Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice

Sphingomonas sp. Hbc-6 alters Arabidopsis metabolites to improve plant growth and drought resistance by manipulating the microbiome

Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which Sphingomonas sp. Hbc-6, a PGPB, promotes Arabidopsis growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example Pseudomonas sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of Arabidopsis and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding.

The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS

The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT's biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17-21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas.

Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics

Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.

Sugarcane apoplast fluid modulates the global transcriptional profile of the diazotrophic bacteria Paraburkholderia tropica strain Ppe8

The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. tropica) strain Ppe8, isolated from sugarcane, is part of the bacterial consortium recommended as inoculant to sugarcane. However, little information has been accumulated regarding this plant-bacterium interaction considering that it colonizes internal sugarcane tissues. Here, we made use of the RNA-Seq transcriptomic analysis to study the influence of sugarcane stalk apoplast fluid on Ppe8 gene expression. The bacterium was grown in JMV liquid medium (100 ml), divided equally and then supplemented with 50 ml of fresh JMV medium or 50 ml of apoplast fluid extracted from sugarcane variety RB867515. Total RNA was extracted 2 hours later, the rRNAs were depleted and mRNAs used to construct libraries to sequence the fragments using Ion Torrent technology. The mapping and statistical analysis were carried out with CLC Genomics Workbench software. The RNA-seq data was validated by RT-qPCR using the reference genes fliP1, paaF, and groL. The data analysis showed that 544 genes were repressed and 153 genes were induced in the presence of apoplast fluid. Genes that induce plant defense responses, genes related to chemotaxis and movements were repressed in the presence of apoplast fluid, indicating that strain Ppe8 recognizes the apoplast fluid as a plant component. The expression of genes involved in bacterial metabolism was regulated (up and down), suggesting that the metabolism of strain Ppe8 is modulated by the apoplast fluid. These results suggest that Ppe8 alters its gene expression pattern in the presence of apoplast fluid mainly in order to use compounds present in the fluid as well as to avoid the induction of plant defense mechanisms. This is a pioneer study showing the role played by the sugarcane apoplast fluid on the global modulation of genes in P. tropica strain Ppe8.

Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent

Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.

A Complex Mechanism Involving LysR and TetR/AcrR That Regulates Iron Scavenger Biosynthesis in Pseudomonas donghuensis HYS

7-Hydroxytropolone (7-HT) is a symmetrical seven-membered heteroatomic ring with a carboxyl group and two hydroxyl groups and was recently reported to be an iron scavenger of Pseudomonas donghuensis HYS. Cluster 1 includes 12 genes related to the synthesis of 7-HT; among these genes, those for two regulators, Orf1 and Orf12, were predicted to regulate 7-HT biosynthesis and to be LysR-type transcriptional regulators (LTTRs) and TetR/AcrR family transcriptional regulators, respectively. Data from real-time quantitative PCR and β-galactosidase and classical siderophore assays indicated that the transcription levels of orf1 and orf12, as well as those of crucial genes orf6 to orf9, were repressed under high-iron conditions. The deletion of orf1 and orf12 led to an absence of 7-HT and a decrease in orf6-orf9 expression. Orf1 and Orf12 were essential for the production of 7-HT through orf6-orf9 These two regulators are regulated by the Gac/Rsm system; Orf1 facilitates the expression of Orf12, and Orf12 concomitantly stimulates the expression of orf6-orf9 to synthesize 7-HT. The overexpression of Orf12 decreased 7-HT yields, possibly through decreased orf6-orf9 expression. This work thus outlines a complex mechanism regulating the biosynthesis of the iron scavenger 7-HT in P. donghuensis HYS. The synergy between Orf1 and Orf12 ensures that 7-HT acts as an iron chelator despite being toxic to bacteria and provides new ideas for the novel regulation of dual-functional secondary metabolism and research on 7-HT and its derivates in other bacteria.IMPORTANCE A complex regulation mechanism including two regulators, LysR and TetR/AcrR, in the biosynthesis of the novel iron scavenger 7-hydroxytropolone (7-HT) was verified in Pseudomonas donghuensis HYS. The coaction of LysR Orf1 and TetR/AcrR Orf12 may balance the toxicity and iron chelation of 7-HT in P. donghuensis HYS to overcome iron deficiency, as well as improve the bacterial competitiveness under iron-scarce conditions because of the toxicity of 7-HT toward other bacteria, making the accurate regulation of 7-HT biosynthesis indispensable. This regulation mechanism may be ubiquitous in the Pseudomonas putida group but may better explain the group's strong adaptability.

Impact of Seed Exudates on Growth and Biofilm Formation of Bacillus amyloliquefaciens ALB629 in Common Bean

We aimed to unravel the events which favor the seed-rhizobacterium Bacillus amyloliquefaciens strain ALB629 (hereafter ALB629) interaction and which may interfere with the rhizobacterium colonization and growth on the spermosphere of common bean. Seed exudates from common bean were tested in vitro for ALB629 biofilm formation and bacterial growth. Furthermore, the performance of ALB629 on plant-related variables under drought stress was checked. Seed exudates (1 and 5% v/v) increased ALB629 biofilm formation. Additionally, the colony forming units for ALB629 increased both in culture and on the bean seed surface. The bean seed exudates up-regulated biofilm operons in ALB629 TasA and EpsD by ca. two and sixfold, respectively. The high-performance liquid chromatography (HPLC)-coupled with MS showed that malic acid is present as a major organic acid component in the seed exudates. Seeds treated with ALB629 and amended with malic acid resulted in seedlings with a higher bacterial concentration, induced plant drought tolerance, and promoted plant growth. We showed that seed exudates promote growth of ALB629 and malic acid was identified as a major organic acid component in the bean seed exudates. Our results also show that supplementation of ALB629 induced drought tolerance and growth in plants. The research pertaining to the biological significance of seed exudates in plant–microbe interaction is unexplored field and our work shows the importance of seed exudates in priming both growth and tolerance against abiotic stress.