Host microbe interactions
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Rescooped by Sachin from Host:microbe Interactions
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Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication?

Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication? | Host microbe interactions | Scoop.it
Both extracellular RNAs and extracellular vesicles (EVs) have recently garnered attention as novel mediators of intercellular communication in eukaryotes and prokaryotes alike. EVs not only permit export of RNA, but also facilitate delivery and trans-kingdom exchange of these and other biomolecules, for instance between microbes and their hosts. In this Opinion article, we propose that EV-mediated export of RNA represents a universal mechanism for interkingdom and intrakingdom communication that is conserved among bacterial, archaeal, and eukaryotic microbes. We speculate how microbes might use EV RNA to influence target cell gene expression or manipulate host immune responses.

Via Jonathan Plett
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Rescooped by Sachin from The Plant Microbiome
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Microbial interactions within the plant holobiont | Microbiome |

Microbial interactions within the plant holobiont | Microbiome | | Host microbe interactions | Scoop.it
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a “holobiont.” Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.

Via Stéphane Hacquard
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Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes - ScienceDirect

Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes - ScienceDirect | Host microbe interactions | Scoop.it
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves, and have been used as taxonomic marker since the early 20th century. These structures are present in very diverse taxa, including dicots (Rubiaceae and Primulaceae) and monocots (Dioscorea). The symbionts colonize the plants throughout their life cycles and contribute bioactive secondary metabolites to the association. In this review, we present recent progress in the understanding of these plant–bacteria symbioses, including the modes of transmission, distribution and roles of the symbionts.
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Extracellular vesicles as key mediators of plant–microbe interactions

Extracellular vesicles as key mediators of plant–microbe interactions | Host microbe interactions | Scoop.it
Extracellular vesicles (EVs) are lipid compartments capable of trafficking proteins, lipids, RNA and metabolites between cells. Plant cells have been shown to secrete EVs during immune responses, but virtually nothing is known about their formation, contents or ultimate function. Recently developed methods for isolating plant EVs have revealed that these EVs are enriched in stress response proteins and signaling lipids, and appear to display antifungal activity. Comparison to work on animal EVs, and the observation that host-derived small interfering RNAs and microRNAs can silence fungal genes, suggests that plant EVs may also mediate trans-kingdom RNA interference. Many fundamental questions remain, however, regarding how plant EVs are produced, how they move, and if and how they are taken up by target cells.
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Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016)

Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016) | Host microbe interactions | Scoop.it

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as ‘selfish’ genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host–microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a ‘two-speed’ genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.


Via Kamoun Lab @ TSL, Francis Martin, Giannis Stringlis, Steve Marek
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Rescooped by Sachin from Microbes, plant immunity, and crop science
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Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice | Host microbe interactions | Scoop.it
Bacterial-fungal interactions are widely found in distinct environments and contribute to ecosystem processes. Previous studies of these interactions have mostly been performed in soil, and only limited studies of aerial plant tissues have been conducted. Here we show that a seed-borne plant pathogenic bacterium, Burkholderia glumae (Bg), and an air-borne plant pathogenic fungus, Fusarium graminearum (Fg), interact to promote bacterial survival, bacterial and fungal dispersal, and disease progression on rice plants, despite the production of antifungal toxoflavin by Bg. We perform assays of toxoflavin sensitivity, RNA-seq analyses, lipid staining and measures of triacylglyceride content to show that triacylglycerides containing linolenic acid mediate resistance to reactive oxygen species that are generated in response to toxoflavin in Fg. As a result, Bg is able to physically attach to Fg to achieve rapid and expansive dispersal to enhance disease severity.

Via Nicolas Denancé
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Rescooped by Sachin from Microbes and Microbiomes
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Genomic features of bacterial adaptation to plants

Genomic features of bacterial adaptation to plants | Host microbe interactions | Scoop.it
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe–microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Via Matt Agler
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Steve Marek's curator insight, December 19, 2017 10:30 AM
"identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes"
WillistonPlantPath's curator insight, December 20, 2017 2:43 PM
484 bacterial genomes. wow.
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Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin

Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin | Host microbe interactions | Scoop.it
Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin
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Rescooped by Sachin from Host Microbe Interactions
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Plant microbial diversity is suggested as the key to future biocontrol and health trends | FEMS Microbiology Ecology | Oxford Academic

Plant microbial diversity is suggested as the key to future biocontrol and health trends | FEMS Microbiology Ecology | Oxford Academic | Host microbe interactions | Scoop.it
The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species. The beneficial interplay of the host and its microbiome is responsible for maintaining the health of the holobiont, while diseases are often correlated with microbial dysbioses. Microbial diversity was identified as a key factor in preventing diseases and can be implemented as a biomarker in plant protection strategies. Targeted and predictive biocontrol approaches are possible by developing microbiome-based solutions. Moreover, combined breeding and biocontrol strategies maintaining diversity and ecosystem health are required. The analysis of plant microbiome data has brought about a paradigm shift in our understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.

