Modulation of nitrogen metabolism of maize plants inoculated with Azospirillum brasilense and Herbaspirillum seropedicae

Impact of historical soil management on the interaction of plant-growth-promoting bacteria with maize (Zea mays L.)

Edaphic factors can modulate the effects of microbial inoculants on crop yield promotion. Given the potential complexity of microbial inoculant responses to diverse soil management practices, we hypothesize that sustainable management of soil and water irrigation may improve soil quality and enhance the effects of plant growth-promoting bacteria (PGPB). Consequently, the primary objective was to assess the effectiveness of microbial inoculants formulated with Herbaspirillum seropedicae (Hs) and Azospirillum brasilense (Ab) on maize growth in soils impacted by different historical conservation management systems. We evaluated two soil management systems, two irrigation conditions, and four treatments: T0 - without bioinoculant and 100% doses of NPK fertilization; T1 - Hs + humic substances and 40% of NPK fertilization; T2 - Ab and 40% of NPK fertilization; T3 - co-inoculation (Hs + Ab) and 40% of NPK fertilization. Using a reduced fertilization dose (40% NPK) associated with microbial inoculants proved efficient in increasing maize shoot dry mass : on average, there was a 16% reduction compared to the treatment with 100% fertilization. In co-inoculation (Hs + Ab), the microbial inoculants showed a mutualistic effect on plant response, higher than isolate ones, especially increasing the nitrogen content in no-tillage systems irrigated by swine wastewater. Under lower nutrient availability and higher biological soil quality, the microbial bioinputs positively influenced root development, instantaneous water use efficiency, stomatal conductance, and nitrogen contents.

Complete genome analysis of sugarcane root associated endophytic diazotroph Pseudomonas aeruginosa DJ06 revealing versatile molecular mechanism involved in sugarcane development

Sugarcane is an important sugar and bioenergy source and a significant component of the economy in various countries in arid and semiarid. It requires more synthetic fertilizers and fungicides during growth and development. However, the excess use of synthetic fertilizers and fungicides causes environmental pollution and affects cane quality and productivity. Plant growth-promoting bacteria (PGPB) indirectly or directly promote plant growth in various ways. In this study, 22 PGPB strains were isolated from the roots of the sugarcane variety GT42. After screening of plant growth-promoting (PGP) traits, it was found that the DJ06 strain had the most potent PGP activity, which was identified as Pseudomonas aeruginosa by 16S rRNA gene sequencing. Scanning electron microscopy (SEM) and green fluorescent protein (GFP) labeling technology confirmed that the DJ06 strain successfully colonized sugarcane tissues. The complete genome sequencing of the DJ06 strain was performed using Nanopore and Illumina sequencing platforms. The results showed that the DJ06 strain genome size was 64,90,034 bp with a G+C content of 66.34%, including 5,912 protein-coding genes (CDSs) and 12 rRNA genes. A series of genes related to plant growth promotion was observed, such as nitrogen fixation, ammonia assimilation, siderophore, 1-aminocyclopropane-1-carboxylic acid (ACC), deaminase, indole-3-acetic acid (IAA) production, auxin biosynthesis, phosphate metabolism, hydrolase, biocontrol, and tolerance to abiotic stresses. In addition, the effect of the DJ06 strain was also evaluated by inoculation in two sugarcane varieties GT11 and B8. The length of the plant was increased significantly by 32.43 and 12.66% and fresh weight by 89.87 and 135.71% in sugarcane GT11 and B8 at 60 days after inoculation. The photosynthetic leaf gas exchange also increased significantly compared with the control plants. The content of indole-3-acetic acid (IAA) was enhanced and gibberellins (GA) and abscisic acid (ABA) were reduced in response to inoculation of the DJ06 strain as compared with control in two sugarcane varieties. The enzymatic activities of oxidative, nitrogen metabolism, and hydrolases were also changed dramatically in both sugarcane varieties with inoculation of the DJ06 strain. These findings provide better insights into the interactive action mechanisms of the P. aeruginosa DJ06 strain and sugarcane plant development.

