scholarly journals Disease-induced changes in plant microbiome assembly and functional adaptation

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Min Gao ◽  
Chao Xiong ◽  
Cheng Gao ◽  
Clement K. M. Tsui ◽  
Meng-Meng Wang ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pathogenic Fungi ◽  
Functional Adaptation ◽  
Diseased Plant ◽  
Beneficial Bacteria ◽  
Ecological Processes ◽  
Beneficial Microbes ◽  
Pathogen Invasion ◽  
Microbiome Assembly ◽  
Plant Microbiome

Abstract Background The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. Results The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants. Conclusions Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture.

scholarly journals Disease-induced Changes in Plant Microbiome Assembly and Functional Adaptation

2020 ◽  
Author(s):  
Min Gao ◽  
Chao Xiong ◽  
Cheng Gao ◽  
Clement K.M. Tsui ◽  
Xin Zhou ◽  
...  
Keyword(s):  
Pathogenic Fungi ◽  
Reproductive Organ ◽  
Functional Adaptation ◽  
Diseased Plant ◽  
Critical Data ◽  
Genes Encoding ◽  
Ecological Importance ◽  
Occurrence Patterns ◽  
Microbiome Assembly ◽  
Plant Microbiome

Abstract Background: Plant microbiome is an integral part of the host influencing its growth and health. The increasing evidence indicates that plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogen, but the ecological mechanisms that govern plant microbiome assembly and functions under disease in both below and aboveground compartments are not fully understood. Here we examined both bacterial and fungal communities from soils (rhizosphere and bulk soil) and multiple plant compartments (e.g. root, stem, and fruit) of chili pepper (Capsicum annuum L.) at two pepper production sites, and explored how Fusarium wilt disease (FWD) affect the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. Results: Our data demonstrated that FWD had less impact on reproductive organ (fruit) than on vegetative organs (root and stem), with the strongest impact in the stem upper epidermis. Fungal intra-kingdom networks presented lower stabilities and their communities were more sensitive to FWD than the bacterial communities. Moreover, the diseased pepper was more susceptible to colonization by other pathogenic fungi, but they may recruit potential beneficial bacteria to facilitate host or offspring survival, and FWD may enhance the ecological importance of fungal taxa in the interkingdom network. Further, metagenomic analysis revealed that several potential protective functional genes encoding detoxify and biofilm formation were significantly enriched in the diseased pepper.Conclusion: Together, these results significantly advance our understanding of pepper microbiome assembly and functions under biotic stress. Our work highlights the diseased plant and the aboveground compartments harbor a potential of beneficial microbiomes and functions that, in concert, can provide potential critical data for harnessing the plant microbiome for sustainable agriculture.

scholarly journals Morphological and Molecular Diversity of Ginger (Zingiber officinale Roscoe) Pathogenic Fungi in Chilga District, North Gondar, Ethiopia

2022 ◽  
Vol 2 ◽  
Author(s):  
Sefinew Tilahun ◽  
Marye Alemu ◽  
Mesfin Tsegaw ◽  
Nega Berhane
Keyword(s):  
Causative Agent ◽  
Fungal Pathogens ◽  
Pathogenic Fungus ◽  
Management Strategies ◽  
Infected Plant ◽  
Pathogenic Fungi ◽  
Zingiber Officinale ◽  
Morphological Characterization ◽  
Molecular Techniques ◽  
Diseased Plant

