Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).
Google Scholar
Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu Rev. Plant Biol. 64, 807–838 (2013).
Google Scholar
Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).
Google Scholar
Venturelli, O. S. et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol. Syst. Biol. 14, e8157 (2018).
Google Scholar
Foster, K. R. & Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845–1850 (2012).
Google Scholar
Helfrich, E. J. N. et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat. Microbiol. 3, 909–919 (2018).
Google Scholar
Coyte, K. Z. & Rakoff-Nahoum, S. Understanding competition and cooperation within the mammalian gut microbiome. Curr. Biol. 29, 538–544 (2019).
Google Scholar
Turner, T. R. et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J. 7, 2248–2258 (2013).
Google Scholar
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).
Google Scholar
Müller, 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
Lugtenberg, B. & Kamilova, F. Plant-growth-promoting Rhizobacteria. Annu. Rev. Microbiol. 63, 541–556 (2009).
Google Scholar
Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (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
Shekhawat, K. et al. Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci. EMBO Rep. 22, e51049 (2021).
Google Scholar
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).
Google Scholar
Bodenhausen, N., Bortfeld-Miller, M., Ackermann, M. & Vorholt, J. A. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10, e1004283 (2014).
Google Scholar
Reisberg, E. E., Hildebrandt, U., Riederer, M. & Hentschel, U. Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves. PLoS ONE 8, e78613 (2013).
Google Scholar
Kniskern, J. M., Traw, M. B. & Bergelson, J. Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol. Plant Microbe Interact. 20, 1512–1522 (2007).
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
Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).
Google Scholar
Hassani, M. A., Duran, P. & Hacquard, S. Microbial interactions within the plant holobiont. Microbiome 6, 58 (2018).
Google Scholar
Lidicker, W. Z. Clarification of interactions in ecological systems. Bioscience 29, 475–477 (1979).
Google Scholar
Schlechter, R. O., Miebach, M. & Remus-Emsermann, M. N. P. Driving factors of epiphytic bacterial communities: a review. J. Adv. Res. 19, 57–65 (2019).
Google Scholar
Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).
Google Scholar
Grosskopf, T. & Soyer, O. S. Synthetic microbial communities. Curr. Opin. Microbiol. 18, 72–77 (2014).
Google Scholar
Blair, P. M. et al. Exploration of the biosynthetic potential of the Populus microbiome. mSystems 3, e00045-00018 (2018).
Google Scholar
Suda, W., Nagasaki, A. & Shishido, M. Powdery mildew-infection changes bacterial community composition in the phyllosphere. Microbes Environ. 24, 217–223 (2009).
Google Scholar
Manching, H. C., Balint-Kurti, P. J. & Stapleton, A. E. Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization. Front. Plant Sci. 5, 403 (2014).
Google Scholar
Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, 100235 (2016).
Google Scholar
Layeghifard, M., Hwang, D. M. & Guttman, D. S. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol. 25, 217–228 (2017).
Google Scholar
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
Google Scholar
Carr, A., Diener, C., Baliga, N. S. & Gibbons, S. M. Use and abuse of correlation analyses in microbial ecology. ISME J. 13, 2647–2655 (2019).
Google Scholar
Vorholt, J. A., Vogel, C., Carlström, 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
Knief, C., Frances, L. & Vorholt, J. A. Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb. Ecol. 60, 440–452 (2010).
Google Scholar
Fan, J., Crooks, C. & Lamb, C. High-throughput quantitative luminescence assay of the growth in planta of Pseudomonas syringae chromosomally tagged with Photorhabdus luminescens luxCDABE. Plant J. 53, 393–399 (2008).
Google Scholar
Carlström, 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
Vogel, C. M., Potthoff, D. M., Schäfer, 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
Chen, I.-M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, 751–763 (2020).
Google Scholar
Ortiz, A., Vega, N. M., Ratzke, C. & Gore, J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. ISME J. 15, 2131–2145 (2021).
Google Scholar
Goberna, M. & Verdú, M. Predicting microbial traits with phylogenies. ISME J. 10, 959–967 (2016).
Google Scholar
Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).
Google Scholar
Cahill, J. F., Kembel, S. W., Lamb, E. G. & Keddy, P. A. Does phylogenetic relatedness influence the strength of competition among vascular plants? Perspect. Plant Ecol. 10, 41–50 (2008).
