Brown, W. L. Jr. & Wilson, E. O. Character displacement. Syst. Biol. 5, 49–64 (1956).
Stuart, Y. E. & Losos, J. B. Ecological character displacement: glass half full or half empty? Trends Ecol. Evol. 28, 402–408 (2013).
Google Scholar
Schluter, D. & McPhail, J. D. Ecological character displacement and speciation in sticklebacks. Am. Nat. 140, 85–108 (1992).
Google Scholar
Tilman, D., May, R. M., Lehman, C. L. & Nowak, M. A. Habitat destruction and the extinction debt. Nature 371, 65–66 (1994).
Google Scholar
Ghoul, M. & Mitri, S. The ecology and evolution of microbial competition. Trends Microbiol. 24, 833–845 (2016).
Google Scholar
Pfennig, D. W., Rice, A. M. & Martin, R. A. Ecological opportunity and phenotypic plasticity interact to promote character displacement and species coexistence. Ecology 87, 769–779 (2006).
Google Scholar
Bruno, J. F., Stachowicz, J. J. & Bertness, M. D. Inclusion of facilitation into ecological theory. Trends Ecol. Evol. 18, 119–125 (2003).
Google Scholar
Day, T. & Young, K. A. Competitive and facilitative evolutionary diversification. Bioscience 54, 101–109 (2004).
Google Scholar
Stachowicz, J. J. Mutualism, facilitation, and the structure of ecological communities. Bioscience 51, 235–246 (2001).
Google Scholar
Stuart, Y. E., Inkpen, S. A., Hopkins, R. & Bolnick, D. I. Character displacement is a pattern: so, what causes it? Biol. J. Linn. Soc. 121, 711–715 (2017).
Google Scholar
Brockhurst, M. A., Hochberg, M. E., Bell, T. & Buckling, A. Character displacement promotes cooperation in bacterial biofilms. Curr. Biol. 16, 2030–2034 (2006).
Google Scholar
Ellis, C. N., Traverse, C. C., Mayo-Smith, L., Buskirk, S. W. & Cooper, V. S. Character displacement and the evolution of niche complementarity in a model biofilm community. Evolution 69, 283–293 (2015).
Google Scholar
Rainey, P. B., Buckling, A., Kassen, R. & Travisano, M. The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol. Evol. 15, 243–247 (2000).
Google Scholar
Turner, P. E., Souza, V. & Lenski, R. E. Tests of ecological mechanisms promoting the stable coexistence of two bacterial genotypes. Ecology 77, 2119–2129 (1996).
Google Scholar
Xavier, J. B. & Foster, K. R. Cooperation and conflict in microbial biofilms. Proc. Natl. Acad. Sci. USA 104, 876–881 (2007).
Google Scholar
Westeberhard, M. J. Phenotypic plasticity and the origins of diversity. Annu. Rev. Ecol. Evol. Syst. 20, 249–278 (1989).
Google Scholar
Turcotte, M. M. & Levine, J. M. Phenotypic plasticity and species coexistence. Trends Ecol. Evol. 31, 803–813 (2016).
Google Scholar
Pfennig, D. W. & Pfennig, K. S. Development and evolution of character displacement. Ann NY Acad Sci. 1256, 89–107 (2012).
Google Scholar
Finkel, O. M., Castrillo, G., Herrera Paredes, S., Salas Gonzalez, I. & Dangl, J. L. Understanding and exploiting plant beneficial microbes. Curr. Opin. Plant Biol. 38, 155–163 (2017).
Google Scholar
Muller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The plant microbiota: systems-level insights and perspectives. Annu. Rev. Genet. 50, 211–234 (2016).
Google Scholar
Schlaeppi, K. & Bulgarelli, D. The plant microbiome at work. Mol. Plant Microbe Interact. 28, 212–217 (2015).
Google Scholar
Leveau, J. H. & Lindow, S. E. Appetite of an epiphyte: quantitative monitoring of bacterial sugar consumption in the phyllosphere. Proc. Natl. Acad. Sci. USA 98, 3446–3453 (2001).