Ginger diseases caused by fungal pathogens have become one of the most serious problems causing reduced production around the world. It has also caused a major problem among farmers in different parts of Ethiopia resulting in a huge decline in rhizome yield. However, the exact causative agents of this disease have not been identified in the state. Although there are few studies related to pathogenic fungus identification, molecular level identification of fungal pathogen was not done in the area. Therefore, this study was undertaken to isolate and characterized the fungal causative agent of ginger disease from the diseased plant and the soil samples collected around the diseased plant from Chilga district, Gondar, Ethiopia. Samples from infected ginger plants and the soil around the infected plant were collected. Culturing and purification of isolates were made using Potato Dextrose Agar supplemented with antibacterial agent chloramphenicol. The morphological characterization was done by structural identification of the isolates under the microscope using lactophenol cotton blue stains. Isolated fungi were cultured and molecular identification was done using an internal transcribed spacer (ITS) of ribosomal DNA (rDNA). A total of 15 fungal morphotypes including 11 Aspergillus spp. (73.3%), 2 Penicillium spp. (13.3%), and single uncultured fungus clone S23 were isolated from the samples representing all the plant organs and the soil. Aspergillus spp. (73.3%) was the most common and seems to be the major causative agent. To the best of our knowledge, this is the first report of ginger pathogenic fungi in Ethiopia identified using ITS rDNA molecular techniques. This study will lay foundation for the development of management strategies for fungal diseases infecting ginger.

scholarly journals A Composite Bioinoculant Based on the Combined Application of Beneficial Bacteria and Fungi

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 220 ◽  
Author(s):  
Henrietta Allaga ◽  
Bettina Bóka ◽  
Péter Poór ◽  
Viktor Dávid Nagy ◽  
Attila Szűcs ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Plant Pathogens ◽  
Azotobacter Vinelandii ◽  
Pathogenic Fungi ◽  
Screening Strategy ◽  
Plant Residues ◽  
Beneficial Bacteria ◽  
Tomato Plants ◽  
Bacteria And Fungi

A composite soil bioinoculant containing beneficial bacteria and fungi was developed for biocontrol of plant pathogens, phosphorous mobilization, stem degradation, humification, and nitrogen fixation. A Trichoderma asperellum isolate with outstanding in vitro antagonistic abilities toward a series of plant pathogenic fungi was included as a potential biocontrol component. The selected strain was also shown to promote growth and increase photosynthetic activity of tomato plants. For phosphorous mobilization and stem degradation, a Trichoderma atrobrunneum strain was selected, which produced cellulose-degrading enzymes even in the absence of stem residues, while this ability increased 10–15-fold in the presence of ground maize stem. The strain was also shown to produce large amounts of enzymes liberating organically bound phosphorous, as well as cellulase and xylanase activities in solid-state fermentation on various plant residues. A Streptomyces albus strain with excellent peroxidase-producing abilities was selected as a potential humus-producing component, while an Azotobacter vinelandii strain with the potential to provide excess nitrogen for crops was included for nitrogen fixation. The assembled soil bioinoculant had positive effect on the uptake of certain important macro- and microelements (potassium, sodium, and manganese) from the soil by field-grown tomato plants. The applied screening strategy proved to be applicable for the assembly of a composite soil bioinoculant with notable application potentials.

scholarly journals Bacillus atrophaeus HAB-5 secretion metabolites preventing occurrence of systemic diseases in tobacco plant

2019 ◽  
Vol 156 (1) ◽  
pp. 159-172 ◽  
Author(s):  
Mamy Jayne Nelly Rajaofera ◽  
Yi Wang ◽  
Zaheer Amed Jatoi ◽  
Pengfei Jin ◽  
Hongguang Cui ◽  
...  
Keyword(s):  
Tobacco Plant ◽  
Regulatory Gene ◽  
Pathogenic Fungi ◽  
Cotton Field ◽  
Bacillus Atrophaeus ◽  
Tobacco Leaves ◽  
Healthy Environment ◽  
Pathogen Invasion ◽  
Synthetic Pesticide ◽  
Antimicrobial Metabolites

