References
-
Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470–480 (2018).
-
McLaughlin, S., Zhalnina, K., Kosina, S., Northen, T. R. & Sasse, J. The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nat. Commun. 14, 1649 (2023).
-
Jansson, J. K., McClure, R. & Egbert, R. G. Soil microbiome engineering for sustainability in a changing environment. Nat. Biotechnol. 1–13, https://doi.org/10.1038/s41587-023-01932-3 (2023).
-
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).
-
Wang, N. R. et al. Commensal pseudomonas fluorescens strains protect arabidopsis from closely related pseudomonas pathogens in a colonization-dependent manner. mBio 13, e02892–21 (2022).
-
Acharya, S. M. et al. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME Commun. 3, 1–9 (2023).
-
Huang, A. C. et al. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364, eaau6389 (2019).
-
Levy, A. et al. Genomic features of bacterial adaptation to plants. Nat. Genet. 50, 138–150 (2018).
-
Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).
-
Lebeis, S. L. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).
-
Pieterse, C. M. J. et al. Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium. Plant Soil 461, 245–263 (2021).
-
Berendsen, R. L. et al. Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417. BMC Genomics 16, 539 (2015).
-
Van Wees, S. C., Van der Ent, S. & Pieterse, C. M. Plant immune responses triggered by beneficial microbes. Curr. Opin. Plant Biol. 11, 443–448 (2008).
-
Yu, K. et al. Rhizosphere-associated pseudomonas suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Curr. Biol. 29, 3913–3920.e4 (2019).
-
Cole, B. J. et al. Genome-wide identification of bacterial plant colonization genes. PLOS Biol. 15, e2002860 (2017).
-
Stringlis, I. A. et al. Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists. Plant J. 93, 166–180 (2018).
-
Bjornson, M., Pimprikar, P., Nürnberger, T. & Zipfel, C. The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity. Nat. Plants 7, 579–586 (2021).
-
Verbon, E. H. et al. Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions. Mol. Plant 16, 1160–1177 (2023).
-
Humphrys, M. S. et al. Simultaneous transcriptional profiling of bacteria and their host cells. PLOS One 8, e80597 (2013).
-
Marsh, J. W., Humphrys, M. S. & Myers, G. S. A. A laboratory methodology for dual RNA-sequencing of bacteria and their host cells in vitro. Front. Microbiol. 8, 1830(2017).
-
Westermann, A. J., Barquist, L. & Vogel, J. Resolving host–pathogen interactions by dual RNA-seq. PLOS Pathog 13, e1006033 (2017).
-
Donaldson, G. P. et al. Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nat. Microbiol. 5, 746–756 (2020).
-
Andrés-Barrao, C. et al. Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187–induced plant salt stress tolerance. Proc. Natl. Acad. Sci. 118, e2107417118 (2021).
-
Vannier, N. et al. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota. Nat. Commun. 14, 8274 (2023).
-
Kumar, N. et al. Efficient enrichment of bacterial mRNA from host-bacteria total RNA samples. Sci. Rep. 6, 34850 (2016).
-
Nobori, T. et al. Transcriptome landscape of a bacterial pathogen under plant immunity. Proc. Natl. Acad. Sci. 115, E3055–E3064 (2018).
-
Roux, B. et al. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J 77, 817–837 (2014).
-
Ma, Q., Bücking, H., Gonzalez Hernandez, J. L. & Subramanian, S. Single-cell RNA sequencing of plant-associated bacterial communities. Front. Microbiol. 10, 2452 (2019).
-
Johns, N. I. et al. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nat. Methods 15, 323–329 (2018).
-
Jones, E. M. et al. A scalable, multiplexed assay for decoding GPCR-ligand interactions with RNA sequencing. Cell Syst. 8, 254–260.e6 (2019).
