Driving factors of epiphytic bacterial communities: A review

Vorholt, 2012, Microbial life in the phyllosphere, Nat Rev Microbiol, 10, 828, 10.1038/nrmicro2910

Remus-Emsermann, 2014, Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization, Environ Microbiol, 16, 2329, 10.1111/1462-2920.12482

Leveau J. Microbial Communities in the Phyllosphere. In: Riederer M, Müller C, editors. Biology of the Plant Cuticle, vol. 23, Oxford, UK: Blackwell Publishing Ltd; 2006, p. 334–67.

Bai, 2015, Functional overlap of the Arabidopsis leaf and root microbiota, Nature, 528, 364, 10.1038/nature16192

Knief, 2010, Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere, ISME J, 4, 719, 10.1038/ismej.2010.9

Redford, 2010, The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves, Environ Microbiol, 12, 2885, 10.1111/j.1462-2920.2010.02258.x

Vogel, 2016, The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health, New Phytol, 212, 192, 10.1111/nph.14036

Vogel, 2012, 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, 10.1128/AEM.00639-12

Innerebner, 2011, Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system, Appl Environ Microbiol, 77, 3202, 10.1128/AEM.00133-11

Mendes, 2013, The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol Rev, 37, 634, 10.1111/1574-6976.12028

Berg, 2009, Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture, Appl Microbiol Biotechnol, 84, 11, 10.1007/s00253-009-2092-7

Stockwell, 2010, Control of fire blight by Pseudomonas fluorescens A506 and Pantoea vagans C9–1 applied as single strains and mixed inocula, Phytopathology, 100, 1330, 10.1094/PHYTO-03-10-0097

Pusey, 2011, Antibiosis activity of Pantoea agglomerans biocontrol strain E325 against Erwinia amylovora on apple flower stigmas, Phytopathology, 101, 1234, 10.1094/PHYTO-09-10-0253

Ritpitakphong, 2016, The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen, New Phytol, 210, 1033, 10.1111/nph.13808

Glover, 2000, Differentiation in plant epidermal cells, J Exp Bot, 51, 497, 10.1093/jexbot/51.344.497

Nadeau, 2002, Stomatal development in Arabidopsis, Arabidopsis Book, 1, 10.1199/tab.0066

Pillitteri, 2013, Stomatal development in Arabidopsis, Arabidopsis Book, 11, 10.1199/tab.0162

Werker, 2000, Trichome diversity and development, Adv Bot Res, 1

Zhao, 2016, A new function of plant trichomes, Nat Plants, 2, 10.1038/nplants.2016.96

Riederer, 2001, Protecting against water loss: analysis of the barrier properties of plant cuticles, J Exp Bot, 52, 2023, 10.1093/jexbot/52.363.2023

Schreiber L, Schönherr J. Water and solute permeability of plant cuticles: measurement and data analysis. Springer Science & Business Media; 2009.

Barthlott, 1997, Purity of the sacred lotus, or escape from contamination in biological surfaces, Planta, 202, 1, 10.1007/s004250050096

Sadler, 2016, Wax and cutin mutants of Arabidopsis: quantitative characterization of the cuticular transport barrier in relation to chemical composition, Biochim Biophys Acta, 1861, 1336, 10.1016/j.bbalip.2016.03.002

Monier, 2004, Frequency, size, and localization of bacterial aggregates on bean leaf surfaces, Appl Environ Microbiol, 70, 346, 10.1128/AEM.70.1.346-355.2004

Shiraishi, 2015, Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy, Sci Rep, 5, srep09719, 10.1038/srep09719

Esser, 201591, Spatial scales of interactions among bacteria and between bacteria and the leaf surface, FEMS Microbiol Ecol

Remus-Emsermann, 2012, Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere, ISME J, 6, 756, 10.1038/ismej.2011.209

Monier, 2003, Differential survival of solitary and aggregated bacterial cells promotes aggregate formation on leaf surfaces, Proc Natl Acad Sci USA, 100, 15977, 10.1073/pnas.2436560100

Morris, 1997, Methods for observing microbial biofilms directly on leaf surfaces and recovering them for isolation of culturable microorganisms, Appl Environ Microbiol, 63, 1570, 10.1128/AEM.63.4.1570-1576.1997

Brewer, 1991, Functional interaction between leaf trichomes, leaf wettability and the optical properties of water droplets, Plant Cell Environ, 14, 955, 10.1111/j.1365-3040.1991.tb00965.x

Burch, 2014, The hygroscopic biosurfactant syringafactin produced by Pseudomonas syringae enhances fitness on leaf surfaces during fluctuating humidity, Environ Microbiol, 16, 2086, 10.1111/1462-2920.12437

