Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria

Thermal and salt stress effects on the survival of plant growth-promoting bacteria Azospirillum brasilense in inoculants for maize cultivation

BACKGROUND

The plant growth-promoting bacteria (PGPB) Azospirillum brasilense is widely used as an inoculant for important grass crops, providing numerous benefits to the plants. However, one limitation to develop viable commercial inoculants is the control of PGPB survival, requiring strategies that guarantee their survival during handling and field application. The application of sublethal stress appears to be a promising strategy to increase bacterial cells tolerance to adverse environmental conditions since previous stress induces the activation of physiological protection in bacterial cell. In this work, we evaluated the effects of thermal and salt stresses on the survival of inoculant containing A. brasilense Ab-V5 and Ab-V6 strains and we monitored A. brasilense viability in inoculated maize roots after stress treatment of inoculant.

RESULTS

Thermal stress application (> 35 °C) in isolated cultures for both strains, as well as salt stress [sodium chloride (NaCl) concentrations > 0.3 mol L-1], resulted in growth rate decline. The A. brasilense enumeration in maize roots obtained by propidium monoazide quantitative polymerase chain reaction (PMA-qPCR), for inoculated maize seedlings grown in vitro for 7 days, showed that there is an increased number of viable cells after the salt stress treatment, indicating that A. brasilense Ab-V5 and Ab-V6 strains are able to adapt to salt stress (0.3 mol L-1 NaCl) growth conditions.

CONCLUSION

Azospirillum brasilense Ab-V5 and Ab-V6 strains had potential for osmoadaptation and salt stress, resulting in increased cell survival after inoculation in maize plants. © 2024 Society of Chemical Industry.

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.

Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T

Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4^T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4^T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.

Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition

Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

Brachypodium: 20 years as a grass biology model system; the way forward?

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.

Targeted and Untargeted Metabolomic Analyses Reveal Organ Specificity of Specialized Metabolites in the Model Grass Brachypodium distachyon

Brachypodium distachyon, because of its fully sequenced genome, is frequently used as a model grass species. However, its metabolome, which constitutes an indispensable element of complex biological systems, remains poorly characterized. In this study, we conducted comprehensive, liquid chromatography-mass spectrometry (LC-MS)-based metabolomic examination of roots, leaves and spikes of Brachypodium Bd21 and Bd3-1 lines. Our pathway enrichment analysis emphasised the accumulation of specialized metabolites representing the flavonoid biosynthetic pathway in parallel with processes related to nucleotide, sugar and amino acid metabolism. Similarities in metabolite profiles between both lines were relatively high in roots and leaves while spikes showed higher metabolic variance within both accessions. In roots, differences between Bd21 and Bd3-1 lines were manifested primarily in diterpenoid metabolism, while differences within spikes and leaves concerned nucleotide metabolism and nitrogen management. Additionally, sulphate-containing metabolites differentiated Bd21 and Bd3-1 lines in spikes. Structural analysis based on MS fragmentation spectra enabled identification of 93 specialized metabolites. Among them phenylpropanoids and flavonoids derivatives were mainly determined. As compared with closely related barley and wheat species, metabolic profile of Brachypodium is characterized with presence of threonate derivatives of hydroxycinnamic acids.

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25-30 plants h-1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH4NO3 the benefit appears through N fixation, while at 0.5 mM NH4NO3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

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.

Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis

Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.

Plant growth-promoting mechanisms and genetic diversity of bacteria strains isolated from Brachiaria humidicola and Brachiaria decumbens

Plant growth-promoting bacteria (PGPB) have received great interest in recent decades. However, PGPB mechanisms remain poorly understood in forage species. We aimed to evaluate roots endophytic and rhizospheric bacteria strains from Brachiaria humidicola and Brachiaria decumbens. The strains were evaluated for biological nitrogen-fixing in saline stress (0 to 10.0 g L-1 of NaCl), N-acyl homoserine lactones and indole-like compounds (ILC) production, the activity of hydrolytic enzymes, and inorganic phosphate solubilization (IPS) under different C sources. The diversity of strains was assessed by BOX-PCR. About 58% of strains were positive for BNF. High salinity levels reduced the growth and BNF. About 58% produced N-acyl homoserine lactones. The ILC was present in 39% of strains. Cellulase, polygalacturonase, pectate lyase, and amylase production were observed in 77, 14, 22, and 25% of strains, respectively. The IPS was observed in 44, 81, and 87% of isolates when glucose, mannitol and sucrose were used, respectively. Comparing two plant species and niches, the strains associated with B. humidicola and root endophytic presented more PGPB mechanisms than others. We found high strain diversity, of which 64% showed similarity lower than 70%. These results can be supporting the bioproducts development to increase forage grasses production in tropical soils.

High-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities

Much effort has been placed on developing microbial inoculants to replace or supplement fertilizers to improve crop productivity and environmental sustainability. However, many studies ignore the dynamics of plant-microbe interactions and the genotypic specificity of the host plant on the outcome of microbial inoculation. Thus, it is important to study temporal plant responses to inoculation in multiple genotypes within a single species. With the implementation of high-throughput phenotyping, the dynamics of biomass and nitrogen (N) accumulation of four sorghum genotypes with contrasting N-use efficiency were monitored upon the inoculation with synthetic microbial communities (SynComs) under high and low-N. Five SynComs comprising bacteria isolated from field grown sorghum were designed based on the overall phylar composition of bacteria and the enriched host compartment determined from a field-based culture independent study of the sorghum microbiome. We demonstrated that the growth response of sorghum to SynCom inoculation is genotype-specific and dependent on plant N status. The sorghum genotypes that were N-use inefficient were more susceptible to the colonization from a diverse set of inoculated bacteria as compared to the N-use efficient lines especially under low-N. By integrating high-throughput phenotyping with sequencing data, our findings highlight the roles of host genotype and plant nutritional status in determining colonization by bacterial synthetic communities.

Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals

Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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.

Correlative surface imaging reveals chemical signatures for bacterial hotspots on plant roots

A universal sample holder allows correlative imaging analysis of plant roots to reveal chemical signatures for bacterial hotspots.

Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops

Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.

Enhanced drought tolerance in seedlings of Neotropical tree species inoculated with plant growth-promoting bacteria

The inoculation of tree species with plant growth-promoting bacteria (PGPB) has emerged as an important strategy for the acclimation of seedlings by improving plant tolerance to biotic and abiotic stresses. This study aimed to evaluate the effects of inoculation with bacterial species (Azospirillum brasilense - Ab-V5, Bacillus sp., Azomonas sp. and Azorhizophillus sp.) on the growth and physiology of the Neotropical tree species Trema micrantha and Cariniana estrellensis under drought conditions. When associated with Ab-V5 and Azomonas sp., T. micrantha showed increased protein in the leaves, starch in the leaves and roots, photosynthesis, instantaneous carboxylation efficiency and root and shoot dry mass. Moreover, there were reductions in hydrogen peroxide, lipid peroxidation, water potential and proline. In C. estrellensis associated with Ab-V5, higher values of photosynthesis and instantaneous carboxylation efficiency were observed, in addition to higher starch content in the leaves and roots and higher protein content in the leaves; lower hydrogen peroxide and lipid peroxidation contents were also observed. The associations of T. micrantha with Ab-V5 and Azomonas sp. and C. estrellensis with Ab-V5 favored the activation of metabolic processes under drought, leading to greater drought tolerance. This work demonstrates the effects of compatible associations of Neotropical tree and PGPB species and suggests that the identification of compatible PGPB strains can result in tree seedlings with increased tolerance to abiotic stresses, such as drought.

Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils

Considering the heavy metal risk to soil microbiota and agro-ecosystems, the study was designed to determine metal toxicity to bacteria and to find metal tolerant bacteria carrying multifarious plant growth promoting activities and to assess their impact on chickpea cultivated in stressed soils. Metal tolerant strain SFP1 recognized as Pseudomonas aeruginosa employing 16S rRNA gene sequence determination showed maximum tolerance to Cr (400 μg/ml) and Ni (800 μg/ml) and produced variable amounts of indole acetic acid, HCN, NH₃, and ACC deaminase and could solubilize insoluble phosphates even under Cr (VI) and Ni stress. Metal tolerant P. aeruginosa reduced toxicity of Cr (VI) and Ni and concomitantly enhanced the performance of chickpea grown under stressed and conventional soils. At 144 mg Cr kg^-1, the measured parameters of a bacterial strain was significantly enhanced, but it was lower compared to those recorded at 660 mg Ni kg^-1. The strain SFP1 demonstrated maximum increase in seed yield (81%) and grain protein (16%) at 660 mg Ni kg^-1 over uninoculated and untreated control. Stressed plants had more proline, antioxidant enzymes, and metal concentrations in plant tissues. P. aeruginosa, however, remarkably declined the level of stress markers (proline and APX, SOD, CAT, and GR), as well as with Cr (VI) and Ni uptake by chickpea. Conclusively, P. aeruginosa strain SFP1 due to its dual metal tolerant ability, capacity to secrete plant growth promoting regulators even under metal stress and potential to mitigate metal toxicity, could be developed as microbial inoculant for enhancing chickpea production in Cr and Ni contaminated soils.

Advances in microbe-assisted reclamation of heavy metal contaminated soils over the last decade: A review

Contamination of agricultural soils with trace metals present lethal consequences in terms of diverse ecological and environmental problems that entail entry of metal in food chain, soil deterioration, plant growth suppression, yield reduction and alteration in microbial community. Metal polluted soils have become a major concern for scientists around the globe. Phytoremediation involves the hyperaccumulation of metals in different plant parts. Phytoremediation of metals from polluted soils could be enhanced through inoculation with metal resistant plant growth promoting (PGP) bacteria. These PGP bacteria not only promote plant growth but also enhance metal uptake by plants. There are a number of reports in the literature where PGP bacterial inoculation improves metal accumulation in different plant parts without influencing plant growth. Therefore, there is a need to select PGP bacterial strains which possess the potential to improve plant growth as well as expedite the phytoremediation of metals. In this review, we have discussed the mechanisms possessed by PGP bacteria to promote plant growth and phytoremediation of metals. The central part of this review deals with the recent advances in microbial assisted-phytoremediation of metals.

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage

Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar (Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar (G. barbadense L.) by high-throughput sequencing technology. Six bacterial phyla were found dominantly in cotton rhizosphere bacterial community including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. The abundance of Acidobacteria, Cyanobacteria, Firmicutes, Planctomycetes and Proteobacteria were largely influenced by cotton root. Bacterial α-diversity in rhizosphere was lower than that of bulk soil in nutrient-rich soil, but higher in cotton continuous cropping field soil. The β-diversity in nutrient-rich soil was greater than that in continuous cropping field soil. The community structure of the rhizosphere bacteria varied significantly during different developmental stages. Our results provided insights into the dynamics of cotton rhizosphere bacterial community and would facilitate to improve cotton growth and development through adjusting soil bacterial community structure artificially.

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat.