Related references
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Summary: Bacillus velezensis, a model species for plant-associated bacilli, can mobilize a substantial part of its metabolome upon perceiving its soil-dwelling competitor Pseudomonas. This metabolite response includes polyketides, bioactive lipopeptides, and antibiotics, contributing to defense, biofilm formation, and enhanced motility. The secondary siderophore pyochelin produced by Pseudomonas was identified as an info-chemical triggering this response, highlighting a new facet of siderophore-mediated interactions in microbial conversations of the rhizosphere community.
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Barbara Kraigher et al.
Summary: The study found that the pattern of surface colonization by swarming mixtures is influenced by kin types, with closely related strains colonizing together and less related strains showing competitive exclusion. The outcome of nonkin swarm expansion depends on the initial ratio of competing strains, and the addition of surfactin can complement the swarming defect of nonkin mutants. Close encounters in nonkin mixtures lead to territorial exclusion, limiting the exploitation of surfactin by nonkin nonproducers.
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Ecology
Mei Li et al.
Summary: The rhizosphere microbiome plays a crucial role in defending against soilborne pathogens, and inhibiting the growth of pathogen helpers may be effective in reducing pathogen densities. This approach could potentially become a sustainable strategy for pathogen control.
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Hemanoel Passarelli-Araujo et al.
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MICROBIOLOGICAL RESEARCH
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Nicole R. Wang et al.
Summary: Plants form commensal associations with soil microorganisms, creating a root microbiome that provides protection against pathogens. However, the mechanisms of how microbiota contribute to pathogen protection are still unclear. By studying a model system of plant-pathogen-microbiome interactions, researchers discovered that commensal strains closely related to the pathogen were more likely to protect against pathogenesis. They also found that commensal colonization level was highly predictive of protection and identified genes involved in membrane modifications that are required for pathogen protection. These findings provide insights into the mechanisms of host protection by microbiota and have implications for microbiome engineering in dysbiotic soil systems.
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Summary: Microbiome engineering is increasingly utilized to address challenges in health, agriculture, and climate, but the failure to consider barriers to organism establishment, particularly in terms of biotic interactions, may hinder the long-term success of engineering solutions.
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Clara Margot Heiman et al.
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Xuhui Deng et al.
Summary: Stimulating the development of soil suppressiveness against certain pathogens through the manipulation of the rhizosphere microbiome has been shown to be an effective way to reduce pesticide use in agriculture. In this study, we investigated the mechanisms behind the suppression of bacterial wilt disease in tomato plants by the rhizosphere microbiome. We found that changes in community composition, rather than the abundance of biocontrol strains, were responsible for the disease suppressiveness observed in long-term field experiments with bio-organic fertilizers. Metagenomics analysis revealed that certain families of bacteria, such as Sphingomonadaceae and Xanthomonadaceae, were enriched in the rhizosphere when pathogen invasion occurred. Further experiments confirmed that these bacteria were able to significantly reduce pathogen abundance and increase the abundance of genes associated with nonribosomal peptide synthesis. Our findings suggest that priming the soil microbiome with bio-organic fertilizers can promote the development of reactive bacterial communities in the rhizosphere, which contribute to disease suppression.
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Wenshan Zheng et al.
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Maureen O'Callaghan et al.
Summary: The growing global market for soil microbial inoculants in agriculture is driven by the need to increase sustainable crop production without harming the environment. A better understanding of the ecology and modes of action of inoculant strains is crucial to optimize their efficacy and targeted use.
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Shaojun Pan et al.
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Morgan Price et al.
Summary: To discover novel catabolic enzymes and transporters, the researchers combined high-throughput genetic data from 29 bacteria with an automated tool. They used GapMind to annotate the uptake and catabolism of compounds in bacterial and archaeal genomes, and systematically examined the gaps in predicted pathways. They identified new pathways or enzymes for the utilization of various compounds and annotated numerous enzymes and transporters.
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Chen Chen et al.
Summary: This study identifies a new mechanism in which plant growth-promoting bacteria (PGPB) affect DNA methylation in roots to promote plant growth. The results show that the assembly of the rhizosphere microbiome is driven by plant development, and DNA methylation modifications in roots remain functional even after the elimination of the inoculum from the microbiome.
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Sunde Xu et al.
Summary: This study identified the bacterial microbiome associated with fungal fruiting bodies and discovered an effective bacterium, Pantoea agglomerans ZJU23, that suppresses fungal growth and infection. The study also identified a key antifungal compound, Herbicolin A, secreted by ZJU23, and determined its biosynthetic gene cluster. Herbicolin A demonstrated potent efficacy against various fungal pathogens both in vitro and in planta, and showed a distinct mode of action. Additionally, Herbicolin A exhibited higher activity against human opportunistic fungal pathogens than clinically used fungicides.
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Athina Gavriilidou et al.