AbstractFinding synthetic pesticide alternatives for health and a healthy environment has become a crucial issue for scientific research. A number of studies have reported efficacy of Bacillus species on promoting plant development, as well as protecting plants against pathogen invasion, especially pathogenic fungi and bacteria. However, little was known about Bacillus species in controlling viral diseases. In this study, Bacillus atrophaeus strain HAB-5, isolated from cotton field, Xinjiang, China efficiently promoted the growth of tobacco plants. According to the results, the treatment with the strain HAB-5 increased the expression of NtEXP1 and NtEXP2. Then the Tobacco mosaic virus (TMV)/ Nicotiana tobacco system was employed to evaluate virus resistance induced by strain HAB-5. Tobacco leaves were treated with antimicrobial metabolites of strain HAB-5 (1 mg/mL), and 12 h later the treated leaves were challenged with TMV via rub-inoculation. The results showed that disease symptoms were obviously compromised by tobacco leaves treated with strain HAB-5, and the viral accumulation level was reduced extensively. Moreover, it was found that the signaling regulatory gene (NPR1), defense genes (PR-1a, PR-1b, Chia5), and hypertensive response related genes (Hsr203J, Hin1) were up-regulated in plants treated with the metabolites. Altogether, these accumulated results strongly support strain HAB-5 to be a biological controlling agent against TMV.

scholarly journals Bacillus subtilis and Pseudomonas fluorescens Trigger Common and Distinct Systemic Immune Responses in Arabidopsis thaliana Depending on the Pathogen Lifestyle

Vaccines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 503
Author(s):  
Ngoc Huu Nguyen ◽  
Patricia Trotel-Aziz ◽  
Sandra Villaume ◽  
Fanja Rabenoelina ◽  
Adrian Schwarzenberg ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Immune Responses ◽  
Signaling Pathways ◽  
Pseudomonas Syringae ◽  
Systemic Resistance ◽  
Functional Study ◽  
Marker Genes ◽  
Beneficial Bacteria ◽  
Bacillus Spp ◽  
Immune Pathways

Plants harbor various beneficial bacteria that modulate their innate immunity, resulting in induced systemic resistance (ISR) against various pathogens. However, the immune mechanisms underlying ISR triggered by Bacillus spp. and Pseudomonas spp. against pathogens with different lifestyles are not yet clearly elucidated. Here, we show that root drenching of Arabidopsis plants with Pseudomonas fluorescensPTA-CT2 and Bacillus subtilis PTA-271 can induce ISR against the necrotrophic fungus B. cinerea and the hemibiotrophic bacterium Pseudomonas syringae Pst DC3000. In the absence of pathogen infection, both beneficial bacteria do not induce any consistent change in systemic immune responses. However, ISR relies on priming faster and robust expression of marker genes for the salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) signaling pathways upon pathogen challenge. These responses are also associated with increased levels of SA, JA, and abscisic acid (ABA) in the leaves of bacterized plants after infection. The functional study also points at priming of the JA/ET and NPR1-dependent defenses as prioritized immune pathways in ISR induced by both beneficial bacteria against B. cinerea. However, B. subtilis-triggered ISR against Pst DC3000 is dependent on SA, JA/ET, and NPR1 pathways, whereas P. fluorescens-induced ISR requires JA/ET and NPR1 signaling pathways. The use of ABA-insensitive mutants also pointed out the crucial role of ABA signaling, but not ABA concentration, along with JA/ET signaling in primed systemic immunity by beneficial bacteria against Pst DC3000, but not against B. cinerea. These results clearly indicate that ISR is linked to priming plants for enhanced common and distinct immune pathways depending on the beneficial strain and the pathogen lifestyle.

scholarly journals Fusarium Oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis Thaliana Roots

2021 ◽  
Author(s):  
Enoch Narh Kudjordjie ◽  
Kourosh Hooshmand ◽  
Rumakanta Sapkota ◽  
Inge S. Fomsgaard ◽  
Mogens Nicolaisen
Keyword(s):  
Arabidopsis Thaliana ◽  
Fusarium Oxysporum ◽  
Fungal Pathogen ◽  
Plant Disease ◽  
Differential Resistance ◽  
Amplicon Sequencing ◽  
Interactive Effects ◽  
Pathogen Invasion ◽  
Plant Disease Control ◽  
Microbiome Assembly