Google Scholar
Lindow, S. E. & Leveau, J. H. Phyllosphere microbiology. Curr. Opin. Biotechnol. 13, 238–243 (2002).
Google Scholar
Meyer, K. M. & Leveau, J. H. Microbiology of the phyllosphere: a playground for testing ecological concepts. Oecologia 168, 621–629 (2012).
Google Scholar
Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA 106, 16428–16433 (2009).
Google Scholar
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).
Google Scholar
Carlstrom, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Google Scholar
Vorholt, J. A., Vogel, C., Carlstrom, C. I. & Müller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe. 22, 142–155 (2017).
Google Scholar
Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).
Google Scholar
Bodenhausen, N., Horton, M. W. & Bergelson, J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE 8, e56329 (2013).
Google Scholar
Horton, M. W. et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat. Commun. 5, 5320 (2014).
Google Scholar
Roman-Reyna, V. et al. Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project. Rice (NY) 13, 72 (2020).
Google Scholar
Zarraonaindia, I. et al. The soil microbiome influences grapevine-associated microbiota. mBio. 6, e02527–14 (2015).
Google Scholar
Laforest-Lapointe, I. & Whitaker, B. K. Decrypting the phyllosphere microbiota: progress and challenges. Am. J. Bot. 106, 171–173 (2019).
Google Scholar
Baldotto, L. E. B. & Olivares, F. L. Phylloepiphytic interaction between bacteria and different plant species in a tropical agricultural system. Can. J. Microbiol. 54, 918–931 (2008).
Google Scholar
Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003).
Google Scholar
Monier, J. M. & Lindow, S. E. Differential survival of solitary and aggregated bacterial cells promotes aggregate formation on leaf surfaces. Proc. Natl. Acad. Sci. USA 100, 15977–15982 (2003).
Google Scholar
Monier, J. M. & Lindow, S. E. Frequency, size, and localization of bacterial aggregates on bean leaf surfaces. Appl. Environ. Microbiol. 70, 346–355 (2004).
Google Scholar
Morris, C. E., Monier, J. M. & Jacques, M. A. A technique To quantify the population size and composition of the biofilm component in communities of bacteria in the phyllosphere. Appl. Environ. Microbiol. 64, 4789–4795 (1998).
Google Scholar
Remus-Emsermann, M. N. P. et al. Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization. Environ. Microbiol. 16, 2329–2340 (2014).
Google Scholar
Remus-Emsermann, M. N. P. & Schlechter, R. O. Phyllosphere microbiology: at the interface between microbial individuals and the plant host. New Phytol. 218, 1327–1333 (2018).
Google Scholar
Gourion, B., Rossignol, M. & Vorholt, J. A. A proteomic study of Methylobacterium extorquens reveals a response regulator essential for epiphytic growth. Proc. Natl. Acad. Sci. USA 103, 13186–13191 (2006).
Google Scholar
Jacobs, J. L., Carroll, T. L. & Sundin, G. W. The role of pigmentation, ultraviolet radiation tolerance, and leaf colonization strategies in the epiphytic survival of phyllosphere bacteria. Microb. Ecol. 49, 104–113 (2005).
Google Scholar
Müller, D. B., Schubert, O. T., Rost, H., Aebersold, R. & Vorholt, J. A. Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization. Mol. Cell. Proteom. 15, 3256–3269 (2016).
Google Scholar
Ochsner, A. M. et al. Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol. Microbiol. 111, 1152–1166 (2019).
Google Scholar
Helmann, T. C., Deutschbauer, A. M. & Lindow, S. E. Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast. Proc. Natl. Acad. Sci. USA 116, 18900–18910 (2019).
Google Scholar
Nobori, T. et al. Transcriptome landscape of a bacterial pathogen under plant immunity. Proc. Natl. Acad. Sci. USA 115, E3055–E3064 (2018).
