Vivanco, J. M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790–803 (2014).
Derksen, H., Rampitsch, C. & Daayf, F. Signaling cross-talk in plant disease resistance. Plant Sci. 207, 79–87 (2013).
Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).
Wang, M. & Cernava, T. Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity. Environ. Sci. Ecotechnol. 4, 100061 (2020).
Cheng, Y. T., Zhang, L. & He, S. Y. Plant–microbe interactions facing environmental challenge. Cell Host Microbe 26, 183–192 (2019).
Berg, G., Grube, M., Schloter, M. & Smalla, K. Unraveling the plant microbiome: looking back and future perspectives. Front. Microbiol. 5, 148 (2014).
Duran, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983 (2018).
Turner, T. R., James, E. K. & Poole, P. S. The plant microbiome. Genome Biol. 14, 209 (2013).
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).
Kwak, M.-J. et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100 (2018).
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).
Haney, C. H., Samuel, B. S., Bush, J. & Ausubel, F. M. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat. Plants 1, 15051 (2015).
Liu, H., Brettell, L. E. & Singh, B. Linking the phyllosphere microbiome to plant health. Trends Plant Sci. 25, 841–844 (2020).
Fan, X. et al. Microenvironmental interplay predominated by beneficial Aspergillus abates fungal pathogen incidence in paddy environment. Environ. Sci. Technol. 53, 13042–13052 (2019).
Shade, A., Jacques, M. A. & Barret, M. Ecological patterns of seed microbiome diversity, transmission, and assembly. Curr. Opin. Microbiol. 37, 15–22 (2017).
Nelson, E. B. The seed microbiome: origins, interactions, and impacts. Plant Soil 422, 7–34 (2017).
Sultan, S. E. Phenotypic plasticity for plant development, function and life history. Trends Plant Sci. 5, 537–542 (2000).
Wang, M. et al. Indole-3-acetic acid produced by Burkholderia heleia acts as a phenylacetic acid antagonist to disrupt tropolone biosynthesis in Burkholderia plantarii. Sci. Rep. 6, 22596 (2016).
Miwa, S. et al. Identification of the three genes involved in controlling production of a phytotoxin tropolone in Burkholderia plantarii. J. Bacteriol. 198, 1604–1609 (2016).
Solis, R., Bertani, I., Degrassi, G., Devescovi, G. & Venturi, V. Involvement of quorum sensing and RpoS in rice seedling blight caused by Burkholderia plantarii. FEMS Microbiol. Lett. 259, 106–112 (2006).
Truyens, S., Weyens, N., Cuypers, A. & Vangronsveld, J. Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ. Microbiol. Rep. 7, 40–50 (2015).
Rybakova, D. et al. The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens. Microbiome 5, 104 (2017).
Bergna, A. et al. Tomato seeds preferably transmit plant beneficial endophytes. Phytobiomes J. 2, 183–193 (2018).
Wassermann, B., Cernava, T., Muller, H., Berg, C. & Berg, G. Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks. Microbiome 7, 108 (2019).
Berg, G. & Raaijmakers, J. M. Saving seed microbiomes. ISME J. 12, 1167–1170 (2018).
Kim, H., Nishiyama, M., Kunito, T. & Oyaizu, H. High population of Sphingomonas species on plant surface. J. Appl. Microbiol. 85, 731–736 (1998).
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Rochefort, A. et al. Influence of environment and host plant genotype on the structure and diversity of the Brassica napus seed microbiota. Phytobiomes J. 3, 326–336 (2019).
Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).
Kim, H., Lee, K. K., Jeon, J., Harris, W. A. & Lee, Y. H. Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed. Microbiome 8, 20 (2020).
Cordovez, V., Dini-Andreote, F., Carrion, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).
Banerjee, S., Schlaeppi, K. & van der Heijden, M. G. A. Keystone taxa as drivers of microbiome structure and functioning. Nat. Rev. Microbiol. 16, 567–576 (2018).
Thomas, F., Corre, E. & Cebron, A. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. ISME J. 13, 1814–1830 (2019).
Wang, H., Zhi, X. Y., Qiu, J., Shi, L. & Lu, Z. Characterization of a novel nicotine degradation gene cluster ndp in Sphingomonas melonis TY and its evolutionary analysis. Front. Microbiol. 8, 337 (2017).
Maeda, H. et al. A rice gene that confers broad-spectrum resistance to β-triketone herbicides. Science 365, 393 (2019).
Bakker, P., Pieterse, C. M. J., de Jonge, R. & Berendsen, R. L. The soil-borne legacy. Cell 172, 1178–1180 (2018).
Scholthof, K. B. The disease triangle: pathogens, the environment and society. Nat. Rev. Microbiol. 5, 152–156 (2007).
Barillot, C. D. C., Sarde, C. O., Bert, V., Tarnaud, E. & Cochet, N. A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system. Ann. Microbiol. 63, 471–476 (2013).
Maeda, Y. et al. Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences. Int. J. Syst. Evol. Microbiol. 56, 1031–1038 (2006).
Takeuchi, T., Sawada, H., Suzuki, F. & Matsuda, I. Specific detection of Burkolderia plantarii and B. glumae by PCR using primers selected from the 16S–23S rDNA spacer regions. Ann. Phytopath. Soc. Japan 63, 455–462 (1997).
Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).
Kusstatscher, P. et al. Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets. Microbiome 7, 112 (2019).
Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. & Dangl, J. L. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10, 999–1002 (2013).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).
Ayyagari, V. S. & Sreerama, K. Evaluation of haplotype diversity of Achatina fulica (Lissachatina) [Bowdich] from Indian sub-continent by means of 16S rDNA sequence and its phylogenetic relationships with other global populations. 3 Biotech 7, 252 (2017).
Lu, J. et al. Induced jasmonate signaling leads to contrasting effects on root damage and herbivore performance. Plant Physiol. 167, 1100–1116 (2015).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Anders, S., Pyl, P. T. & Huber, W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Deng, X., Zhou, Y., Zheng, W., Bai, L. & Zhou, X. Dissipation dynamic and final residues of oxadiargyl in paddy fields using high-performance liquid chromatography-tandem mass spectrometry coupled with modified QuEChERS method. Int. J. Environ. Res. Public Health 15, 1680 (2018).
Lang, Z. et al. Isolation and characterization of a quinclorac-degrading Actinobacteria Streptomyces sp. strain AH-B and its implication on microecology in contaminated soil. Chemosphere 199, 210–217 (2018).
Sun, M., Li, H. & Jaisi, D. P. Degradation of glyphosate and bioavailability of phosphorus derived from glyphosate in a soil–water system. Water Res. 163, 114840 (2019).
Source: Ecology - nature.com
