scholarly journals Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alba Pacheco-Moreno ◽  
Francesca L Stefanato ◽  
Jonathan J Ford ◽  
Christine Trippel ◽  
Simon Uszkoreit ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Plant Colonization ◽  
Potato Field ◽  
Strong Correlations ◽  
In Planta ◽  
Genetic Determinants ◽  
Specialized Metabolites ◽  
Commercial Potato ◽  
Pathogen Inhibition ◽  
Dynamic Population

Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.

scholarly journals Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

2019 ◽  
Author(s):  
Francesca L. Stefanato ◽  
Christine Trippel ◽  
Simon Uszkoreit ◽  
Laura Ferrafiat ◽  
Lucia Grenga ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Plant Colonization ◽  
Potato Field ◽  
Strong Correlations ◽  
Genetic Determinants ◽  
Specialized Metabolites ◽  
Commercial Potato ◽  
Pathogen Inhibition ◽  
Dynamic Population ◽  
Potato Pathogens

AbstractAgricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant growth and preventing disease. However, the genetic determinants of this beneficial activity are only partially understood, especially in relation to specialized metabolite production. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in commercial potato field soils and identify strong correlations between specialized metabolite biosynthetic pathways and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.

Dynamics of fungal pathogens in host plant tissues

1995 ◽  
Vol 73 (S1) ◽  
pp. 1275-1283 ◽  
Author(s):  
Shigehito Takenaka
Keyword(s):  
Host Plant ◽  
Species Interactions ◽  
Fungal Biomass ◽  
Quantitative Methods ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Molecular Methods ◽  
Plant Colonization ◽  
Fungal Colonization ◽  
Plant Tissues

To develop efficient control measures against fungal plant pathogens, the dynamics of host plant colonization during disease development and the interactions among fungi within host plant tissues need to be clarified. These studies require accurate quantitative estimation of specific fungal biomass in plant tissues. This has been approached by direct-microscopic methods, cultural methods, chemical determinations of fungal components, serological methods, and molecular methods. Among these methods, serological and molecular methods provide rapid, specific, and sensitive quantitative measures of fungal biomass in host plant tissues. Therefore, studies on fungal dynamics of host plant colonization using these two methods are presented. Some examples of species interactions among pathogenic fungi within host plants, such as synergism and competition, are reviewed and the usefulness of serological and molecular methods for studies on these interactions is presented. These quantitative methods will provide helpful information for understanding the ecology of plant pathogenic fungi, such as the dynamics of host plant colonization and species interactions. Key words: quantitative methods, fungal biomass, ELISA, PCR, fungal colonization, species interaction.

scholarly journals In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

2019 ◽  
Author(s):  
Tatsuya Nobori ◽  
Yiming Wang ◽  
Jingni Wu ◽  
Sara Christina Stolze ◽  
Yayoi Tsuda ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pseudomonas Syringae ◽  
Protein Level ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Bacterial Virulence ◽  
In Planta ◽  
Bacterial Gene ◽  
Global Food Security

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

scholarly journals PHIALOMYCES MACROSPORUS REDUCES CERCOSPORA COFFEICOLA SURVIVAL ON SYMPTOMATIC COFFEE LEAVES

2019 ◽  
Vol 14 (1) ◽  
pp. 1
Author(s):  
Marie Caroline Ferreira Laborde ◽  
Deila Magna dos Santos Botelho ◽  
Gabriel Alfonso Alvarez Rodriguez ◽  
Mário Lúcio Vilela de Resende ◽  
Marisa Vieira de Queiroz ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Disease Rate ◽  
In Planta ◽  
Necrotrophic Pathogen ◽  
Initial Inoculum ◽  
Saprobe Fungi ◽  
Cercospora Coffeicola ◽  
Brown Eye Spot

