Comparative Multi-Omics Survey Reveals Novel Specialized Metabolites and Biosynthetic Gene Clusters Under GacS Control in Pseudomonas donghuensis Strain SVBP6.

In Pseudomonas donghuensis SVBP6, isolated from an agricultural field, the well-conserved Gac-Rsm pathway upregulates biosynthesis of the antifungal compound 7-hydroxytropolone (7-HT). However, 7-HT does not fully explain the strain's Gac-Rsm-dependent antimicrobial activity. Here, we combined comparative transcriptomic, proteomic, and metabolomic approaches to identify novel GacS-dependent biosynthetic gene clusters (BGC) and/or extracellular specialized metabolites.

Small Regulatory RNAs of the Rsm Clan in Pseudomonas.

Bacteria of the genus Pseudomonas are ubiquitous on Earth due to their great metabolic versatility and adaptation to fluctuating environments and different hosts. Some groups are important animal/human and plant pathogens, whereas others are studied for their biotechnological applications, including bioremediation, biological control of phytopathogens and plant growth promotion. Notably, their adaptability is mediated by various signal transduction systems, with the post-transcriptional Gac-Rsm cascade playing a key role.

Variability in Maize Seed Bacterization and Survival Correlating with Root Colonization by Isolates with Plant-Probiotic Traits.

Seed treatment with plant growth-promoting bacteria represents the primary strategy to incorporate them into agricultural ecosystems, particularly for crops under extensive management, such as maize. In this study, we evaluated the seed bacterization levels, root colonization patterns, and root competitiveness of a collection of autochthonous isolates that have demonstrated several plant-probiotic abilities in vitro. Our findings indicate that the seed bacterization level, both with and without the addition of various protectants, is specific to each strain, including their response to seed pre-hydration.

An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia.

The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs.

Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas.

In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable.

Azospirillum baldaniorum Sp245 exploits Pseudomonas fluorescens A506 biofilm to overgrow in dual-species macrocolonies.

Biofilms are essential for plant-associated bacteria to colonize their host. In this work, we analysed the interaction of Azospirillum baldaniorum Sp245 and Pseudomonas fluorescens A506 in mixed macrocolony biofilms. We identified certain culture conditions where A.

Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium sp. nov. strain 1008.

sp. strain 1008 was isolated from the rhizosphere of field grown wheat plants at the tillering stage in an agricultural plot near Pergamino city, Argentina. Based on its phosphate solubilizing capacity and the production of IAA, strain 1008 was formulated as an inoculant for bacterization of wheat seeds and subjected to multiple field assays within the period 2010-2017.

Structural studies on the O-specific polysaccharide of the lipopolysaccharide from Pseudomonas donghuensis strain SVBP6, with antifungal activity against the phytopathogenic fungus Macrophomina phaseolina.

An O-specific polysaccharide (OPS) was isolated from the lipopolysaccharide (LPS) of Pseudomonas donghuensis SVBP6, a bacterium with a broad-spectrum antifungal activity in vitro, particularly that against Macrophomina phaseolina. This latter is one of the most virulent and dangerous pathogens of plants, including soybean which is an economically important crop in Argentina today. The OPS was studied by sugar analysis and spectroscopy (1D and 2D H and C NMR) showing the following trisaccharide repeating unit: →6)-ɑ-D-ManpNAc-(1 → 3)-β-l-Rhap-(1 → 4)-β-D-Glcp-(1→.

Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria.

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus .

Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs.

7-hydroxytropolone is the main metabolite responsible for the fungal antagonism of Pseudomonas donghuensis strain SVBP6.

Pseudomonas donghuensis strain SVBP6, an isolate from an agricultural plot in Argentina, displays a broad-spectrum and diffusible antifungal activity, which requires a functional gacS gene but could not be ascribed yet to known secondary metabolites typical of Pseudomonas biocontrol species. Here, we report that Tn5 mutagenesis allowed the identification of a gene cluster involved in both the fungal antagonism and the production of a soluble tropolonoid compound. The ethyl acetate extract from culture supernatant showed a dose-dependent inhibitory effect against the phytopathogenic fungus Macrophomina phaseolina.

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization.

Bacteria of the Azospirillum and Pseudomonas genera are ubiquitous members of the rhizosphere, where they stimulate plant growth. Given the outstanding capacity of pseudomonads to antagonize other microorganisms, we analyzed the interaction between these two bacterial groups to identify determinants of their compatibility. We could establish that, when in direct contact, certain Pseudomonas strains produce lethality on Azospirillum brasilense cells using an antibacterial type 6 secretion system.

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6.

Plant-growth promotion has been linked to the Pseudomonas genus since the beginning of this research field. In this work, we mined the genome of an Argentinean isolate of the recently described species P. donghuensis.

Guidelines for Inferring and Characterizing a Family of Bacterial trans-Acting Small Noncoding RNAs.

So far, every sequenced bacterial transcriptome encompasses hundreds of small regulatory noncoding RNAs (sRNAs). From those sRNAs that have been already characterized, we learned that their regulatory functions could span over almost every bacterial process, mostly acting at the posttranscriptional control of gene expression (Wagner and Romby, Adv Genet 90:133-208, 2015). Canonical molecular mechanisms of sRNA action have been described to rely on both sequence and/or structural traits of the RNA molecule.

