The phyllosphere microbiome shifts toward combating melanose pathogen

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: April 2, 2022

Plants can recruit beneficial microbes to enhance their ability defend against pathogens. However, in contrast the intensively studied roles of rhizosphere microbiome suppressing plant pathogens, collective community-level change and effect phyllosphere response pathogen invasion remains largely elusive.Here, we integrated 16S metabarcoding, shotgun metagenomics culture-dependent methods systematically investigate changes between infected uninfected citrus leaves by Diaporthe citri, a fungal causing melanose disease worldwide. Multiple features suggested shift upon D. citri infection, highlighted marked reduction community evenness, emergence large numbers new microbes, intense microbial network. We also identified from functional perspectives leaves, such as enriched functions for iron competition potential antifungal traits, with genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated could positively affect performance under challenge, reductions index ranging 65.7 88.4%. Among them, Pantoea asv90 Methylobacterium asv41 "recruited microbes" exhibited antagonistic activities both vitro vivo, including inhibition spore germination and/or mycelium growth. Sphingomonas spp. presented characteristics were found be main contributor enrichment complex outer membrane receptor protein leaves. Moreover, asv20 showed stronger suppression iron-deficient conditions than iron-sufficient conditions, suggesting role during action.Overall, our study revealed how microbiomes differed pathogen, mechanisms observed might have helped plants cope pressure. Our findings provide novel insights into understanding responses challenge. Video abstract.

Language: Английский

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A phage tail–like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria

Science, Journal Year: 2024, Volume and Issue: 384(6701)

Published: June 13, 2024

Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in killing activity, although there is limited evidence that this specificity drives bacterial population dynamics. Here, we identified intact phage and derived a metapopulation of wild plant-associated Pseudomonas genomes. We discovered the most abundant viral cluster encodes remnant resembling tail called tailocin, which bacteria have co-opted competitors. Each pathogenic carries one few distinct tailocin variants target variable polysaccharides outer membrane co-occurring strains. Analysis herbarium samples from past 170 years revealed same receptor persisted populations. These results suggest genetic diversity be mined develop targeted "tailocin cocktails" for microbial control.

Language: Английский

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The Leaf Microbiome of Arabidopsis Displays Reproducible Dynamics and Patterns throughout the Growing Season

mBio, Journal Year: 2022, Volume and Issue: 13(3)

Published: April 14, 2022

Leaves are primarily responsible for the plant's photosynthetic activity. Thus, changes in leaf microbiota, which includes deleterious and beneficial microbes, can have far-reaching effects on plant fitness productivity. Identifying processes microorganisms that drive these over a lifetime is, therefore, crucial. In this study, we analyzed temporal dynamics microbiome of Arabidopsis thaliana, integrating both composition microbe-microbe interactions via study microbial networks. Field-grown

Language: Английский

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Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(9), P. 2280 - 2289

Published: June 29, 2022

Leaf microbiomes play crucial roles in plant health, making it important to understand the origins and functional relevance of their diversity. High strain-level leaf bacterial genetic diversity is known be relevant for interactions with hosts, but little about its multitude diverse co-colonizing microorganisms. In leaves, nutrients like amino acids are major regulators microbial growth activity. Using metabolomics apoplast fluid, we found that different species genus Flaveria considerably differ concentrations high-cost acids. We investigated how these differences affect community assembly by enriching bacteria vitro only sucrose or + as possible carbon sources. Enrichments from F. robusta were dominated Pantoea sp. Pseudomonas sp., regardless source. The latter was unable grow on alone persisted sucrose-only enrichment thanks exchange metabolites Individual strains enrichments had high similarity still displayed clear niche partitioning, enabling distinct cross-feed parallel. also closely related, individuals enriched trinervia fed more poorly than those robusta. This can explained part environment, since some cross-feeding selected for, when experimentally evolved a poor (sucrose-only) environment against rich (sucrose acids) one. Together, our work shows functionally strongly suggests resource shape thereby indirectly drive

Language: Английский

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Differential Responses of Methylobacterium and Sphingomonas Species to Multispecies Interactions in the Phyllosphere

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Jan. 1, 2025

ABSTRACT The leaf surface, known as the phylloplane, presents an oligotrophic and heterogeneous environment due to its topography uneven distribution of resources. Although it is a challenging environment, leaves support abundant bacterial communities that are spatially structured. However, factors influencing these spatial patterns not well understood. To study changes in population density bacteria synthetic communities, behaviour two common groups Arabidopsis thaliana microbiota— Methylobacterium (methylobacteria) Sphingomonas (sphingomonads)—was examined. Using consisting or three species, hypothesis was tested presence third species affects interaction other species. Results indicated methylobacteria exhibit greater sensitivity densities patterns, with higher intra‐genus competition lower aggregation compared sphingomonads. Pairwise comparisons were insufficient explain shifts observed three‐species suggesting higher‐order interactions influence structuring complex communities. This emphasises role multispecies determining community dynamics on phylloplane.

Language: Английский

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Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype

Peer Community Journal, Journal Year: 2023, Volume and Issue: 3

Published: Oct. 4, 2023

Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity phenotypic effects of these that constitute a primary inoculum plant microbiota is mostly unknown. Here, we studied transmission bacteria from radish seeds to seedlings using inoculation individual seed-borne strains synthetic communities (SynComs) under in vitro conditions. The SynComs were composed highly abundant prevalent, sub-dominant, or rare bacterial seed taxa. We monitored each strain alone gyrB gene amplicon sequencing assessed their impacts on phenotype. All successfully colonized able reconstruct richness gradient (6, 8 12 strains) both seedlings. Stenotrophomonas rhizophila became dominant three but most had variable success (i.e increasing, stable decreasing transition) also depended SynCom richness. Most no effect phenotypes, with exception Pseudomonas viridiflava Paenibacillus sp. which detrimental development. Abnormal morphologies observed proportions decreased at highest level. Interestingly, some previously identified as core (Pseudomonas viridiflava, Erwinia persicina) associated phenotypes either isolation SynComs. These results confirm microbiome includes pathogenic not only commensal mutualistic Altogether, show effectively manipulate diversity thus represents promising tool better understand early stages assembly. This study highlights strong differences between native colonization survival habitats.

Language: Английский

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Roles of microbiota in autoimmunity in Arabidopsis leaves

Nature Plants, Journal Year: 2024, Volume and Issue: 10(9), P. 1363 - 1376

Published: Sept. 6, 2024

Over the past three decades, researchers have isolated plant mutants that show constitutively activated defence responses in absence of pathogen infection. These are called autoimmune and typically dwarf and/or bearing chlorotic/necrotic lesions. Here, from a genetic screen for Arabidopsis genes involved maintaining normal leaf microbiota, we identified TIP GROWTH DEFECTIVE 1 (TIP1), which encodes an S-acyltransferase, as key player guarding leaves against abnormal microbiota level composition under high-humidity conditions. The tip1 mutant has several characteristic phenotypes classical mutants, including stature, showing lesions, having high basal gene expression. Gnotobiotic experiments revealed largely dependent on presence axenic plants markedly reduced phenotypes. We found dependency is shared by 'lesion mimic'-type Arabidopsis. It worth noting caused mutations two Nucleotide-Binding, Leucine-Rich Repeat (NLR) do not require can even be partially alleviated microbiota. Our results therefore suggest existence at least classes autoimmunity (microbiota-dependent versus microbiota-independent) plants. observed interplay between lesion mimic class reminiscent interactions dysbiosis animal kingdom. parallels highlight intricate relationship host immunity microbial communities across various biological systems.

Language: Английский

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The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava

New Phytologist, Journal Year: 2023, Volume and Issue: 240(5), P. 1961 - 1975

Published: Sept. 4, 2023

The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common in phyllosphere of European Arabidopsis thaliana populations. Belonging to P. syringae complex, it genetically phenotypically distinct from well-characterized sensu stricto. Despite its prevalence, we lack knowledge how A. responds native isolates at molecular level. Here, characterize host response an - pathosystem. We measured growth axenic infections used immune mutants, transcriptomics, metabolomics determine defense pathways influencing susceptibility infection. Infection with increased jasmonic acid (JA) levels expression ethylene pathway marker genes. a susceptible accession was delayed compared tolerant one. Mechanical injury rescued susceptibility, consistent involvement JA. JA/ethylene important for suppression viridiflava, yet capacity varies between accessions. Our results shed light on can suppress ever-present but further studies are needed understand evades this spread broadly across

Language: Английский

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A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 17, 2023

Abstract Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence their impact on natural populations is limited. Here we identified viral sequences in a metapopulation wild plant-associated Pseudomonas spp. genomes. We discovered that most abundant cluster does not encode an intact phage but instead encodes tailocin - phage-derived element bacteria use kill competitors for interbacterial warfare. Each pathogenic sp. strain carries one few distinct variants, which target variable polysaccharides outer membrane co-occurring strains. Analysis historic herbarium samples from last 170 years revealed same and receptor variants have persisted at least two centuries, suggesting continued defined set haplotypes receptors. These results indicate genetic diversity can be mined develop targeted “tailocin cocktails” microbial control. One-Sentence Summary Bacterial pathogens host-associated repurposed prophage competitors.

Language: Английский

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Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(10), P. 2748 - 2758

Published: Sept. 6, 2024

Abstract Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but factors driving their geographic variation largely unknown. Here, using 16S ribosomal DNA shotgun sequencing, we characterized associations Arabidopsis thaliana leaf microbiome with host genetics climate variables from 267 populations in species’ native range Europe. Comparing distribution 575 major bacterial amplicon variants (phylotypes), discovered that composition A. segregates along a latitudinal gradient. The clines predicted metrics drought, also spatial host. To validate relative effects drought genotype conducted common garden field study, finding 10% core bacteria to be affected directly 20% genetic drought. These data provide valuable resource for plant field, identified suggesting can indirectly shape via microbiome.

Language: Английский

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