Summary: By analyzing a large number of bacterial genomes and metagenome assembled genomes (MAGs), it was found that only about 3% of the potential natural products encoded in bacterial genomes have been characterized. The study also identified the genus level as an appropriate taxonomic rank for comparing the biosynthetic diversity of secondary metabolites, with Streptomyces bacteria encoding the largest diversity. Additionally, less-studied taxa such as Weeksellaceae, Myxococcaceae, Pleurocapsa, and Nostocaceae were found to have the potential to produce diverse secondary metabolites that require further investigation.
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Or Shalev et al.
Summary: The community structure in the plant-associated microbiome is influenced by interactions between the host and microbes, as well as among different microbes. In this study, the researchers found that commensal Pseudomonas strains can induce a host response that selectively inhibits specific pathogenic strains, providing plant protection. The extent of this protection depends on the genetic variation of the host plant.
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Panji Cahya Mawarda et al.
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Mathilde Nordgaard et al.
Summary: Bacillus subtilis can promote plant growth and protect plants against disease. Through experiments in Arabidopsis thaliana, it was found that B. subtilis can rapidly adapt to the environment, showing increased root colonization and robust biofilm formation. However, there was a fitness disadvantage for evolved isolates in a non-selective environment. The research also demonstrated increased root colonization by evolved isolates in the presence of other soil microbes.
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Ecology
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Yian Gu et al.
Summary: Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. This binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities.
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Wanze Chen et al.
Summary: Live-seq is a novel single-cell transcriptomic profiling approach that preserves cell viability during RNA extraction, allowing for the correlation analysis between a cell's ground-state transcriptome and its downstream molecular or phenotypic behavior. It accurately stratifies diverse cell types and states without major cellular perturbations, and can be used to map a cell's trajectory and evaluate gene effects on cell phenotypes.
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Dorota Kawa et al.
Summary: Root responses to environmental stresses are specific to cell types and developmental stages. Interactions with microorganisms elicit unique transcriptional responses, while changes in cell wall and cell integrity can serve as barriers against pests.
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Carmen Escudero-Martinez et al.
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Multidisciplinary Sciences
Ben O. Oyserman et al.
Summary: In this study, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
NATURE COMMUNICATIONS
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Multidisciplinary Sciences
Connor Sharp et al.
Summary: Humans and many other species carry a large set of beneficial microbes, and the vital relationships with these microbes only work when hosts can control their microbiome and suppress wayward symbionts. Cooperation evolution is not only driven by mutual benefits, but also relies on host control and constraints limiting symbiont counter evolution.
NATURE COMMUNICATIONS
(2022)
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Ecology
Philippe Piccardi et al.
Summary: The study investigated the competition between microbial invaders and resident microbes under different environmental conditions, finding that invaders were more likely to colonize a toxic medium in the presence of resident communities, while invasive species that could survive alone had a higher success rate in benign environments when residents were absent. Through experiments, it was shown that early colonists may exclude future invaders through a priority effect.
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Ecology
Morten Lindqvist Hansen et al.
Summary: Soil and rhizosphere microbiomes play important roles in suppressing plant pathogens through the production of antagonistic secondary metabolites. This study investigates how interactions within the Pseudomonas genus affect their production of antimicrobial metabolites. The researchers found that P. capeferrum species can modulate secondary metabolite production in P. protegens through two distinct mechanisms. They also discovered that the interaction between the two species leads to changes in specific metabolite production. These findings have implications for improving the efficacy of biocontrol strains and consortia.
Review
Plant Sciences
Henry W. G. Birt et al.
Summary: Plant roots are influenced by a variety of microbial taxa, and the interactions between plants and microbes at the root-soil interface are affected by variations in root phenotypes. Manipulating root phenotypes allows for targeted manipulation of plant-associated microbes, which can have significant impacts on plant health.
FRONTIERS IN PLANT SCIENCE
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Gabriela Purtschert-Montenegro et al.
Summary: Research has found that the plant root colonizer Pseudomonas putida strain IsoF is able to use a type IVB secretion system (T4BSS) to kill a wide range of soil and plant-associated Gram-negative bacteria, invade existing biofilms, and protect tomato plants against the phytopathogen Ralstonia solanacearum.
NATURE MICROBIOLOGY
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Doroteia Alves Ferreira et al.
Summary: The study revealed a significant positive correlation between soil microbial diversity and the symbiosis between plants and arbuscular mycorrhizal fungi (AMF). This finding contradicts the diversity-invasibility hypothesis and highlights the potential overall helper effect of soil biodiversity on plant-AMF symbiosis.
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Sang-Moo Lee et al.
Summary: The study showed that enrichment of protective microbiota in the rhizosphere facilitates disease suppression, while disruption of protective rhizobacteria can increase the incidence of disease. Artificial disruption of Gram-positive bacteria in rhizosphere soil resulted in higher occurrence of bacterial wilt in tomatoes. Identification of specific Gram-positive bacteria species in healthy rhizosphere soil contributed to plant immunity activation and enhanced plant disease resistance.
Article
Microbiology
Christian Froschel et al.
