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Plant-Associated Pseudomonads

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 35038

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Dr. Jacob G. Malone

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Guest Editor

John Innes Centre, Norwich Research Park, Norwich, UK
Interests: Pseudomonas signal transduction in response to environmental stimuli; bacterial infection and colonisation mechanisms in both plants and humans; identifying bacterial genes and pathways that suppress plant disease and contribute to plant health

Dr. Rafael Rivilla

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Guest Editor

Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
Interests: plant-microbe interactions; Pseudomonas; plant probiotics; bioremediation; motility; rhizosphere colonization
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Special Issue Information

Dear Colleagues,

The genus Pseudomonas is one of the widest and most diverse bacterial genera, with more than 200 species named to date. Pseudomonads are versatile Proteobacteria that are able to dwell in many environments with different life-styles. A large number of important Pseudomonas species have been isolated from plant environments, including the rhizosphere, phylosphere, and endophytic compartments. In these environments, pseudomonads can have either a pathogenic or a saprophytic life-style. Many strains and species have shown a role in promoting plant growth and are therefore considered Plant-Growth-Promoting Bacteria (PGPB). Plant growth promotion by pseudomonads has been attributed to various mechanisms, such as the improvement of plant nutrition (biofertilization), antagonism towards phytopathogens (biocontrol) or modifying the plant hormone balance. In each case, the actions of Pseudomonas spp. play important roles in altering the relationship between plants and the environment.

This Special Issue will cover all aspects of the interactions of pseudomonads with their host plants as well as the biology of plant-interacting pseudomonads. It will also cover the interactions of plant-associated pseudomonads with other microorganisms present in the plant microbiome.

Dr. Jacob G. Malone
Dr. Rafael Rivilla
Guest Editors

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Keywords

Pseudomonas
Pseudomonas fluorescens, Pseudomonas syringae, Pseudomonas protegens etc.
Plant growth promoting (rhizo)bacteria
Phytopathogenic pseudomonads
Plant microbe interactions
Rhizosphere
Phylosphere
Endophytic
Inoculant
Biocontrol
Biofertilization
Phytostimulation
Microbiome

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Published Papers (11 papers)

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Editorial

Jump to: Research

3 pages, 183 KiB

Open AccessEditorial

Plant-Associated Pseudomonads

by Rafael Rivilla and Jacob G. Malone

Microorganisms 2023, 11(5), 1216; https://doi.org/10.3390/microorganisms11051216 - 6 May 2023

Viewed by 1052

Abstract

Bacteria belonging to the genus Pseudomonas (the pseudomonads) are a group of Gammaproteobacteria that are characterized by a high metabolic versatility and adaption to different ecological niches [...] Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

Research

Jump to: Editorial

22 pages, 5501 KiB

Open AccessArticle

Pseudomonas bijieensis Strain XL17 within the P. corrugata Subgroup Producing 2,4-Diacetylphloroglucinol and Lipopeptides Controls Bacterial Canker and Gray Mold Pathogens of Kiwifruit

by Md. Arshad Ali, Jinyan Luo, Temoor Ahmed, Jiannan Zhang, Ting Xie, Dejiang Dai, Jingyong Jiang, Jie Zhu, Sabry Hassan, Jamal A. Alorabi, Bin Li and Qianli An

Microorganisms 2022, 10(2), 425; https://doi.org/10.3390/microorganisms10020425 - 12 Feb 2022

Cited by 17 | Viewed by 3545

Abstract

Kiwifruit worldwide suffers from the devastating diseases of bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) and gray mold caused by Botrytis cinerea. Here, an endophytic bacterium XL17 isolated from a rape crown gall was screened out for its potent antagonistic activities against Psa and B. cinerea. Strain XL17 and its cell-free culture filtrate (CF) inhibited the growth of Psa and B. cinerea, Psa-associated leaf necrosis, and B. cinerea-associated kiwifruit necrosis. Electron microscopy showed that XL17 CF could damage the cell structures of Psa and B. cinerea. Genome-based taxonomy revealed that strain XL17 belongs to Pseudomonas bijieensis within the P. corrugata subgroup of the P. fluorescens species complex. Among the P. corrugata subgroup containing 31 genomospecies, the presence of the phl operon responsible for the biosynthesis of the phenolic polyketide 2,4-diacetylphloroglucinol (DAPG) and the absence of the lipopeptide/quorum sensing island can serve as the genetic marker for the determination of a plant-protection life style. HPLC detected DAPG in extracts from XL17 CF. MALDI-TOF-MS analysis revealed that strain XL17 produced cyclic lipopeptides of the viscosin family and orfamide family. Together, phenotypic, genomic, and metabolic analyses identified that P. bijieensis XL17 producing DAPG and cyclic lipopeptides can be used to control bacterial canker and gray mold pathogens of kiwifruit. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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13 pages, 1818 KiB