Multiomic Approaches Reveal Hormonal Modulation and Nitrogen Uptake and Assimilation in the Initial Growth of Maize Inoculated with Herbaspirillum seropedicae

Herbaspirillum seropedicae is an endophytic bacterium that can fix nitrogen and synthesize phytohormones, which can lead to a plant growth-promoting effect when used as a microbial inoculant. Studies focused on mechanisms of action are crucial for a better understanding of the bacteria-plant interaction and optimization of plant growth-promoting response. This work aims to understand the underlined mechanisms responsible for the early stimulatory growth effects of H. seropedicae inoculation in maize. To perform these studies, we combined transcriptomic and proteomic approaches with physiological analysis. The results obtained eight days after inoculation (d.a.i) showed increased root biomass (233 and 253%) and shoot biomass (249 and 264%), respectively, for the fresh and dry mass of maize-inoculated seedlings and increased green content and development. Omics data analysis, before a positive biostimulation phenotype (5 d.a.i.) revealed that inoculation increases N-uptake and N-assimilation machinery through differentially expressed nitrate transporters and amino acid pathways, as well carbon/nitrogen metabolism integration by the tricarboxylic acid cycle and the polyamine pathway. Additionally, phytohormone levels of root and shoot tissues increased in bacterium-inoculated-maize plants, leading to feedback regulation by the ubiquitin-proteasome system. The early biostimulatory effect of H. seropedicae partially results from hormonal modulation coupled with efficient nutrient uptake-assimilation and a boost in primary anabolic metabolism of carbon-nitrogen integrative pathways.

The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops

Agriculture is facing increasing challenges with regard to achieving sustainable growth in productivity without negatively impacting the environment. The use of bioinoculants is emerging as a sustainable solution for agriculture, especially bioinoculants based on diazotrophic bacteria. Brazil is at the forefront of studies intended to identify beneficial diazotrophic bacteria, as well as in the molecular characterization of this association on both the bacterial and plant sides. Here we highlight the main advances in molecular studies to understand the benefits brought to plants by diazotrophic bacteria. Different molecular pathways in plants are regulated both genetically and epigenetically, providing better plant performance. Among them, we discuss the involvement of genes related to nitrogen metabolism, cell wall formation, antioxidant metabolism, and regulation of phytohormones that can coordinate plant responses to environmental factors. Another important aspect in this regard is how the plant recognizes the microorganism as beneficial. A better understanding of plant–bacteria–environment interactions can assist in the future formulation of more efficient bioinoculants, which could in turn contribute to more sustainable agriculture practices.

Effects of Chemical Fertilization and Microbial Inoculum on Bacillus subtilis Colonization in Soybean and Maize Plants

Plant growth-promoting endophytic microorganisms in agriculture have been expanding in Brazil and are an excellent strategy to face the challenges of current agriculture, such as reducing production costs with fewer environmental impacts, without detriment to productivity. However, little is known about the factors that can affect the colonization of endophytic such as inoculant concentration and mineral fertilization. The present study aimed to evaluate the influence of these factors on soybean and maize crops and found that for soybean crops, the highest Bacillus subtilis concentration of 1 × 10⁴ and 1 × 10¹⁰ CFU ml⁻¹ promoted the highest number of recovered bacteria, when there was no mineral fertilization. However, mineral fertilization limited the number of recovered bacteria, suggesting that mineral fertilization interferes with endophytic colonization. For maize crops, the highest number of recovered bacteria occurred from the concentration of 1 × 10⁶ CFU ml⁻¹, not differing from the highest concentrations. A mineral fertilization dose of 25% promoted the greatest B. subtilis recovery compared to the other treatments. Regarding plant development, the highest microbial inoculum concentrations did not necessarily promote greater positive growth promotion effects compared to the concentration of 1 × 10⁴ CFU ml⁻¹ for both crops. The results also suggest that the higher number of endophytic bacteria recovered in the plant does not necessarily affect plant growth in the same proportion. For soybean plants, there is a strong tendency that with the increase in the B. subtilis inoculant concentration, the need for mineral fertilization doses to achieve the same plant development is consequently increased, and inoculations with 1 × 10⁵ and 1 × 10⁶ CFU ml⁻¹ with fertilization doses between 44% and 62% are the ideal combinations for greater plant development. In maize plants, the best growth promotion response (height) was obtained using inoculation concentration of 1 × 10² and 1 × 10¹⁰ CFU ml⁻¹, increasing according to the increase in fertilization doses. The findings suggest, for soybean crop, that these high inoculum concentrations required more photosynthetic metabolites from the plants and more nutrients from the soil. Thus, the need for mineral fertilization for plant growth must be increased.

Melatonin improves nitrogen metabolism during grain filling under drought stress

Drought affects the normal growth and development of soybeans. Melatonin reportedly alleviates drought stress-induced growth inhibition and plant injury, thus, its foliar application presumably has considerable potential in agriculture. However, few studies have investigated the mechanism responsible for its effects on soybean nitrogen metabolism. In this study, pot culture and plant physiological detection, qPCR, and other methods were used for analysis. The purpose of this study was to explore the effects of melatonin and melanin on glutathione metabolism. The results showed that drought stress led to an increase in soluble protein and proline content, concomitantly with a decrease in the activity of nitrogen metabolism-related key enzymes, an increase in inorganic nitrogen content, and a reduction in nitrogen accumulation and transport. Exogenous melatonin application under drought stress significantly increased the expression of key genes involved in nitrogen metabolism and the activity of key enzymes including, GOGAT, NR, Gs and GDH. Enhanced enzyme activity promotes the conversion of nitrate nitrogen in plants, increases proline, soluble protein, and ureide contents, and, consequently, nitrogen accumulation. Altogether, these changes were conducive to greater nitrogen assimilation and transport. Therefore, under drought stress, melatonin application upregulated key genes involved in nitrogen metabolism, thereby enhancing the activity of related enzymes and restoring growth, stable biomass production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01219-y.