Schreiber, 2005, Polar paths of diffusion across plant cuticles: new evidence for an old hypothesis, Ann Bot, 95, 1069, 10.1093/aob/mci122

Schönherr, 2006, Characterization of aqueous pores in plant cuticles and permeation of ionic solutes, J Exp Bot, 57, 2471, 10.1093/jxb/erj217

Beattie, 2011, Water relations in the interaction of foliar bacterial pathogens with plants, Annu Rev Phytopathol, 49, 533, 10.1146/annurev-phyto-073009-114436

Schreiber, 2005, Plant-microbe interactions: identification of epiphytic bacteria and their ability to alter leaf surface permeability, New Phytol, 166, 589, 10.1111/j.1469-8137.2005.01343.x

Krimm, 2005, Epiphytic microorganisms on strawberry plants (Fragaria ananassa cv. Elsanta): identification of bacterial isolates and analysis of their interaction with leaf surfaces, FEMS Microbiol Ecol, 53, 483, 10.1016/j.femsec.2005.02.004

van der Wal, 2011, Modelling sugar diffusion across plant leaf cuticles: the effect of free water on substrate availability to phyllosphere bacteria, Environ Microbiol, 13, 792, 10.1111/j.1462-2920.2010.02382.x

Remus-Emsermann, 2013, Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R, Genome Announc, 1, 10.1128/genomeA.00036-13

Tecon, 2016, Symplasmata are a clonal, conditional, and reversible type of bacterial multicellularity, Sci Rep, 6, 31914, 10.1038/srep31914

Leveau, 2001, Appetite of an epiphyte: quantitative monitoring of bacterial sugar consumption in the phyllosphere, Proc Natl Acad Sci USA, 98, 3446, 10.1073/pnas.061629598

Remus-Emsermann, 2011, Quantification of lateral heterogeneity in carbohydrate permeability of isolated plant leaf cuticles, Front Microbiol, 2, 197

Ohshiro, 2016, Effects of soil types and fertilizers on growth, yield, and quality of edible Amaranthus tricolor lines in Okinawa, Japan, Plant Prod Sci, 19, 61, 10.1080/1343943X.2015.1128087

Quan M, Liang J. The influences of four types of soil on the growth, physiological and biochemical characteristics of Lycoris aurea (L’ Her.) Herb. Scientific Reports 2017;7. doi: 10.1038/srep43284.

Meiners, 2017, Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species, Oecologia, 183, 1155, 10.1007/s00442-017-3833-4

Agler, 2016, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS Biol, 14, 10.1371/journal.pbio.1002352

Remus-Emsermann, 2018, Phyllosphere microbiology: at the interface between microbial individuals and the plant host, New Phytol, 218, 1327, 10.1111/nph.15054

Delmotte, 2009, Community proteogenomics reveals insights into the physiology of phyllosphere bacteria, Proc Natl Acad Sci USA, 106, 16428, 10.1073/pnas.0905240106

Knief, 2012, Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice, ISME J, 6, 1378, 10.1038/ismej.2011.192

Bodenhausen, 2013, Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana, PLoS ONE, 8, 10.1371/journal.pone.0056329

Durand, 2018, Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: community characterization and isolation of Hg-resistant plant growth-promoting bacteria, Sci Total Environ, 622–623, 1165, 10.1016/j.scitotenv.2017.12.069

Levy, 2018, Genomic features of bacterial adaptation to plants, Nat Genet, 50, 138, 10.1038/s41588-017-0012-9

Lambais, 2017, Phyllosphere metaproteomes of trees from the Brazilian atlantic forest show high levels of functional redundancy, Microb Ecol, 73, 123, 10.1007/s00248-016-0878-6

Tecon, 2012, The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology, Environ Microbiol, 14, 1325, 10.1111/j.1462-2920.2012.02715.x

Franklin, 2007, Statistical analysis of spatial structure in microbial communities, The Spatial Distribution of Microbes in the Environment, 31, 10.1007/978-1-4020-6216-2_2

Tecon, 2018, Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces, Proc Natl Acad Sci USA, 115, 9791, 10.1073/pnas.1808274115

Monier, 2005, Spatial organization of dual-species bacterial aggregates on leaf surfaces, Appl Environ Microbiol, 71, 5484, 10.1128/AEM.71.9.5484-5493.2005

Vacher, 2016, The phyllosphere: microbial jungle at the plant-climate interface, Annu Rev Ecol Evol Syst, 47, 1, 10.1146/annurev-ecolsys-121415-032238

Nemergut, 2013, Patterns and processes of microbial community assembly, Microbiol Mol Biol Rev, 77, 342, 10.1128/MMBR.00051-12

Zhou J, Ning D. Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev 2017;81. doi: 10.1128/MMBR.00002-17.