-
Crook, N., Ferreiro, A., Condiotte, Z. & Dantas, G. Transcript barcoding illuminates the expression level of synthetic constructs in E. coli nissle residing in the mammalian gut. ACS Synth. Biol. 9, 1010–1021 (2020).
-
Jores, T. et al. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. Nat. Plants, https://doi.org/10.1038/s41477-021-00932-y (2021).
-
Wang, G. et al. CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria. Nat. Microbiol. 4, 2498–2510 (2019).
-
Wang, B. et al. CRAGE-duet facilitates modular assembly of biological systems for studying plant–microbe interactions. ACS Synth. Biol. 9, 2610–2615 (2020).
-
Cho, B.-K. et al. The transcription unit architecture of the Escherichia coli genome. Nat. Biotechnol. 27, 1043–1049 (2009).
-
Wurtzel, O. et al. The single-nucleotide resolution transcriptome of pseudomonas aeruginosa grown in body temperature. PLOS Pathog 8, e1002945 (2012).
-
Filiatrault, M. J. et al. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLOS ONE 6, e29335 (2011).
-
Salgado, H., Moreno-Hagelsieb, G., Smith, T. F. & Collado-Vides, J. Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. 97, 6652–6657 (2000).
-
Tjaden, B. A computational system for identifying operons based on RNA-seq data. Methods 176, 62–70 (2020).
-
Lugtenberg, B. J. J., Dekkers, L. & Bloemberg, G. V. Molecular determinants of rhizosphere colonization by pseudomonas. Annu. Rev. Phytopathol. 39, 461–490 (2001).
-
Muñoz-Elías, E. J. & McKinney, J. D. Carbon metabolism of intracellular bacteria. Cell. Microbiol. 8, 10–22 (2006).
-
Chen, H., Shiroguchi, K., Ge, H. & Xie, X. S. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol. Syst. Biol. 11, 781 (2015).
-
Waters, L. S. & Storz, G. Regulatory RNAs in bacteria. Cell 136, 615–628 (2009).
-
Winnen, B., Hvorup, R. N. & Saier, M. H. The tripartite tricarboxylate transporter (TTT) family. Res. Microbiol. 154, 457–465 (2003).
-
Brocker, M., Schaffer, S., Mack, C. & Bott, M. Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA. J. Bacteriol. 191, 3869 (2009).
-
Finkel, O. M. et al. A single bacterial genus maintains root growth in a complex microbiome. Nature 587, 103–108 (2020).
-
De Weger, L. A. et al. Flagella of a plant-growth-stimulating Pseudomonas fluorescens strain are required for colonization of potato roots. J. Bacteriol. 169, 2769–2773 (1987).
-
Sivakumar, R. et al. Evaluation of INSeq To Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization. G3 GenesGenomesGenetics 9, 651–661 (2019).
-
Pankievicz, V. C. S. et al. RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. Plant Mol. Biol. 90, 589–603 (2016).
-
Nobori, T. et al. Dissecting the cotranscriptome landscape of plants and their microbiota. EMBO Rep. 23, e55380 (2022).
-
WOJTASZEK, P. Oxidative burst: an early plant response to pathogen infection. Biochem. J. 322, 681–692 (1997).
-
Ebel, J. & Mithöfer, A. Early events in the elicitation of plant defence. Planta 206, 335–348 (1998).
-
Danhorn, T. & Fuqua, C. Biofilm formation by plant-associated bacteria. Annu. Rev. Microbiol. 61, 401–422 (2007).
-
Rudrappa, T., Biedrzycki, M. L. & Bais, H. P. Causes and consequences of plant-associated biofilms. FEMS Microbiol. Ecol. 64, 153–166 (2008).
-
Callewaert, L. et al. A new family of lysozyme inhibitors contributing to lysozyme tolerance in gram-negative bacteria. PLOS Pathog. 4, e1000019 (2008).