Inoculation of Herbaspirillum seropedicae strain SmR1 increases biomass in maize roots DKB 390 variety in the early stages of plant development

Herbaspirillum seropedicae is a plant growth-promoting bacteria isolated from diverse plant species. In this work, the main objective was to investigate the efficiency of H. seropedicae strain SmR1 in colonizing and increasing maize growth (DKB 390 variety) in the early stages of development under greenhouse conditions. Inoculation with H. seropedicae resulted in 19.43 % (regarding High and Low N controls) and 10.51% (regarding Low N control) in mean of increase of root biomass, for 1^st and 2^nd greenhouse experiments, respectively, mainly in the initial stages of plant development, at 21 days after emergence (DAE). Quantification of H. seropedicae in roots and leaves was performed by quantitative PCR. H. seropedicae was detected only in maize inoculated roots by qPCR, and a slight decrease in DNA copy number g^-1 of fresh root weight was observed from 7 to 21 DAE, suggesting that there was initial effective colonization on maize plants. H. seropedicae strain SmR1 efficiently increased maize root biomass exhibiting its potential to be used as inoculant in agricultures systems.

The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria

The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co²⁺, Fe³⁺, Mo^2 +, V⁵⁺, Zn²⁺), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.

Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid

Bacterial transcriptome profiling in the presence of plant fluids or extracts during microbial growth may provide relevant information on plant-bacteria interactions. Here, RNA sequencing (RNA-Seq) was used to determine the transcriptomic profile of Herbaspirillum seropedicae strain HRC54 at the early stages of response to sugarcane apoplastic fluid. Differentially expressed gene (DEG) analysis was performed using the DESeq2 and edgeR packages, followed by functional annotation using Blast2GO and gene ontology enrichment analysis using the COG and KEGG databases. After 2 h of sugarcane apoplastic fluid addition to the H. seropedicae HRC54 culture, respectively, 44 and 45 genes were upregulated and downregulated. These genes were enriched in bacterial metabolism (e.g., oxidoreductase and transferase), ABC transporters, motility, secretion systems, and signal transduction. RNA-Seq expression profiles of 12 genes identified in data analyses were verified by RT-qPCR. The results suggested that H. seropedicae HRC54 recognized sugarcane apoplastic fluid as the host signal, and some DEGs were closely involved at the early stages of the establishment of plant-bacteria interactions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02848-y.

Effect of Chemical Fertilization on the Impacts of Plant Growth-Promoting Rhizobacteria in Maize Crops

The use of chemical fertilizers strongly promotes productivity in agricultural crops; therefore, large amounts of chemical fertilizers have been used. The use of plant growth-promoting bacteria may be a strategy to reduce the use of chemical fertilizers; however, little is known about the effect of chemical fertilization on the performance of these bacteria through plant-microbe interactions. The present study aimed to verify the performance of Bacillus subtilis, Azospirillum brasilense, B. pumilus, B. amyloliquefaciens, Herbaspirillum seropedicae, Gluconacetobacter diazotrophicus, and the mixtures A. brasilense + B. subtilis, B. pumilus + B. amyloliquefaciens, and H. seropedicae + G. diazotrophicus on parameters such as nitrogen and phosphorus extraction from soil, the concentrations of these nutrients in maize plants, and plant growth in both fertilized and unfertilized soil. The results showed that H. seropedica increased the nitrogen content by 6.6 g kg^-1 in leaves and 2.2 g kg^-1 in the root when comparing the unfertilized with the fertilized condition. G. diazotrophicus increased the nitrogen content by 3.7 g kg^-1 in leaves and 2.4 g kg^-1 in the root. B. pumilus increased the phosphorous content by 1.7 g kg^-1 in leaves, and B. amyloliquefaciens increased the phosphorous content by 0.61 g kg^-1. The present study showed that even though the bacteria presented good performance related to plant growth under fertilized conditions, H. seropedicae, G. diazotrophicus, B. pumilus, and B. amyloliquefaciens could be used in the maize crop with a reduced chemical fertilization dose.

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix⁺) or a fix^- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix^- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix^- strain, perhaps reflecting a plant defense response.