Via Ryohei Thomas Nakano
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Rescooped by Sachin from Plant Immunity And Microbial Effectors
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The Beautiful Intelligence of Bacteria and Other Microbes

The Beautiful Intelligence of Bacteria and Other Microbes | Host microbe interactions | Scoop.it
Bacterial biofilms and slime molds are more than crude patches of goo. Detailed time-lapse microscopy reveals how they sense and explore their surroundings,

Via IPM Lab
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Rescooped by Sachin from Soil microbial interactions
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Biophysical processes supporting the diversity of microbial life in soil - FEMS Microbiology Reviews

Biophysical processes supporting the diversity of microbial life in soil - FEMS Microbiology Reviews | Host microbe interactions | Scoop.it

Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.


Via Max-Bernhard Ballhausen
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Rescooped by Sachin from Plant Pathogens
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New insights into plant–microbe interactions through advances in fungal genetics

New insights into plant–microbe interactions through advances in fungal genetics | Host microbe interactions | Scoop.it
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Via Yogesh Gupta
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Rescooped by Sachin from MycorWeb Plant-Microbe Interactions
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Seeing is believing: imaging the delivery of pathogen effectors during plant infection

Pathogenic microbes manipulate their plant host by interfering with a plethora of cellular processes (Asai & Shirasu, 2015; Pelgrom & Van den Ackerveken, 2016). To hijack the cellular machinery of the plant, pathogens deliver effector proteins inside host cells by mechanisms that are often not fully understood. In this issue of New Phytologist, Wang et al. (pp. 205–215) provide convincing, live cell-imaging footage of the delivery into plant cells of a host-translocated RXLR effector by the oomycete pathogen Phytophthora infestans. The late blight pathogen deploys an unconventional protein secretion route for this. Together with recent live cell-imaging data on effector traffic in other plant–pathogen interactions, discussed later, we have begun to grasp that invading filamentous microbes use unconventional secretory routes to deliver their sabotage tools into plant cells.

This is the long-awaited experimental confirmation of RXLR effector delivery through haustoria into plant cells.

Many microbial pathogens of plants have a biotrophic lifestyle and grow on living host tissues – a delicate process that is well balanced and timed in order to preserve the integrity of host tissue during infection. A crucial feature of biotrophic interactions is the suppression of plant immunity that is required for pathogens to exploit their host without being blocked (Asai & Shirasu, 2015). It is well known that pathogenic microbes translocate suites of effector proteins and interfering metabolites into plant cells to manipulate host processes. Bacterial pathogens have evolved sophisticated translocation machineries, e.g. Type III and Type IV secretion systems that act as microsyringes to deliver effectors directly into host cells. Although it will not be further discussed in this Commentary, the delivery of Type III effectors was recently visualized using the GFP strand system, allowing Henry et al. (2017) to investigate the temporal and spatial delivery of Pseudomonas effectors during the infection of Arabidopsis and tomato

Via Francis Martin
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Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India

Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India | Host microbe interactions | Scoop.it
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Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha

Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha | Host microbe interactions | Scoop.it
A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE‐3‐ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss‐ and gain‐of‐function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss‐of‐function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR‐resistant MpARF3 alleles are auxin‐insensitive, suggesting that class C ARFs act in a context‐dependent fashion. We conclude that two modules independently evolved to regulate a pre‐existing ARF transcriptional network. Whereas the auxin‐TIR1‐AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.
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Rescooped by Sachin from Microbiome and plant immunity
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Root exudates of stressed plants stimulate and attract Trichoderma soil fungi

Root exudates of stressed plants stimulate and attract Trichoderma soil fungi | Host microbe interactions | Scoop.it
Plant roots release complex mixtures of bioactive molecules including compounds that affect the activity and modify the composition of the rhizosphere microbiome. In this work, we investigated the initial phase of the interaction between tomato and an effective biocontrol strain of Trichoderma harzianum (T22). We found that root exudates (RE), obtained from plants grown in a split root system and exposed to a choice of biotic and abiotic stress factors (wounding, salt, pathogen attack), stimulate the growth and act as chemoattractants of the biocontrol fungus. On the other hand, some of the treatments did not result in an enhanced chemotropism on Fusarium oxysporum f. sp. lycopersici, indicating a mechanism that may be selective for non-pathogenic microbes. The involvement of peroxidases and oxylipins, both known to be released by roots in response to stress, was demonstrated by using RE fractions containing these molecules and their commercial purified analogues, testing the effect of a specific inhibitor, and characterizing the complex pattern of these metabolites released by tomato roots both locally and systemically.

