Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight

Vrieze, Mout De; Varadarajan, Adithi R.; Schneeberger, Kerstin; Bailly, Aurélien; Rohr, Rudolf P.; Ahrens, Christian H.; Weisskopf, Laure

doi:10.3389/fmicb.2020.00857

Cited by 38 publications

(33 citation statements)

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“…Conceptually, the model was designed to integrate genotype data with phenotypic information and to leverage the wealth of existing public genetic resources and functional genomics data sets. A complete, fully resolved genome sequence is one critical element 31 , 57 , which recently allowed linking of genotypic differences of nine Pseudomonas plant microbiome isolates with their varying biocontrol potential 58 . While a complete genome existed for P. aeruginosa PAO1 2 , only three fragmented Illumina-based genome assemblies were available for MPAO1, the parental strain of the popular UW transposon mutant library 21 .…”

Section: Discussionmentioning

confidence: 99%

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

Varadarajan

Allan

Valentin

et al. 2020

npj Biofilms Microbiomes

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Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.

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Section: Discussionmentioning

confidence: 99%

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

Varadarajan

Allan

Valentin

et al. 2020

npj Biofilms Microbiomes

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“…For instance, whole-genome sequencing of both wild-type and a pigmentless mutant strain of the antagonist Metschnikowia pulcherrima allowed to identify Snf2 as a regulator of antifungal activity (Gore-Lloyd et al, 2019). Thereby, links from the genotype to a phenotype can be suggested, as has been shown in systems for potential biocontrol strains and different host plant varieties (De Vrieze et al, 2020). An important approach to reduce the number of candidate genes provided from genome comparisons are transcriptomics studies.…”

Section: An Integrated Strategy To Harness Compost Microbiomes For Plmentioning

confidence: 99%

“…In addition, the de novo assembly of complete genomes of isolates that show a suppressive effect, offer unprecedented opportunities to move beyond studying the composition of compost microbiomes toward obtaining a mechanistic understanding of the beneficial effects that individual strains and consortia of strains can exert, and to elucidate direct causal effects (i.e., specific genes or pathways involved in suppression). The great potential of this approach has been shown for both strains isolated from natural soils that exert suppressive effects against pathogens (Mendes et al, 2011;De Vrieze et al, 2015;De Vrieze et al, 2020), as well as for strains isolated from the phyllosphere (Gore-Lloyd et al, 2019).…”

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Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

et al. 2020

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“…Similarly, promising results were obtained in our previous studies exploring the potential of Pseudomonas strains isolated from the potato microbiome for late blight control [ 6 , 21 , 22 , 30 , 31 ]. We have recently identified some candidate genes putatively involved in this anti- Phytophthora activity, among which those encoding production of the respiratory toxin HCN [ 20 ]. Here, we verified the involvement of this known particular biocontrol trait and quantified its relative contribution to the overall anti-oomycete activity of two cyanogenic Pseudomonas using in vitro and leaf disk experiments.…”

Section: Discussionmentioning

confidence: 99%

“…In a recent comparative genomics study investigating the putative genetic determinants underlying the anti- Phytophthora activity of potato-associated Pseudomonas strains, we observed that the strains showing strong in vitro inhibition of P. infestans mycelial growth all harbored the HCN locus in their genome [ 20 ]. We therefore asked the question of the relative contribution of this particular biocontrol trait to the overall protective effect of cyanogenic Pseudomonas known for their strong biocontrol activity against different pathogens like Phytophthora infestans , Helminthosporium solani , Rhizoctonia solani , Fusarium oxysporum, and Dickeya dianthicola [ 6 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans

et al. 2020

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Plants face many biotic and abiotic challenges in nature; one of them is attack by disease-causing microbes. Phytophthora infestans, the causal agent of late blight is one of the most prominent pathogens of the potato responsible for multi-billion-dollar losses every year. We have previously reported that potato-associated Pseudomonas strains inhibited P. infestans at various developmental stages. A comparative genomics approach identified several factors putatively involved in this anti-oomycete activity, among which was the production of hydrogen cyanide (HCN). Here, we report the relative contribution of HCN emission to the overall anti-Phytophthora activity of two cyanogenic Pseudomonas strains, P. putida R32 and P. chlororaphis R47. To quantify this contribution, we generated HCN-negative mutants (Δhcn) and compared their activities to those of their respective wild types in different experiments assessing P. infestans mycelial growth, zoospore germination, and infection of potato leaf disks. Using in vitro experiments allowing only volatile-mediated interactions, we observed that HCN accounted for most of the mycelial growth inhibition (57% in R47 and 80% in R32). However, when allowing both volatile and diffusible compound-mediated interactions, HCN only accounted for 1% (R47) and 18% (R32) of mycelial growth inhibition. Likewise, both mutants inhibited zoospore germination in a similar way as their respective wild types. More importantly, leaf disk experiments showed that both wild-type and Δhcn strains of R47 and R32 were able to limit P. infestans infection to a similar extent. Our results suggest that while HCN is a major contributor to the in vitro volatile-mediated restriction of P. infestans mycelial growth, it does not play a major role in the inhibition of other disease-related features such as zoospore germination or infection of plant tissues.

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Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight

Cited by 38 publications

References 100 publications

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans

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