Google Scholar
Pulawska, J. et al. Transcriptome analysis of Xanthomonas fragariae in strawberry leaves. Sci. Rep. 10, 20582 (2020).
Knief, C. et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6, 1378–1390 (2012).
Google Scholar
Innerebner, G., Knief, C. & Vorholt, J. A. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77, 3202–3210 (2011).
Google Scholar
Vogel, C., Innerebner, G., Zingg, J., Guder, J. & Vorholt, J. A. Forward genetic in planta screen for identification of plant-protective traits of Sphingomonas sp Strain Fr1 against Pseudomonas syringae DC3000. Appl. Environ. Microbiol. 78, 5529–5535 (2012).
Google Scholar
Ryffel, F. et al. Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves. ISME J. 10, 632–643 (2016).
Google Scholar
Vogel, C. M., Potthoff, D. B., Schafer, M., Barandun, N. & Vorholt, J. A. Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen. Nat. Microbiol. 6, 1537–1548 (2021).
Google Scholar
Pfeilmeier, S. et al. The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nat. Microbiol. 6, 852–864 (2021).
Google Scholar
Maier, B. A. et al. A general non-self response as part of plant immunity. Nat. Plants 7, 696–705 (2021).
Google Scholar
Breton, C., Snajdrova, L., Jeanneau, C., Koca, J. & Imberty, A. Structures and mechanisms of glycosyltransferases. Glycobiology 16, 29r–37r (2006).
Google Scholar
Tao, F., Swarup, S. & Zhang, L. H. Quorum sensing modulation of a putative glycosyltransferase gene cluster essential for Xanthomonas campestris biofilm formation. Environ. Microbiol. 12, 3159–3170 (2010).
Google Scholar
Zhou, M. X., Zhu, F., Dong, S. L., Pritchard, D. G. & Wu, H. A novel glucosyltransferase is required for glycosylation of a serine-rich adhesin and biofilm formation by Streptococcus parasanguinis. J. Biol. Chem. 285, 12140–12148 (2010).
Google Scholar
Becker, A. et al. Regulation of succinoglycan and galactoglucan biosynthesis in Sinorhizobium meliloti. J. Mol. Microbiol. Biotechnol. 4, 187–190 (2002).
Google Scholar
Halder, U., Banerjee, A. & Bandopadhyay, R. Structural and functional properties, biosynthesis, and patenting trends of bacterial succinoglycan: a review. Indian J. Microbiol. 57, 278–284 (2017).
Google Scholar
Niehaus, K. & Becker, A. The role of microbial surface polysaccharides in the Rhizobium-legume interaction. Sub-Cell. Biochem. 29, 73–116 (1998).
Google Scholar
Ellis, H. R. Mechanism for sulfur acquisition by the alkanesulfonate monooxygenase system. Bioorg. Chem. 39, 178–184 (2011).
Google Scholar
Marco, M. L., Legac, J. & Lindow, S. E. Pseudomonas syringae genes induced during colonization of leaf surfaces. Environ. Microbiol. 7, 1379–1391 (2005).
Google Scholar
Yu, X. L. et al. Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites. Proc. Natl. Acad. Sci. USA 110, E425–E434 (2013).
Google Scholar
Cai, S. J. & Inouye, M. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J. Biol. Chem. 277, 24155–24161 (2002).
Google Scholar
Freeman, B. C. et al. Physiological and transcriptional responses to osmotic stress of two Pseudomonas syringae strains that differ in epiphytic fitness and osmotolerance. J. Bacteriol. 195, 4742–4752 (2013).
Google Scholar
Scheublin, T. R. et al. Transcriptional profiling of gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds. Environ. Microbiol. 16, 2212–2225 (2014).
Google Scholar
Felix, G., Duran, J. D., Volko, S. & Boller, T. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J. 18, 265–276 (1999).
Google Scholar
Macho, A. P. & Zipfel, C. Plant PRRs and the activation of innate immune signaling. Mol. Cell 54, 263–272 (2014).