Open AccessArticle

Drought and Plant Community Composition Affect the Metabolic and Genotypic Diversity of Pseudomonas Strains in Grassland Soils

by Claudia Breitkreuz, Thomas Reitz, Elke Schulz and Mika Tapio Tarkka

Microorganisms 2021, 9(8), 1677; https://doi.org/10.3390/microorganisms9081677 - 7 Aug 2021

Cited by 8 | Viewed by 2916

Abstract

Climate and plant community composition (PCC) modulate the structure and function of microbial communities. In order to characterize how the functional traits of bacteria are affected, important plant growth-promoting rhizobacteria of grassland soil communities, pseudomonads, were isolated from a grassland experiment and phylogenetically and functionally characterized. The Miniplot experiment was implemented to examine the mechanisms underlying grassland ecosystem changes due to climate change, and it investigates the sole or combined impact of drought and PCC (plant species with their main distribution either in SW or NE Europe, and a mixture of these species). We observed that the proportion and phylogenetic composition of nutrient-releasing populations of the Pseudomonas community are affected by prolonged drought periods, and to a minor extent by changes in plant community composition, and that these changes underlie seasonality effects. Our data also partly showed concordance between the metabolic activities and 16S phylogeny. The drought-induced shifts in functional Pseudomonas community traits, phosphate and potassium solubilization and siderophore production did not follow a unique pattern. Whereas decreased soil moisture induced a highly active phosphate-solubilizing community, the siderophore-producing community showed the opposite response. In spite of this, no effect on potassium solubilization was detected. These results suggest that the Pseudomonas community quickly responds to drought in terms of structure and function, the direction of the functional response is trait-specific, and the extent of the response is affected by plant community composition. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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14 pages, 2984 KiB

Open AccessArticle

Two Pathway-Specific Transcriptional Regulators, PltR and PltZ, Coordinate Autoinduction of Pyoluteorin in Pseudomonas protegens Pf-5

by Qing Yan, Mary Liu, Teresa Kidarsa, Colin P. Johnson and Joyce E. Loper

Microorganisms 2021, 9(7), 1489; https://doi.org/10.3390/microorganisms9071489 - 13 Jul 2021

Cited by 6 | Viewed by 2549

Abstract

Antibiotic biosynthesis by microorganisms is commonly regulated through autoinduction, which allows producers to quickly amplify the production of antibiotics in response to environmental cues. Antibiotic autoinduction generally involves one pathway-specific transcriptional regulator that perceives an antibiotic as a signal and then directly stimulates transcription of the antibiotic biosynthesis genes. Pyoluteorin is an autoregulated antibiotic produced by some Pseudomonas spp. including the soil bacterium Pseudomonas protegens Pf-5. In this study, we show that PltR, a known pathway-specific transcriptional activator of pyoluteorin biosynthesis genes, is necessary but not sufficient for pyoluteorin autoinduction in Pf-5. We found that pyoluteorin is perceived as an inducer by PltZ, a second pathway-specific transcriptional regulator that directly represses the expression of genes encoding a transporter in the pyoluteorin gene cluster. Mutation of pltZ abolished the autoinducing effect of pyoluteorin on the transcription of pyoluteorin biosynthesis genes. Overall, our results support an alternative mechanism of antibiotic autoinduction by which the two pathway-specific transcriptional regulators PltR and PltZ coordinate the autoinduction of pyoluteorin in Pf-5. Possible mechanisms by which PltR and PltZ mediate the autoinduction of pyoluteorin are discussed. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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21 pages, 3727 KiB

Open AccessArticle

HrpL Regulon of Bacterial Pathogen of Woody Host Pseudomonas savastanoi pv. savastanoi NCPPB 3335

by Alba Moreno-Pérez, Cayo Ramos and Luis Rodríguez-Moreno

Microorganisms 2021, 9(7), 1447; https://doi.org/10.3390/microorganisms9071447 - 5 Jul 2021