Faust, 2012, Microbial interactions: from networks to models, Nat Rev Microbiol, 10, 538, 10.1038/nrmicro2832

Großkopf, 2014, Synthetic microbial communities, Curr Opin Microbiol, 18, 72, 10.1016/j.mib.2014.02.002

Freimoser, 2016, Tritagonist as a new term for uncharacterised microorganisms in environmental systems, ISME J, 10, 1, 10.1038/ismej.2015.92

Niu, 2017, Simplified and representative bacterial community of maize roots, Proc Natl Acad Sci USA, 114, E2450, 10.1073/pnas.1616148114

Suda, 2009, Powdery mildew-infection changes bacterial community composition in the phyllosphere, Microbes Environ, 24, 217, 10.1264/jsme2.ME09114

Koskella, 2014, Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities, FEMS Microbiol Rev, 38, 916, 10.1111/1574-6976.12072

Koskella, 2013, Phage-mediated selection on microbiota of a long-lived host, Curr Biol, 23, 1256, 10.1016/j.cub.2013.05.038

Morella, 2018, The impact of bacteriophages on phyllosphere bacterial abundance and composition, Mol Ecol, 27, 2025, 10.1111/mec.14542

Begon, 2010

Mercier, 2000, Role of leaf surface sugars in colonization of plants by bacterial epiphytes, Appl Environ Microbiol, 66, 369, 10.1128/AEM.66.1.369-374.2000

Zelezniak, 2015, Metabolic dependencies drive species co-occurrence in diverse microbial communities, Proc Natl Acad Sci USA, 112, 6449, 10.1073/pnas.1421834112

Freilich, 2011, Competitive and cooperative metabolic interactions in bacterial communities, Nat Commun, 2, 589, 10.1038/ncomms1597

Narwani, 2017, Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae, J Ecol, 105, 580, 10.1111/1365-2745.12759

Fukami, 2015, Historical contingency in community assembly: integrating niches, species pools, and priority effects, Annu Rev Ecol Evol Syst, 46, 1, 10.1146/annurev-ecolsys-110411-160340

Wilson, 1994, Ecological similarity and coexistence of epiphytic ice-nucleating (Ice+) pseudomonas syringae strains and a non-ice-nucleating (Ice-) biological control agent, Appl Environ Microbiol, 60, 3128, 10.1128/AEM.60.9.3128-3137.1994

Smith, 1982, Bias in estimating niche overlap, Ecology, 63, 1248, 10.2307/1938851

Laforest-Lapointe, 2016, Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species, PeerJ, 4, 10.7717/peerj.2367

Schlaeppi K, Dombrowski N, Oter RG, Ver Loren van Themaat E, Schulze-Lefert P. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA 2014;111:585–92.

Coleman-Derr, 2016, Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species, New Phytol, 209, 798, 10.1111/nph.13697

Wagner, 2016, Host genotype and age shape the leaf and root microbiomes of a wild perennial plant, Nat Commun, 7, 12151, 10.1038/ncomms12151

Horton, 2014, Genome-wide association study of Arabidopsis thaliana leaf microbial community, Nat Commun, 5, 5320, 10.1038/ncomms6320

Bodenhausen, 2014, A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota, PLoS Genet, 10, 10.1371/journal.pgen.1004283

Kembel, 2014, Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest, Proc Natl Acad Sci USA, 111, 13715, 10.1073/pnas.1216057111

Rastogi, 2012, Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce, ISME J, 6, 1812, 10.1038/ismej.2012.32

Copeland, 2015, Seasonal community succession of the phyllosphere microbiome, Mol Plant Microbe Interact, 28, 274, 10.1094/MPMI-10-14-0331-FI

Lebeis, 2015, Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa, Science, 349, 860, 10.1126/science.aaa8764

Boller, 2009, A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors, Annu Rev Plant Biol, 60, 379, 10.1146/annurev.arplant.57.032905.105346

Monaghan, 2012, Plant pattern recognition receptor complexes at the plasma membrane, Curr Opin Plant Biol, 15, 349, 10.1016/j.pbi.2012.05.006

Chinchilla, 2006, The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception, Plant Cell, 18, 465, 10.1105/tpc.105.036574

Zipfel, 2004, Bacterial disease resistance in Arabidopsis through flagellin perception, Nature, 428, 764, 10.1038/nature02485

Stringlis, 2018, Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists, Plant J, 93, 166, 10.1111/tpj.13741

Jones, 2006, The plant immune system, Nature, 444, 323, 10.1038/nature05286

Mukhtar, 2011, Independently evolved virulence effectors converge onto hubs in a plant immune system network, Science, 333, 596, 10.1126/science.1203659