Google Scholar
Hopsu-Havu, V. K. & Glenner, G. G. A new dipeptide naphthylamidase hydrolyzing glycyl-prolyl-beta-naphthylamide. Histochemie 7, 197–201 (1966).
Google Scholar
Kavi Kishor, P. B., Hima Kumari, P., Sunita, M. S. & Sreenivasulu, N. Role of proline in cell wall synthesis and plant development and its implications in plant ontogeny. Front. Plant Sci. 6, 544 (2015).
Google Scholar
Chipperfield, J. R. & Ratledge, C. Salicylic acid is not a bacterial siderophore: a theoretical study. Biometals 13, 165–168 (2000).
Google Scholar
Visca, P., Ciervo, A., Sanfilippo, V. & Orsi, N. Iron-regulated salicylate synthesis by Pseudomonas Spp. J. Gen. Microbiol. 139, 1995–2001 (1993).
Google Scholar
Seifert, G. J., Barber, C., Wells, B., Dolan, L. & Roberts, K. Galactose biosynthesis in Arabidopsis: genetic evidence for substrate channeling from UDP-D-galactose into cell wall polymers. Curr. Biol. 12, 1840–1845 (2002).
Google Scholar
Zablackis, E., Huang, J., Muller, B., Darvill, A. G. & Albersheim, P. Characterization of the cell-wall polysaccharides of Arabidopsis thaliana leaves. Plant Physiol. 107, 1129–1138 (1995).
Google Scholar
Santos-Beneit, F. The Pho regulon: a huge regulatory network in bacteria. Front. Microbiol. 6, 402 (2015).
Google Scholar
Mortimer, J. C. et al. An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14. Plant J. 83, 413–426 (2015).
Google Scholar
Honer Zu Bentrup, K., Miczak, A., Swenson, D. L. & Russell, D. G. Characterization of activity and expression of isocitrate lyase in Mycobacterium avium and Mycobacterium tuberculosis. J. Bacteriol. 181, 7161–7167 (1999).
Google Scholar
Reinscheid, D. J., Eikmanns, B. J. & Sahm, H. Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme. J. Bacteriol. 176, 3474–3483 (1994).
Google Scholar
Groisman, E. A., Chiao, E., Lipps, C. J. & Heffron, F. Salmonella typhimurium phoP virulence gene is a transcriptional regulator. Proc. Natl. Acad. Sci. USA 86, 7077–7081 (1989).
Google Scholar
Lamarche, M. G., Wanner, B. L., Crepin, S. & Harel, J. The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis. FEMS Microbiol. Rev. 32, 461–473 (2008).
Google Scholar
Jameson, G. N., Cosper, M. M., Hernandez, H. L., Johnson, M. K. & Huynh, B. H. Role of the [2Fe-2S] cluster in recombinant Escherichia coli biotin synthase. Biochemistry 43, 2022–2031 (2004).
Sirithanakorn, C. & Cronan, J. E. Biotin, a universal and essential cofactor: synthesis, ligation and regulation. FEMS Microbiol. Rev. 45, fuab003 (2021).
Google Scholar
Choi-Rhee, E. & Cronan, J. E. Biotin synthase is catalytic in vivo, but catalysis engenders destruction of the protein. Chem. Biol. 12, 461–468 (2005).
Google Scholar
Wilmes, P. et al. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2, 853–864 (2008).
Google Scholar
Beier, S., Rivers, A. R., Moran, M. A. & Obernosterer, I. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures. ISME J. 9, 1141–1151 (2015).
Google Scholar
Kim, H. et al. High population of Sphingomonas species on plant surface. J. Appl. Microbiol. 85, 731–736 (1998).
Google Scholar
Singh, P., Santoni, S., Weber, A., This, P. & Peros, J. P. Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures. Sci. Rep. 9, 14294 (2019).
Kosma, D. K. et al. The impact of water deficiency on leaf cuticle lipids of Arabidopsis. Plant Physiol. 151, 1918–1929 (2009).