Cited by 6 | Viewed by 2796

Abstract

The Pseudomonas savastanoi species comprises a group of phytopathogenic bacteria that cause symptoms of disease in woody hosts. This is mediated by the rapid activation of a pool of virulence factors that suppress host defences and hijack the host’s metabolism to the pathogen’s benefit. The hrpL gene encodes an essential transcriptional regulator of virulence functions, including the type III secretion system (T3SS), in pathogenic bacteria. Here, we analyzed the contribution of HrpL to the virulence of four pathovars (pv.) of P. savastanoi isolated from different woody hosts (oleander, ash, broom, and dipladenia) and characterized the HrpL regulon of P. savastanoi pv. savastanoi NCPPB 3335 using two approaches: whole transcriptome sequencing (RNA-seq) and the bioinformatic prediction of candidate genes containing an hrp-box. Pathogenicity tests carried out for the P. savastanoi pvs. showed that HrpL was essential for symptom development in both non-host and host plants. The RNA-seq analysis of the HrpL regulon in P. savastanoi revealed a total of 53 deregulated genes, 49 of which were downregulated in the ΔhrpL mutant. Bioinformatic prediction resulted in the identification of 50 putative genes containing an hrp-box, 16 of which were shared with genes previously identified by RNA-seq. Although most of the genes regulated by HrpL belonged to the T3SS, we also identified some genes regulated by HrpL that could encode potential virulence factors in P. savastanoi. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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17 pages, 1254 KiB

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The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

by Adrián Pintado, Isabel Pérez-Martínez, Isabel M. Aragón, José Antonio Gutiérrez-Barranquero, Antonio de Vicente, Francisco M. Cazorla and Cayo Ramos

Microorganisms 2021, 9(7), 1388; https://doi.org/10.3390/microorganisms9071388 - 25 Jun 2021

Cited by 7 | Viewed by 2995

Abstract

The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of strain AVO110. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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14 pages, 10278 KiB

Open AccessArticle

Transposon Mutagenesis of Pseudomonas syringae Pathovars syringae and morsprunorum to Identify Genes Involved in Bacterial Canker Disease of Cherry

by Helen C. Neale, Michelle T. Hulin, Richard J. Harrison, Robert W. Jackson and Dawn L. Arnold

Microorganisms 2021, 9(6), 1328; https://doi.org/10.3390/microorganisms9061328 - 18 Jun 2021

Cited by 3 | Viewed by 3901

Abstract

Bacterial canker of Prunus, affecting economically important stone fruit crops including cherry, peach, apricot and plum, is caused by the plant pathogen Pseudomonas syringae (P.s.). Strains from two pathovars—P.s. pv. syringae (Pss) and P.s. pv. morsprunorum race 1 (PsmR1) and 2 (PsmR2)—in three phylogenetically distant clades have convergently evolved to infect Prunus. The bacteria enter woody tissues through wounds and leaf scars, causing black necrotic cankers. Symptoms are also produced on blossom, fruit and leaves. Little is known about the mechanisms P.s. uses to colonise tree hosts such as Prunus. Here, we created transposon (Tn) mutant libraries in one strain of P.s. from each of the three clades and screened the mutants on immature cherry fruit to look for changes in virulence. Mutants (242) with either reduced or enhanced virulence were detected and further characterised by in vitro screens for biofilm formation, swarming ability, and pathogenicity on leaves and cut shoots. In total, 18 genes affecting virulence were selected, and these were involved in diverse functions including motility, type III secretion, membrane transport, amino acid synthesis, DNA repair and primary metabolism. Interestingly, mutation of the effector gene, hopAU1, led to an increase in virulence of Psm R2. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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21 pages, 2186 KiB

Open AccessArticle

Absence of 4-Formylaminooxyvinylglycine Production by Pseudomonas fluorescens WH6 Results in Resource Reallocation from Secondary Metabolite Production to Rhizocompetence

by Viola A. Manning and Kristin M. Trippe

Microorganisms 2021, 9(4), 717; https://doi.org/10.3390/microorganisms9040717 - 31 Mar 2021