<p>Saprobe fungi and necrotrophic pathogens share the same niche within crop stubble and the search for fungi non-pathogenic to plants that are able to displace the plant pathogens from its overwintering substrate contributes to the disease management. Brown eye spot (<em>Cercospora coffeicola</em>) is among the most important coffee diseases, it is caused by a necrotrophic pathogen that has decaying leaves as its major source of inoculum. We have screened saprobe fungi for the ability to reduce <em>C. coffeicola</em> sporulation and viability and determined the possible mechanisms involved in the observed biocontrol. A selected saprobe fungus, <em>Phialomyces macrosporus</em>, reduced the pathogen’s viability by 40% both <em>in vitro</em> and <em>in vivo</em>. The fungus acts through antibiosis and competition for nutrients. It produced both volatile and non-volatile compounds that inhibited <em>C. coffeicola</em> growth, sporulation, and viability. It also produced the tissue maceration enzyme (polygalacturonase), which reduces the pathogen both in detached leaves or in planta. The reduction in the fungal viability either by the saprobe fungus or its polygalacturonase-fraction supernatant resulted in the reduction of the disease rate. Therefore, <em>P. macrosporus </em>is a potential microbial agent that can be used in an integrated management of brown eye spot through the reduction of the initial inoculum of the pathogen that survives and builds up in infected leaves.</p><p> </p>

scholarly journals Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6905 ◽  
Author(s):  
Elena Maria Colombo ◽  
Cristina Pizzatti ◽  
Andrea Kunova ◽  
Claudio Gardana ◽  
Marco Saracchi ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Culture Media ◽  
Screening Methods ◽  
Dual Culture ◽  
In Planta ◽  
In Vitro Method ◽  
In Vitro Methods ◽  
Strain Diversity ◽  
Fungal Plant Pathogens

Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects ofFusariumstrain diversity (N= 5) and culture media (N= 6) on the identification of biological control activity ofStreptomycesstrains (N= 20) againstFusariumpathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media,Fusariumstrain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r= 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays ofStreptomycesBCAs against fungal pathogens.

scholarly journals An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation

2021 ◽  
Author(s):  
Nick Snelders ◽  
Gabriella Petti ◽  
Grardy van den Berg ◽  
Michael Seidl ◽  
Bart Thomma
Keyword(s):  
Life Stage ◽  
Antibacterial Properties ◽  
Plant Evolution ◽  
Effector Proteins ◽  
Plant Colonization ◽  
Antimicrobial Protein ◽  
In Planta ◽  
Antimicrobial Proteins ◽  
Pathogenic Microbes ◽  
Plant Microbiome

Microbes typically secrete a plethora of molecules to promote niche colonization. Soil-dwelling microbes are well-known producers of antimicrobials that are exploited to outcompete microbial co-inhabitants. Also plant pathogenic microbes secrete a diversity of molecules into their environment for niche establishment. Upon plant colonization, microbial pathogens secrete so-called effector proteins that promote disease development. While such effectors are typically considered to exclusively act through direct host manipulation, we recently reported that the soil-borne fungal xylem-colonizing vascular wilt pathogen Verticillium dahliae exploits effector proteins with antibacterial properties to promote host colonization through the manipulation of beneficial host microbiota. Since fungal evolution preceded land plant evolution, we now speculate that a subset of the pathogen effectors involved in host microbiota manipulation evolved from ancient antimicrobial proteins of terrestrial fungal ancestors that served in microbial competition prior to the evolution of plant pathogenicity. Here, we show that V. dahliae has co-opted an ancient antimicrobial protein as effector, named VdAMP3, for mycobiome manipulation in planta. We show that VdAMP3 is specifically expressed to ward off fungal niche competitors during resting structure formation in senescing mesophyll tissues. Our findings indicate that effector-mediated microbiome manipulation by plant pathogenic microbes extends beyond bacteria and also concerns eukaryotic members of the plant microbiome. Finally, we demonstrate that fungal pathogens can exploit plant microbiome-manipulating effectors in a life-stage specific manner, and that a subset of these effectors has evolved from ancient antimicrobial proteins of fungal ancestors that likely originally functioned in manipulation of terrestrial biota.

Soil bacterial communities exhibit systematic spatial variation with landform across a commercial potato field

Geoderma ◽  
2019 ◽  
Vol 335 ◽  
pp. 112-122 ◽  
Author(s):  
Saraswoti Neupane ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sheng Li ◽  
Sean Whitney
Keyword(s):  
Spatial Variation ◽  
Bacterial Communities ◽  
Potato Field ◽  
Soil Bacterial Communities ◽  
Commercial Potato ◽  
Soil Bacterial

scholarly journals Identification of Loci of Pseudomonas syringae pv. actinidiae Involved in Lipolytic Activity and Their Role in Colonization of Kiwifruit Leaves