Weßling, 2014, Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life, Cell Host Microbe, 16, 364, 10.1016/j.chom.2014.08.004

Bonardi, 2012, A new eye on NLR proteins: focused on clarity or diffused by complexity?, Curr Opin Immunol, 24, 41, 10.1016/j.coi.2011.12.006

Jacob, 2013, Evolution and conservation of plant NLR functions, Front Immunol, 4, 297, 10.3389/fimmu.2013.00297

Tsuda, 2009, Network properties of robust immunity in plants, PLoS Genet, 5, 10.1371/journal.pgen.1000772

Dong, 2015, Revealing shared and distinct gene network organization in Arabidopsis immune responses by integrative analysis, Plant Physiol, 167, 1186, 10.1104/pp.114.254292

Tsuda, 2010, Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity, Curr Opin Plant Biol, 13, 459, 10.1016/j.pbi.2010.04.006

Kim, 2014, Mechanisms underlying robustness and tunability in a plant immune signaling network, Cell Host Microbe, 15, 84, 10.1016/j.chom.2013.12.002

Glazebrook, 2005, Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens, Annu Rev Phytopathol, 43, 205, 10.1146/annurev.phyto.43.040204.135923

Ryffel, 2016, Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves, ISME J, 10, 632, 10.1038/ismej.2015.141

Badri, 2009, An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota, Plant Physiol, 151, 2006, 10.1104/pp.109.147462

Reisberg, 2013, Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves, PLoS ONE, 8, 10.1371/journal.pone.0078613

Yamada, 2016, Regulation of sugar transporter activity for antibacterial defense in Arabidopsis, Science, 354, 1427, 10.1126/science.aah5692

Chen, 2010, Sugar transporters for intercellular exchange and nutrition of pathogens, Nature, 468, 527, 10.1038/nature09606

Henry, 2013, Recognition of bacterial plant pathogens: local, systemic and transgenerational immunity, New Phytol, 199, 908, 10.1111/nph.12214

Melotto, 2006, Plant stomata function in innate immunity against bacterial invasion, Cell, 126, 969, 10.1016/j.cell.2006.06.054

Fu, 2013, Systemic acquired resistance: turning local infection into global defense, Annu Rev Plant Biol, 64, 839, 10.1146/annurev-arplant-042811-105606

Toyota, 2018, Glutamate triggers long-distance, calcium-based plant defense signaling, Science, 361, 1112, 10.1126/science.aat7744

Coker, 2015, Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting, Front Plant Sci, 6, 527, 10.3389/fpls.2015.00527

Karrer, 1995, In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries, Proc Natl Acad Sci USA, 92, 3814, 10.1073/pnas.92.9.3814

Guillaume-Gentil, 2016, Tunable single-cell extraction for molecular analyses, Cell, 166, 506, 10.1016/j.cell.2016.06.025

Kerk, 2003, Laser capture microdissection of cells from plant tissues, Plant Physiol, 132, 27, 10.1104/pp.102.018127

Gjetting, 2007, Single-cell transcript profiling of barley attacked by the powdery mildew fungus, Mol Plant Microbe Interact, 20, 235, 10.1094/MPMI-20-3-0235

Birnbaum, 2003, A gene expression map of the Arabidopsis root, Science, 302, 1956, 10.1126/science.1090022

Zhang, 2008, Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei, Plant

Deal, 2010, A simple method for gene expression and chromatin profiling of individual cell types within a tissue, Dev Cell, 18, 1030, 10.1016/j.devcel.2010.05.013

Doyle, 2008, Application of a translational profiling approach for the comparative analysis of CNS cell types, Cell, 135, 749, 10.1016/j.cell.2008.10.029

Ottesen, 2016, Using a control to better understand phyllosphere microbiota, PLoS one, 11, 10.1371/journal.pone.0163482

Doan, 2015, Artificial surfaces in phyllosphere microbiology, Phytopathology, 105, 1036, 10.1094/PHYTO-02-15-0050-RVW

Soffe R, Altenhuber N, Bernach M, Remus-Emsermann M, Nock V. Comparison of replica leaf surface materials for phyllosphere microbiology. engRxiv 2018. doi: 10.31224/osf.io/2pzrv.

Bernach, 2019, Micropatterning of hybrid PDMS for replica leaves, Jpn J Appl Phys, 10.7567/1347-4065/ab0498

Soffe R, Bernach M, Remus-Emsermann MNP, Nock V. PDMS Replica leaf surfaces for phyllosphere microbiology. bioRxiv 2018. doi: https://doi.org/10.1101/523985.