Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp.

Zboralski, Antoine; Filion, Martin

doi:10.1016/j.csbj.2020.11.025

Cited by 73 publications

(41 citation statements)

References 216 publications

(92 reference statements)

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“…Bacterial pathways expressed during rhizosphere colonization control utilization of plant-derived metabolites (Simons et al, 1996(Simons et al, , 1997Camacho-Carvajal, 2001;Lugtenberg and Kamilova, 2009), motility and chemotaxis (de Weert et al, 2002;Lugtenberg and Kamilova, 2009), phase variation (Dekkers et al, 1998;Sanchez-Contreras et al, 2002;van den Broek et al, 2005), outer membrane integrity (de Weert et al, 2006;Lugtenberg and Kamilova, 2009), and the ability to sequester limiting resources (Raaijmakers et al, 1995) and resist environmental stresses (Sarniguet et al, 1995;Miller and Wood, 1996;van Veen et al, 1997;Schnider-Keel et al, 2001). In its spatial and temporal properties, root colonization resembles biofilm formation, and biofilm-related pathways also have been implicated in adhesion to seeds and roots and rhizosphere colonization (Espinosa-Urgel et al, 2000;Hinsa et al, 2003;Yousef-Coronado et al, 2008;Fuqua, 2010;Martinez-Gil et al, 2010;Nielsen et al, 2011;Zboralski and Filion, 2020). Finally, root exudates strongly affect the expression of diverse plant growth promotion and biocontrol genes (Vacheron et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas

et al. 2021

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Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.

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Section: Introductionmentioning

confidence: 99%

Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas

et al. 2021

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“…and Pseudomonas spp. members can not only stimulate induced systemic resistance (ISR) of the host plant and produce antibiotics to suppress pathogens, but also secrete secondary metabolites to promote growth or to enhance abiotic stress tolerance of the host plant [7] , [8] . However, these functions depend on the abiotic conditions and the biological interactions for these members to exert their plant beneficial properties in a rhizosphere community with high species diversity [9] , [10] .…”

Section: Introductionmentioning

confidence: 99%

Rhizosphere microbiome: Functional compensatory assembly for plant fitness

Xun

Shao

Shen

et al. 2021

Computational and Structural Biotechnology Journal

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Environmental pressure to reduce our reliance on agrochemicals and the necessity to increase crop production in a sustainable way have made the rhizosphere microbiome an untapped resource for combating challenges to agricultural sustainability. In recent years, substantial efforts to characterize the structural and functional diversity of rhizosphere microbiomes of the model plant Arabidopsis thaliana and various crops have demonstrated their importance for plant fitness. However, the plant benefiting mechanisms of the rhizosphere microbiome as a whole community rather than as an individual rhizobacterium have only been revealed in recent years. The underlying principle dominating the assembly of the rhizosphere microbiome remains to be elucidated, and we are still struggling to harness the rhizosphere microbiome for agricultural sustainability. In this review, we summarize the recent progress of the driving factors shaping the rhizosphere microbiome and provide community-level mechanistic insights into the benefits that the rhizosphere microbiome has for plant fitness. We then propose the functional compensatory principle underlying rhizosphere microbiome assembly. Finally, we suggest future research efforts to explore the rhizosphere microbiome for agricultural sustainability.

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“…In addition to gaining understanding of gvg cluster regulation, the impact of FVG production on the transcriptome, and the regulation of FVG production by acidic amino acids, we observed that genes necessary for rhizocompetence phenotypes were positively regulated in the absence (or decrease) of FVG. There are several well-documented competence traits common to rhizosphere-colonizing bacteria [ 51 , 52 , 53 , 54 , 55 ]. Motility in Pf is important for root colonization [ 56 ] and highly motile variants have a competitive advantage [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

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

Manning

Trippe

2021

Microorganisms

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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.

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Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp.

Abstract: Graphical abstract

Cited by 73 publications

References 216 publications

Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas

Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas

Rhizosphere microbiome: Functional compensatory assembly for plant fitness

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

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