Google Scholar
Maherali, H. & Klironomos, J. N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746–1748 (2007).
Google Scholar
Duncan, R. P. & Williams, P. A. Ecology – Darwin’s naturalization hypothesis challenged. Nature 417, 608–609 (2002).
Google Scholar
Slingsby, J. A. & Verboom, G. A. Phylogenetic relatedness limits co-occurrence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa. Am. Nat. 168, 14–27 (2006).
Google Scholar
Mayfield, M. M. & Levine, J. M. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett. 13, 1085–1093 (2010).
Google Scholar
Teixeira, P. J. P. L., Colaianni, N. R., Fitzpatrick, C. R. & Dangl, J. L. Beyond pathogens: microbiota interactions with the plant immune system. Curr. Opin. Microbiol. 49, 7–17 (2019).
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
Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 0109 (2017).
Google Scholar
Kehe, J. et al. Positive interactions are common among culturable bacteria. Sci. Adv. 7, eabi7159 (2021).
Google Scholar
Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003).
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
Billick, I. & Case, T. J. Higher-order interactions in ecological communities – what are they and how can they be detected. Ecology 75, 1529–1543 (1994).
Google Scholar
Grilli, J., Barabas, G., Michalska-Smith, M. J. & Allesina, S. Higher-order interactions stabilize dynamics in competitive network models. Nature 548, 210–213 (2017).
Google Scholar
Levine, J. M., Bascompte, J., Adler, P. B. & Allesina, S. Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546, 56–64 (2017).
Google Scholar
Sundarraman, D. et al. Higher-order interactions dampen pairwise competition in the zebrafish gut microbiome. mBio 11, e01667-20 (2020).
Google Scholar
Morris, C. in Encyclopedia for Life Sciences (National Publishing Group, 2002).
Raaijmakers, J. M. & Mazzola, M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu. Rev. Phytopathol. 50, 403–424 (2012).
Google Scholar
Iversen, O. J. & Grov, A. Studies on lysostaphin – separation and characterization of 3 enzymes. Eur. J. Biochem. 38, 293–300 (1973).
Google Scholar
Recsei, P. A., Gruss, A. D. & Novick, R. P. Cloning, sequence, and expression of the lysostaphin gene from Staphylococcus simulans. Proc. Natl Acad. Sci. USA 84, 1127–1131 (1987).
Google Scholar
Kessler, E., Safrin, M., Abrams, W. R., Rosenbloom, J. & Ohman, D. E. Inhibitors and specificity of Pseudomonas aeruginosa LasA. J. Biol. Chem. 272, 9884–9889 (1997).
Google Scholar
Trayer, H. R. & Buckley, C. E. Molecular properties of lysostaphin, a bacteriolytic agent specific for Staphylococcus aureus. J. Biol. Chem. 245, 4842–4846 (1970).
Google Scholar
Heymer, B. & Schmidt, W. C. Purification and characterization of a Streptomyces albus endo-N-acetylmuramidase lytic for group A and other beta hemolytic streptococci. Microbios 12, 51–66 (1975).
Google Scholar
Vollmer, W., Joris, B., Charlier, P. & Foster, S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol. Rev. 32, 259–286 (2008).
Google Scholar
Peyraud, R. et al. Demonstration of the ethylmalonyl-CoA pathway by using C-13 metabolomics. Proc. Natl Acad. Sci. USA 106, 4846–4851 (2009).
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
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
Google Scholar
Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Google Scholar
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).
Google Scholar
Integrated Development Environment for R (R Studio, 2020).
R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).
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).
Google Scholar
Oksanen, J. et al. vegan: Community Ecology Package. R package v. 2.5-7 (2020).
Armenteros, J. J. A. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).
Google Scholar
Gasteiger, E. et al. in The Proteomics Protocols Handbook 571–607 (ed Walker, J. M.) (Humana Press, 2005).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Google Scholar
Bushnell, B. BBMap short read aligner, and other bioinformatic tools (SourceForge, version 38.87); https://sourceforge.net/projects/bbmap
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).
Google Scholar
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Google Scholar
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Google Scholar
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
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