Abstract BackgroundAlthough it is well established that plant metabolomes mediate microbiome assembly, the question of how metabolome-microbiome interactions may prevent pathogen invasion remains to be answered. To address this question, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions, Columbia-0 (Col-0) and Landsberg erecta (Ler-0) with differential resistance profiles to the fungal pathogen Fusarium oxysporum f.sp. mathioli (FOM). We used amplicon sequencing to characterize bacterial (16S) and fungal (ITS2) communities, and we used targeted metabolite analysis across 5 stages of FOM host progression. ResultsWe found that microbiome and metabolome profiles were markedly altered in FOM-inoculated and non-inoculated samples of resistant Col-0 and susceptible Ler-0. Co-occurrence network analysis revealed robust microbial networks in the resistant Col-0 compared to the susceptible Ler-0, during FOM infection. Specific metabolites and microbial OTUs (including indicator and hub OTUs) correlated in both non-inoculated and inoculated Col-0 and Ler-0. The glucosinolates 4-hydroxyglucobrassicin, neoglucobrassicin and indole-3 carbinol, but also phenolic compounds were active in structuring the A. thaliana-microbiome. ConclusionsOur results highlight the interactive effects of host resistance and its associated microbiota on Fusarium infection and progression. These findings shed significant insights into plant inter-omics dynamics during pathogen invasion and could possibly facilitate the exploitation of microbiomes for plant disease control.

Overview of the Interplay Between Cell Wall Integrity Signaling Pathways and Membrane Lipid Biosynthesis in Fungi: Perspectives forAspergillus fumigatus

2020 ◽  
Vol 21 (3) ◽  
pp. 265-283 ◽  
Author(s):  
João Henrique T.M. Fabri ◽  
Marina C. Rocha ◽  
Iran Malavazi
Keyword(s):  
Cell Wall ◽  
Plasma Membrane ◽  
Signaling Pathways ◽  
Fungal Infections ◽  
Invasive Pulmonary Aspergillosis ◽  
Pathogenic Fungi ◽  
Cell Wall Integrity ◽  
Immune Recognition ◽  
Fungal Cell ◽  
Low Efficiency

:The cell wall (CW) and plasma membrane are fundamental structures that define cell shape and support different cellular functions. In pathogenic fungi, such as Aspegillus fumigatus, they not only play structural roles but are also important for virulence and immune recognition. Both the CW and the plasma membrane remain as attractive drug targets to treat fungal infections, such as the Invasive Pulmonary Aspergillosis (IPA), a disease associated with high morbimortality in immunocompromised individuals. The low efficiency of echinocandins that target the fungal CW biosynthesis, the occurrence of environmental isolates resistant to azoles such as voriconazole and the known drawbacks associated with amphotericin toxicity foster the urgent need for fungal-specific drugable targets and/or more efficient combinatorial therapeutic strategies. Reverse genetic approaches in fungi unveil that perturbations of the CW also render cells with increased susceptibility to membrane disrupting agents and vice-versa. However, how the fungal cells simultaneously cope with perturbation in CW polysaccharides and cell membrane proteins to allow morphogenesis is scarcely known. Here, we focus on current information on how the main signaling pathways that maintain fungal cell wall integrity, such as the Cell Wall Integrity and the High Osmolarity Glycerol pathways, in different species often cross-talk to regulate the synthesis of molecules that comprise the plasma membrane, especially sphingolipids, ergosterol and phospholipids to promote functioning of both structures concomitantly and thus, cell viability. We propose that the conclusions drawn from other organisms are the foundations to point out experimental lines that can be endeavored in A. fumigatus.

scholarly journals Characterization of a Novel, Defense-Related Arabidopsis Mutant, cir1, Isolated By Luciferase Imaging

2002 ◽  
Vol 15 (6) ◽  
pp. 557-566 ◽  
Author(s):  
Shane L. Murray ◽  
Catherine Thomson ◽  
Andrea Chini ◽  
Nick D. Read ◽  
Gary J. Loake
Keyword(s):  
Signaling Pathways ◽  
Pseudomonas Syringae ◽  
Constitutive Expression ◽  
Bacterial Pathogen ◽  
Negative Regulator ◽  
Reactive Oxygen Intermediate ◽  
Peronospora Parasitica ◽  
Tomato Dc3000 ◽  
Pathogen Invasion ◽  
Arabidopsis Mutant