Google Scholar
Piffeteau, A. & Gaudry, M. Biotin uptake: influx, efflux and countertransport in Escherichia coli K12. Biochim. Biophys. Acta 816, 77–82 (1985).
Google Scholar
D’Souza, G. et al. Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria. Evolution 68, 2559–2570 (2014).
Google Scholar
Hassani, M. A., Duran, P. & Hacquard, S. Microbial interactions within the plant holobiont. Microbiome 6, 58 (2018).
Google Scholar
Mas, A., Jamshidi, S., Lagadeuc, Y., Eveillard, D. & Vandenkoornhuyse, P. Beyond the black queen hypothesis. ISME J. 10, 2085–2091 (2016).
Google Scholar
Morris, B. E., Henneberger, R., Huber, H. & Moissl-Eichinger, C. Microbial syntrophy: interaction for the common good. FEMS Microbiol. Rev. 37, 384–406 (2013).
Google Scholar
Pacheco, A. R., Moel, M. & Segre, D. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat. Commun. 10, 103 (2019).
Google Scholar
Pande, S. et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J. 8, 953–962 (2014).
Google Scholar
Joyner, D. C. & Lindow, S. E. Heterogeneity of iron bioavailability on plants assessed with a whole-cell GFP-based bacterial biosensor. Microbiol. 146, 2435–2445 (2000).
Google Scholar
Remus-Emsermann, M. N., de Oliveira, S., Schreiber, L. & Leveau, J. H. Quantification of lateral heterogeneity in carbohydrate permeability of isolated plant leaf cuticles. Front. Microbiol. 2, 197 (2011).
Google Scholar
Remus-Emsermann, M. N. P., Tecon, R., Kowalchuk, G. A. & Leveau, J. H. J. Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere. ISME J. 6, 756–765 (2012).
Google Scholar
Peredo, E. L. & Simmons, S. L. Leaf-FISH: microscale imaging of bacterial taxa on phyllosphere. Front. Microbiol. 8, 2669 (2018).
Dar, D., Dar, N., Cai, L. & Newman, D. K. Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. Science 373, eabi4882 (2021).
Google Scholar
Ledermann, R., Strebel, S., Kampik, C. & Fischer, H. M. Versatile vectors for efficient mutagenesis of Bradyrhizobium diazoefficiens and other alphaproteobacteria. Appl. Environ. Microbiol. 82, 2791–2799 (2016).
Google Scholar
Roux, M. et al. The Arabidopsis leucine-rich repeat receptor-like kinases BAK1/SERK3 and BKK1/SERK4 are required for innate immunity to hemibiotrophic and biotrophic pathogens. Plant Cell 23, 2440–2455 (2011).
Google Scholar
Staswick, P. E., Tiryaki, I. & Rowe, M. L. Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation. Plant Cell 14, 1405–1415 (2002).
Google Scholar
Torres, M. A., Dangl, J. L. & Jones, J. D. Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response. Proc. Natl. Acad. Sci. USA 99, 517–522 (2002).
Google Scholar
Cao, H., Glazebrook, J., Clarke, J. D., Volko, S. & Dong, X. The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 88, 57–63 (1997).
Google Scholar
Schlesier, B., Breton, F. & Mock, H. P. A hydroponic culture system for growing Arabidopsis thaliana plantlets under sterile conditions. Plant Mol. Biol. Rep. 21, 449–456 (2003).
Google Scholar
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Google Scholar
Hemmerle, L., Ochsner, A. M., Vonderach, T., Hattendorf, B. & Vorholt, J. A. Mass spectrometry-based approaches to study lanthanides and lanthanide-dependent proteins in the phyllosphere. Methods Enzymol. 650, 215–236 (2021).
Google Scholar
Uhrig, R. G. et al. Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome. Plant Cell Environ. 44, 821–841 (2021).
Google Scholar
Davis, J. J. et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res. 48, D606–D612 (2020).
Google Scholar
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016).
Google Scholar
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).
Google Scholar
Source: Ecology - nature.com