Cited by 3 | Viewed by 2562

Abstract

Pseudomonas fluorescens WH6 produces the non-proteinogenic amino acid 4-formylaminooxyvinylglycine (FVG), a secondary metabolite with antibacterial and pre-emergent herbicidal activities. The gvg operon necessary for FVG production encodes eight required genes: one regulatory (gvgR), two of unknown functional potential (gvgA and C), three with putative biosynthetic function (gvgF, H, and I), and two small ORFs (gvgB and G). To gain insight into the role of GvgA and C in FVG production, we compared the transcriptome of knockout (KO) mutants of gvgR, A, and C to wild type (WT) to test two hypotheses: (1) GvgA and GvgC play a regulatory role in FVG production and (2) non-gvg cluster genes are regulated by GvgA and GvgC. Our analyses show that, collectively, 687 genes, including the gvg operon, are differentially expressed in all KO strains versus WT, representing >10% of the genome. Fifty-one percent of these genes were similarly regulated in all KO strains with GvgC having the greatest number of uniquely regulated genes. Additional transcriptome data suggest cluster regulation through feedback of a cluster product. We also discovered that FVG biosynthesis is regulated by L-glu, L-asp, L-gln, and L-asn and that resources are reallocated in KO strains to increase phenotypes involved in rhizocompetence including motility, biofilm formation, and denitrification. Altogether, differential transcriptome analyses of mutants suggest that regulation of the cluster is multifaceted and the absence of FVG production or its downregulation can dramatically shift the lifestyle of WH6. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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23 pages, 5495 KiB

Open AccessArticle

Co-Cultivation of Fusarium, Alternaria, and Pseudomonas on Wheat-Ears Affects Microbial Growth and Mycotoxin Production

by Annika Hoffmann, Gunnar Lischeid, Matthias Koch, Peter Lentzsch, Thomas Sommerfeld and Marina E. H. Müller

Microorganisms 2021, 9(2), 443; https://doi.org/10.3390/microorganisms9020443 - 20 Feb 2021

Cited by 17 | Viewed by 4321

Abstract

Mycotoxigenic fungal pathogens Fusarium and Alternaria are a leading cause of loss in cereal production. On wheat-ears, they are confronted by bacterial antagonists such as pseudomonads. Studies on these groups’ interactions often neglect the infection process’s temporal aspects and the associated priority effects. In the present study, the focus was on how the first colonizer affects the subsequent ones. In a climate chamber experiment, wheat-ears were successively inoculated with two different strains (Alternaria tenuissima At625, Fusarium graminearum Fg23, or Pseudomonas simiae Ps9). Over three weeks, microbial abundances and mycotoxin concentrations were analyzed and visualized via Self Organizing Maps with Sammon Mapping (SOM-SM). All three strains revealed different characteristics and strategies to deal with co-inoculation: Fg23, as the first colonizer, suppressed the establishment of At625 and Ps9. Nevertheless, primary inoculation of At625 reduced all of the Fusarium toxins and stopped Ps9 from establishing. Ps9 showed priority effects in delaying and blocking the production of the fungal mycotoxins. The SOM-SM analysis visualized the competitive strengths: Fg23 ranked first, At625 second, Ps9 third. Our findings of species-specific priority effects in a natural environment and the role of the mycotoxins involved are relevant for developing biocontrol strategies. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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16 pages, 2507 KiB

Open AccessArticle

Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments

by David Lalaouna, Sylvain Fochesato, Mourad Harir, Philippe Ortet, Philippe Schmitt-Kopplin, Thierry Heulin and Wafa Achouak

Microorganisms 2021, 9(2), 250; https://doi.org/10.3390/microorganisms9020250 - 26 Jan 2021

Cited by 7 | Viewed by 2517

Abstract

In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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25 pages, 2357 KiB

Open AccessArticle

In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads

by Esther Blanco-Romero, Daniel Garrido-Sanz, Rafael Rivilla, Miguel Redondo-Nieto and Marta Martín

Microorganisms 2020, 8(11), 1740; https://doi.org/10.3390/microorganisms8111740 - 6 Nov 2020

Cited by 22 | Viewed by 4000

Abstract

Biofilms are complex structures that are crucial during host–bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of Pseudomonas fluorescens F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in Pseudomonas. Interestingly, we identified novel components: the Pseudomonas acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in P. aeruginosa. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete Pseudomonas genomes. Our analyses show that Pseudomonas populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization. Full article

(This article belongs to the Special Issue Plant-Associated Pseudomonads)

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