Expression of the small regulatory RNA gene mmgR is regulated negatively by AniA and positively by NtrC in Sinorhizobium meliloti 2011.

In the N2-fixing symbiont of alfalfa root nodules, Sinorhizobium meliloti 2011, the mmgR gene encodes a 77 nt small untranslated RNA (sRNA) that negatively regulates the accumulation of polyhydroxybutyrate (PHB) when the bacterium is grown under conditions of surplus carbon (C) in relation to nitrogen (N). We previously showed that the expression of mmgR is primarily controlled at the transcriptional level and that it depends on the cellular N status, although the regulatory mechanism and the factors involved were unknown. In this study, we provide experimental data supporting that: (a) mmgR is induced upon N limitation with the maximum expression found at the highest tested C/N molar ratio in the growth medium; (b) a conserved heptamer TTGTGCA located between the -35 and -10 mmgR promoter elements is necessary and sufficient for induction by N limitation; (c) induction of mmgR requires the N-status regulator NtrC; (d) under C limitation, mmgR transcription is repressed by AniA, a global regulator of C flow; (e) the mmgR promoter contains a conserved dyadic motif (TGC[N3]GCA) partially overlapping the heptamer TTGTGCA, which was also found in the promoters of the PHB-related genes phaP1, phaP2, phaZ and phaR (aniA) of S.

Quantification of Bacterial Polyhydroxybutyrate Content by Flow Cytometry.

We describe here a detailed protocol for the quantification of the intracellular content of polyhydroxybutyrate (PHB) in a population of bacterial cells by flow cytometry, which is based on a consensus of several previously reported works.

A matter of hierarchy: activation of orfamide production by the post-transcriptional Gac-Rsm cascade of Pseudomonas protegens CHA0 through expression upregulation of the two dedicated transcriptional regulators.

In this work, we surveyed the genome of P. protegens CHA0 in order to identify novel mRNAs possibly under the control of the Gac-Rsm cascade that might, for their part, serve to elucidate as-yet-unknown functions involved in the biocontrol of plant pathogens and/or in cellular processes required for fitness in natural environments. In view of the experimental evidence from former studies on the Gac-Rsm cascade, we developed a computational screen supported by a combination of sequence, structural and evolutionary constraints that led to a dataset of 43 potential novel mRNA targets.

The Irr and RirA Proteins Participate in a Complex Regulatory Circuit and Act in Concert To Modulate Bacterioferritin Expression in Ensifer meliloti 1021.

In this work we found that the gene of the rhizobial species , encoding a bacterioferritin iron storage protein, is involved in iron homeostasis and the oxidative stress response. This gene is located downstream of and overlapping the open reading frame (ORF). No well-predicted RirA or Irr boxes were found in the region immediately upstream of the gene although two presumptive RirA boxes and one presumptive Irr box were present in the putative promoter of We demonstrate that gene expression is enhanced under iron-sufficient conditions and that Irr and RirA modulate this expression.

Correction: Quantitative Proteomic Analysis of the Hfq-Regulon in Sinorhizobium meliloti 2011.

[This corrects the article DOI: 10.1371/journal.pone.

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the -Encoded Small RNA MmgR.

Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, -encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In , over 400 sRNAs are expressed under different stimuli.

Interspecific cooperation: enhanced growth, attachment and strain-specific distribution in biofilms through Azospirillum brasilense-Pseudomonas protegens co-cultivation.

Plant-growth-promoting bacteria belonging to Azospirillum and Pseudomonas genera are major inhabitants of the rhizosphere. Both are increasingly commercialized as crops inoculants. Interspecific interaction in the rhizosphere is critical for inoculants aptness.

Major cereal crops benefit from biological nitrogen fixation when inoculated with the nitrogen-fixing bacterium Pseudomonas protegens Pf-5 X940.

A main goal of biological nitrogen fixation research has been to expand the nitrogen-fixing ability to major cereal crops. In this work, we demonstrate the use of the efficient nitrogen-fixing rhizobacterium Pseudomonas protegens Pf-5 X940 as a chassis to engineer the transfer of nitrogen fixed by BNF to maize and wheat under non-gnotobiotic conditions. Inoculation of maize and wheat with Pf-5 X940 largely improved nitrogen content and biomass accumulation in both vegetative and reproductive tissues, and this beneficial effect was positively associated with high nitrogen fixation rates in roots.

Phylogenetic distribution and evolutionary pattern of an α-proteobacterial small RNA gene that controls polyhydroxybutyrate accumulation in Sinorhizobium meliloti.

It has become clear that sRNAs play relevant regulatory functions in bacteria. However, a comprehensive understanding of their biological roles considering evolutionary aspects has not been achieved for most of them. Thus, we have characterized the evolutionary and phylogenetic aspects of the Sinorhizobium meliloti mmgR gene encoding the small RNA MmgR, which has been recently reported to be involved in the regulation of polyhydroxybutyrate accumulation in this bacterium.

Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source.

Small non-coding regulatory RNAs (sRNAs) are key players in post-transcriptional regulation of gene expression. Hundreds of sRNAs have been identified in Sinorhizobium meliloti, but their biological function remains unknown for most of them. In this study, we characterized the expression pattern of the gene encoding the 77-nt sRNA MmgR in S.