2017 ◽  
Vol 107 (6) ◽  
pp. 645-653 ◽  
Author(s):  
Hitendra Kumar Patel ◽  
Patrizia Ferrante ◽  
Meng Xianfa ◽  
Sree Gowrinadh Javvadi ◽  
Sujatha Subramoni ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Lipid A ◽  
Lipolytic Activity ◽  
Genetic Screen ◽  
Economic Losses ◽  
In Planta ◽  
Tn5 Transposon ◽  
Tn5 Mutants ◽  
Transposon Mutants

Bacterial canker disease caused by Pseudomonas syringae pv. actinidiae, an emerging pathogen of kiwifruit plants, has recently brought about major economic losses worldwide. Genetic studies on virulence functions of P. syringae pv. actinidiae have not yet been reported and there is little experimental data regarding bacterial genes involved in pathogenesis. In this study, we performed a genetic screen in order to identify transposon mutants altered in the lipolytic activity because it is known that mechanisms of regulation, production, and secretion of enzymes often play crucial roles in virulence of plant pathogens. We aimed to identify the set of secretion and global regulatory loci that control lipolytic activity and also play important roles in in planta fitness. Our screen for altered lipolytic activity phenotype identified a total of 58 Tn5 transposon mutants. Mapping all these Tn5 mutants revealed that the transposons were inserted in genes that play roles in cell division, chemotaxis, metabolism, movement, recombination, regulation, signal transduction, and transport as well as a few unknown functions. Several of these identified P. syringae pv. actinidiae Tn5 mutants, notably the functions affected in phosphomannomutase AlgC, lipid A biosynthesis acyltransferase, glutamate–cysteine ligase, and the type IV pilus protein PilI, were also found affected in in planta survival and/or growth in kiwifruit plants. The results of the genetic screen and identification of novel loci involved in in planta fitness of P. syringae pv. actinidiae are presented and discussed.

scholarly journals Pseudomonas syringae AlgU Downregulates Flagellin Gene Expression, Helping Evade Plant Immunity

2019 ◽  
Vol 202 (4) ◽  
Author(s):  
Zhongmeng Bao ◽  
Hai-Lei Wei ◽  
Xing Ma ◽  
Bryan Swingle
Keyword(s):  
Gene Expression ◽  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Control Point ◽  
Plant Colonization ◽  
Compensatory Mechanisms ◽  
Flagellin Gene ◽  
Content Type ◽  
Immune Systems ◽  
Plant Infection

ABSTRACT Flagella power bacterial movement through liquids and over surfaces to access or avoid certain environmental conditions, ultimately increasing a cell’s probability of survival and reproduction. In some cases, flagella and chemotaxis are key virulence factors enabling pathogens to gain entry and attach to suitable host tissues. However, flagella are not always beneficial; both plant and animal immune systems have evolved receptors to sense the proteins that make up flagellar filaments as signatures of bacterial infection. Microbes poorly adapted to avoid or counteract these immune functions are unlikely to be successful in host environments, and this selective pressure has driven the evolution of diverse and often redundant pathogen compensatory mechanisms. We tested the role of AlgU, the Pseudomonas extracytoplasmic function sigma factor σE/σ22 ortholog, in regulating flagellar expression in the context of Pseudomonas syringae-plant interactions. We found that AlgU is necessary for downregulating bacterial flagellin expression in planta and that this results in a corresponding reduction in plant immune elicitation. This AlgU-dependent regulation of flagellin gene expression is beneficial to bacterial growth in the course of plant infection, and eliminating the plant’s ability to detect flagellin makes this AlgU-dependent function irrelevant for bacteria growing in the apoplast. Together, these results add support to an emerging model in which P. syringae AlgU functions at a key control point that serves to optimize the expression of bacterial functions during host interactions, including minimizing the expression of immune elicitors and concomitantly upregulating beneficial virulence functions. IMPORTANCE Foliar plant pathogens, like Pseudomonas syringae, adjust their physiology and behavior to facilitate host colonization and disease, but the full extent of these adaptations is not known. Plant immune systems are triggered by bacterial molecules, such as the proteins that make up flagellar filaments. In this study, we found that during plant infection, AlgU, a gene expression regulator that is responsive to external stimuli, downregulates expression of fliC, which encodes the flagellin protein, a strong elicitor of plant immune systems. This change in gene expression and resultant change in behavior correlate with reduced plant immune activation and improved P. syringae plant colonization. The results of this study demonstrate the proximate and ultimate causes of flagellar regulation in a plant-pathogen interaction.

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