In order to identify components of the defense signaling network engaged following attempted pathogen invasion, we generated a novel PR-1∷luciferase (LUC) transgenic line that was deployed in an imaging-based screen to uncover defense-related mutants. The recessive mutant designated cir1 exhibited constitutive expression of salicylic acid (SA), jasmonic acid (JA)/ethylene, and reactive oxygen intermediate-dependent genes. Moreover, this mutation conferred resistance against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and a virulent oomycete pathogen Peronospora parasitica Noco2. Epistasis analyses were undertaken between cir1 and mutants that disrupt the SA (npr1, nahG), JA (jar1), and ethylene (ET) (ein2) signaling pathways. While resistance against both P. syringae pv. tomato DC3000 and Peronospora parasitica Noco2 was partially reduced by npr1, resistance against both of these pathogens was lost in an nahG genetic background. Hence, cir1-mediated resistance is established via NPR1-dependent and -independent signaling pathways and SA accumulation is essential for the function of both pathways. While jar1 and ein2 reduced resistance against P. syringae pv. tomato DC3000, these mutations appeared not to impact cir1-mediated resistance against Peronospora parasitica Noco2. Thus, JA and ET sensitivity are required for cir1-mediated resistance against P. syringae pv. tomato DC3000 but not Peronospora parasitica Noco2. Therefore, the cir1 mutation may define a negative regulator of disease resistance that operates upstream of SA, JA, and ET accumulation.

scholarly journals Multitrait Pseudomonas spp. Isolated from Monocropped Wheat (Triticum aestivum) Suppress Fusarium Root and Crown Rot

2020 ◽  
Vol 110 (3) ◽  
pp. 582-592 ◽  
Author(s):  
Habib Ullah ◽  
Humaira Yasmin ◽  
Saqib Mumtaz ◽  
Zahra Jabeen ◽  
Rabia Naz ◽  
...  
Keyword(s):  
Plant Growth ◽  
Pathogenic Fungi ◽  
Endophytic Bacterium ◽  
Crown Rot ◽  
Common Disease ◽  
Arid Zones ◽  
Bacterial Strains ◽  
Beneficial Bacteria ◽  
Wheat Varieties ◽  
Root And Crown Rot

Fusarium root and crown rot is the most common disease of wheat, especially wheat grown in arid zones where drought is a common issue. The development of environmentally safe approaches to manage diseases of food crops is important for humans. The monocropping system recruits beneficial bacteria that promote plant growth through nutrient solubilization and pathogen suppression. In this study, a field where wheat was monocropped for 5 successive years under rainfed conditions was identified. A total of 29 bacterial isolates were obtained from the rhizosphere, endosphere, and phyllosphere of wheat at its harvesting stage. The Gram-negative bacteria were less prevalent (41%) but the majority (75%) exhibited plant growth-promoting traits. The ability of strains to solubilize nutrients (solubilization index = 2.3 to 4), inhibit pathogenic fungi (25 to 56%), and produce antifungal compounds was highly variable. The rhizobacteria significantly promoted the growth and disease resistance of wheat varieties such as Pirsbak-2015 and Galaxy-2013 by inducing antioxidant enzyme activity (0.2- to 2.1-fold). The bacterial strains were identified as Ochrobactrum spp., Acinetobacter spp., and Pseudomonas mediterranea by 16S rRNA and rpoD sequence analysis. The endophytic bacterium P. mediterranea HU-9 exhibited maximum biocontrol efficacy against wheat root and crown rot diseases with a disease score/disease index from 1.8 to 3.1. The monocropping systems of rainfed agriculture are an ideal source of beneficial bacteria to use as bioinoculants for different crops.

Sign in / Sign up

Export Citation Format

Share Document