-
Yum, S. et al. Structural basis for the recognition of lysozyme by MliC, a periplasmic lysozyme inhibitor in Gram-negative bacteria. Biochem. Biophys. Res. Commun. 378, 244–248 (2009).
-
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
-
Liu, X. et al. Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis. eLife 3, e01990 (2014).
-
Eitzen, K., Sengupta, P., Kroll, S., Kemen, E. & Doehlemann, G. A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme. eLife 10, e65306 (2021).
-
Lee, K.-M. et al. A genetic screen reveals novel targets to render pseudomonas aeruginosa sensitive to lysozyme and cell wall-targeting antibiotics. Front. Cell. Infect. Microbiol. 7, 59 (2017).
-
Torrens, G. et al. Targeting the permeability barrier and peptidoglycan recycling pathways to disarm Pseudomonas aeruginosa against the innate immune system. PLOS One 12, e0181932 (2017).
-
Flores-Cruz, Z. & Allen, C. Ralstonia solanacearum encounters an oxidative environment during tomato infection. Mol. Plant Microbe Interactions 22, 773–782 (2009).
-
Phelan, J. P., Bourgeois, J. S., McCarthy, J. E. & Hu, L. T. A putative xanthine dehydrogenase is critical for Borrelia burgdorferi survival in ticks and mice. Microbiology 169, 001286 (2023).
-
Sasse, J. et al. Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon. Plant Direct 4, e00207 (2020).
-
Palluk, S. et al. De novo DNA synthesis using polymerase-nucleotide conjugates. Nat. Biotechnol. 36, 645–650 (2018).
-
Plesa, C., Sidore, A. M., Lubock, N. B., Zhang, D. & Kosuri, S. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science 359, 343–347 (2018).
-
Sharma, C. M. et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464, 250–255 (2010).
-
Adiconis, X. et al. Comprehensive comparative analysis of 5′-end RNA-sequencing methods. Nat. Methods 15, 505–511 (2018).
-
Yu, K. et al. Transcriptome signatures in Pseudomonas simiae WCS417 shed light on role of root-secreted coumarins in arabidopsis-mutualist communication. Microorganisms 9, 575 (2021).
-
Canarini, A., Kaiser, C., Merchant, A., Richter, A. & Wanek, W. Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli. Front. Plant Sci. 10, 157 (2019).
-
Gliese, N., Khodaverdi, V., Schobert, M. & Görisch, H. AgmR controls transcription of a regulon with several operons essential for ethanol oxidation in Pseudomonas aeruginosa ATCC 17933. Microbiology 150, 1851–1857 (2004).
-
Choi, O. et al. Pyrroloquinoline quinone is a plant growth promotion factor produced by Pseudomonas fluorescens B16. Plant Physiol. 146, 657–668 (2008).
-
Carreño-López, R., Alatorre-Cruz, J. M. & Marín-Cevada, V. Pyrroloquinoline quinone (PQQ): role in plant-microbe interactions. In Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms: Discovery and Applications (eds Singh, H. B., Keswani, C., Reddy, M. S., Sansinenea, E. & García-Estrada, C.) 169–184 (Springer, Singapore, 2019). https://doi.org/10.1007/978-981-13-5862-3_9.
-
Wang, X. et al. Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis. Nat. Metab. 1–14, https://doi.org/10.1038/s42255-024-01024-9 (2024).
-
Boo, A. et al. Synthetic microbe-to-plant communication channels. Nat. Commun. 15, 1817 (2024).
-
Pini, F. et al. Bacterial biosensors for in vivo spatiotemporal mapping of root secretion. Plant Physiol. 174, 1289–1306 (2017).
-
Haskett, T. L. et al. Engineered plant control of associative nitrogen fixation. Proc. Natl. Acad. Sci. 119, e2117465119 (2022).
-
Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).
-
Law, C. W. et al. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5, ISCB Comm J–1408 (2018).
-
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47–e47 (2015).
-
Chen, I.-M. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).
-
Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915 (2019).
-
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