Via Giannis Stringlis
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Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont

Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont | Host microbe interactions | Scoop.it

The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acid, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate L-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell-walls. These compounds could function as C sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 million years ago, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

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Rescooped by Sachin from Agriculture & crop technologies
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Emerging Microbial Biocontrol Strategies For Plant Pathogens

Emerging Microbial Biocontrol Strategies For Plant Pathogens | Host microbe interactions | Scoop.it
Highlights
• Food Security is at risk by an increasing world population and a growing number of crop pathogens.
• Biological control options emerge as promising alternatives to assist crops to fight pathogens.
• Microbial biocontrol success is inconsistent and depends on a number of environmental, ecological and genetic factors.
• This review provides an overview of existing and new microbial biocontrol strategies and how these can be more stable.
• Emerging strategies include long-term plant colonization, microbiome engineering and breeding of microbe-optimized crops.

To address food security, agricultural yields must increase to match the growing human population in the near future. There is now a strong push to develop low-input and more sustainable agricultural practices that include alternatives to chemicals for controlling pests and diseases, a major factor of heavy losses in agricultural production. Based on the adverse effects of some chemicals on human health, the environment and living organisms, researchers are focusing on potential biological control microbes as viable alternatives for the management of pests and plant pathogens. There is a growing body of evidence that demonstrates the potential of leaf and root-associated microbiomes to increase plant efficiency and yield in cropping systems. It is important to understand the role of these microbes in promoting growth and controlling diseases, and their application as biofertilizers and biopesticides whose success in the field is still inconsistent. This review focusses on how biocontrol microbes modulate plant defense mechanisms, deploy biocontrol actions in plants and offer new strategies to control plant pathogens. Apart from simply applying individual biocontrol microbes, there are now efforts to improve, facilitate and maintain long-term plant colonization. In particular, great hopes are associated with the new approaches of using “plant-optimized microbiomes” (microbiome engineering) and establishing the genetic basis of beneficial plant-microbe interactions to enable breeding of “microbe-optimized crops”.

Via Jonathan Lapleau
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Jonathan Lapleau's curator insight, January 23, 9:12 AM
Biocontrol is an emerging and promising field of research and application in order to manage diseases and stresses in crops. Nature is a bio-bank for active compounds, so let's use it !
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Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant

Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant | Host microbe interactions | Scoop.it
Tritrophic interactions involving a biocontrol agent, a pathogen and a plant have been analyzed predominantly from the perspective of the biocontrol agent. We have conducted the first comprehensive transcriptomic analysis of all three organisms in an effort to understand the elusive properties of Pseudozyma flocculosa in the context of its biocontrol activity against Blumeria graminis f.sp. hordei as it parasitizes Hordeum vulgare.
After inoculation of P. flocculosa, the tripartite interaction was monitored over time and samples collected for scanning electron microscopy and RNA sequencing.
Based on our observations, P. flocculosa indirectly parasitizes barley, albeit transiently, by diverting nutrients extracted by B. graminis from barley leaves through a process involving unique effectors. This brings novel evidence that such molecules can also influence fungal–fungal interactions. Their release is synchronized with a higher expression of powdery mildew haustorial effectors, a sharp decline in the photosynthetic machinery of barley and a developmental peak in P. flocculosa. The interaction culminates with a collapse of B. graminis haustoria, thereby stopping P. flocculosa growth, as barley plants show higher metabolic activity.
To conclude, our study has uncovered a complex and intricate phenomenon, described here as hyperbiotrophy, only achievable through the conjugated action of the three protagonists.
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J Exp Bot - Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth

J Exp Bot - Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth | Host microbe interactions | Scoop.it

Extracellular vesicles (EV) are membrane particles released by cells into their environment and are considered to be key players in intercellular communication. EV are produced by all domains of life but limited knowledge about EV in plants is available, although their implication in plant defense has been suggested. We have characterized sunflower EV and tested whether they could interact with fungal cells. EV were isolated from extracellular fluids of seedlings and characterized by transmission electron microscopy and proteomic analysis. These nanovesicles appeared to be enriched in cell wall remodeling enzymes and defense proteins. Membrane-labeled EV were prepared and their uptake by the phytopathogenic fungus Sclerotinia sclerotiorum was verified. Functional tests further evaluated the ability of EV to affect fungal growth. Spores treated with plant EV showed growth inhibition, morphological changes, and cell death. Conclusive evidence on the existence of plant EV is presented and we demonstrate their ability to interact with and kill fungal cells. Our results introduce the concept of cell-to-cell communication through EV in plants.