Summary: The research revealed that plant roots have genetically defined response programs in different cell layers when facing various microbial infections, highlighting the importance of radial organization in root-microbe interactions. The study utilized cell-layer translatomes to gain insights into the different colonization strategies of pathogens and mutualists, providing a valuable resource for crop improvement strategies.
CELL HOST & MICROBE
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Microbiology
Shan Shan Qi et al.
Summary: A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere and play important roles for plant health. Phyllosphere microbial communities assemble predictably and differ functionally from other plant organs or soil communities. The phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but production or activity is dependent upon external signals or cues. Through studying bacteria in the phyllosphere, isolates capable of inhibiting the growth of common bacteria were identified.
ENVIRONMENTAL MICROBIOLOGY
(2021)
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Microbiology
Elhanan Tzipilevich et al.
Summary: The study explored the interaction between plants and beneficial bacteria, revealing that activation of the plant immune system is crucial for efficient bacterial colonization and auxin secretion. A feedback loop was established where bacterial colonization triggers an immune reaction and production of reactive oxygen species, which in turn stimulates auxin production by the bacteria. This mutual feedback loop promotes the fitness of both partners.
CELL HOST & MICROBE
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Multidisciplinary Sciences
Isai Salas-Gonzalez et al.
Summary: Plant roots and animal guts have evolved specialized cell layers to control mineral nutrient homeostasis, tolerating resident microbiota while keeping integrity. In the model plant Arabidopsis thaliana, genes controlling endodermal function contribute to plant microbiome assembly, driven by a regulatory mechanism of endodermal differentiation with profound effects on nutrient homeostasis. This mechanism is linked to the microbiota's capacity to repress responses to the phytohormone abscisic acid in the root, establishing the endodermis as a regulatory hub coordinating microbiota assembly and homeostatic mechanisms.
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Biochemical Research Methods
Helen M. Kurkjian et al.
Summary: Microbial interactions within resident communities and between residents and invaders play a crucial role in determining invasion outcomes. The level of disruption, displacement, augmentation, or resistance of invasions is influenced by the facilitation or inhibition among community members. Understanding these interactions is essential for predicting the success of invasions and interventions in microbial communities.
PLOS COMPUTATIONAL BIOLOGY
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Biotechnology & Applied Microbiology
Zhikang Wang et al.
Summary: Periodic inoculation with phosphate-solubilizing and N-2-fixing bacteria can enhance plant growth and soil nutrients. Repeated inoculations do not increase the benefits from inoculants, and these benefits are not maintained after transplantation. Inoculations impact the succession of resident bacterial communities in bulk soil, primarily influenced by changes in soil pH and nitrate levels.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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Aurelia Emonet et al.
Summary: The study shows that plants restrict immune responses to vulnerable root parts to avoid constitutive responses to rhizosphere microbiota. By expressing the plant flagellin receptor and using fluorescent defense markers, immune responses can be observed at cellular resolution. The research highlights the incompatibility of meristematic activity and defense, emphasizing the importance of cell-resolved studies of plant immune responses.
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Multidisciplinary Sciences
Shahar Alon et al.
Summary: Expansion microscopy is adapted for long-read untargeted and targeted in situ RNA sequencing, enabling highly multiplexed mapping of RNAs from nanoscale to system scale. This technology allows for detailed transcript localization in different cell types and spatial positions, with applications in both animal models and human cancer samples.
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Multidisciplinary Sciences
Jared Kehe et al.
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Hong Li et al.
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Ecology
Tao Tian et al.
Summary: This study reveals that sucrose secreted from plant roots promotes solid surface motility (SSM) and root colonization by Bacillus subtilis through a previously unknown mechanism, suggesting a practical approach to enhance the prevalence of beneficial Bacillus species in plant protection.
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Microbiology
Sofija Andric et al.
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Paulo J. P. L. Teixeira et al.
Summary: Plants have an innate immune system to fight off potential invaders based on the perception of microbial molecules. The root commensal bacteria can modulate a specific sector of the Arabidopsis immune system, highlighting the importance of extracellular strategies for pathogen suppression.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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Microbiology
Christopher Blake et al.
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Daniel Dar et al.
Summary: The par-seqFISH method allows for recording gene expression and spatial context of microbial populations, revealing diverse physiological states coexisting within the same biofilm with high spatial resolution when studying Pseudomonas aeruginosa.
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Erqin Li et al.
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Carlos Molina-Santiago et al.
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Genetics & Heredity
Kazuo Kobayashi
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Kathrin Wippel et al.
Summary: The study reveals that commensal bacteria in root microbiota exhibit host preferences, which are associated with their invasiveness into established root-associated communities, as shown in systematic analyses of synthetic bacterial communities in a gnotobiotic system.
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Yi Song et al.
Summary: The FER receptor kinase mutant fer-8 has an enriched rhizosphere microbiome with Pseudomonas fluorescens, showing that FER-mediated ROS production regulates levels of beneficial pseudomonads. The study identifies FERONIA as a key modulator of rhizosphere Pseudomonas and microbiome composition in Arabidopsis by controlling levels of ROS production.
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