Via LRSV, Francis Martin
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A secreted antibacterial neuropeptide shapes the microbiome of Hydra

A secreted antibacterial neuropeptide shapes the microbiome of Hydra | Host microbe interactions | Scoop.it
Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood. Here, we show that sensory and ganglion neurons in the ectodermal epithelium of the model organism hydra (a member of the animal phylum Cnidaria) secrete neuropeptides with antibacterial activity that may shape the microbiome on the body surface. In particular, a specific neuropeptide, which we call NDA-1, contributes to the reduction of Gram-positive bacteria during early development and thus to a spatial distribution of the main colonizer, the Gram-negative Curvibacter sp., along the body axis. Our findings warrant further research to test whether neuropeptides secreted by nerve cells contribute to the spatial structure of microbial communities in other organisms.

Via Ryohei Thomas Nakano
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Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont

Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont | Host microbe interactions | Scoop.it
A proteobacterial symbiont with the smallest known genome of an extracellular bacterium
provides its host beetle with key enzymes to break down pectin in plant-based food,
giving a striking example of symbiosis and evolutionary adaptation.
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Equol, a Clinically Important Metabolite, Inhibits the Development and Pathogenicity of Magnaporthe oryzae, the Causal Agent of Rice Blast Disease

Equol, a Clinically Important Metabolite, Inhibits the Development and Pathogenicity of Magnaporthe oryzae, the Causal Agent of Rice Blast Disease | Host microbe interactions | Scoop.it
Equol, a metabolite of soybean isoflavone daidzein, has been proven to have various bioactivities related to human health, but little is known on its antifungal activity to plant fungal pathogens. Magnaporthe oryzae is a phytopathogenic fungus that causes rice blast, a devastating disease on rice. Here, we demonstrated that equol influences the development and pathogenicity of M. oryzae. Equol showed a significant inhibition to the mycelial growth, conidial generation and germination, and appressorial formation of M. oryzae. As a result, equol greatly reduced the virulence of M. oryzae on rice and barley leaves. The antifungal activity of equol was also found in several other plant fungal pathogens. These findings expand our knowledge on the bioactivities of equol.

Via Elsa Ballini
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Frontiers | Regulated Forms of Cell Death in Fungi | Microbiology

Frontiers | Regulated Forms of Cell Death in Fungi | Microbiology | Host microbe interactions | Scoop.it
Cell death occurs in all domains of live. While some cells die in an uncontrolled way due to exposure to external cues, other cells die in a regulated manner as part of a genetically encoded developmental program. Like other eukaryotic species, fungi undergo programmed cell death (PCD) in response to various triggers. For example, exposure to external stress conditions can activate PCD pathways in fungi. Calcium redistribution between the extracellular space, the cytoplasm and intracellular storage organelles appears to be pivotal for this kind of cell death. PCD is also part of the fungal life cycle, in which it occurs during sexual and asexual reproduction, aging, and as part of development associated with infection in phytopathogenic fungi. Additionally, a fungal non-self recognition mechanism termed heterokaryon incompatibility (HI) also involves PCD. Some of the molecular players mediating PCD during HI show remarkable similarities to major constituents involved in innate immunity in metazoans and plants. In this review we discuss recent research on fungal PCD mechanisms in comparison to more characterized mechanisms in metazoans. We highlight the role of PCD in fungi in response to exogenic compounds, fungal development and nonself recognition processes and discuss identified intracellular signaling pathways and molecules that regulate fungal PCD.

Via Steve Marek, Francis Martin
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Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives

Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives | Host microbe interactions | Scoop.it
Lignin, most complex and abundant biopolymer on the earth’s surface, attains its stability from intricate polyphenolic units and non-phenolic bonds, making it difficult to depolymerize or separate from other units of biomass. Eccentric lignin degrading ability and availability of annotated genome make Phanerochaete chrysosporium ideal for studying lignin degrading mechanisms. Decoding and understanding the molecular mechanisms underlying the process of lignin degradation will significantly aid the progressing biofuel industries and lead to the production of commercially vital platform chemicals. In this study, we have performed a large-scale metadata analysis to understand the common gene expression patterns of P. chrysosporium during lignin degradation. Gene expression datasets were retrieved from NCBI GEO database and analyzed using GEO2R and Bioconductor packages. Commonly expressed statistically significant genes among different datasets were further considered to understand their involvement in lignin degradation and detoxification mechanisms. We have observed three sets of enzymes commonly expressed during ligninolytic conditions which were later classified into primary ligninolytic, aromatic compound-degrading and other necessary enzymes. Similarly, we have observed three sets of genes coding for detoxification and stress-responsive, phase I and phase II metabolic enzymes. Results obtained in this study indicate the coordinated action of enzymes involved in lignin depolymerization and detoxification-stress responses under ligninolytic conditions. We have developed tentative network of genes and enzymes involved in lignin degradation and detoxification mechanisms by P. chrysosporium based on the literature and results obtained in this study. However, ambiguity raised due to higher expression of several uncharacterized proteins necessitates for further proteomic studies in P. chrysosporium.

Via Francis Martin
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Francis Martin's curator insight, September 23, 2017 3:40 AM
A nice piece of work!