Diversity of root-associated fluorescent pseudomonads as affected by ferritin overexpression in tobacco

Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches

4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.

Importance of the Rhizosphere Microbiota in Iron Biofortification of Plants

Increasing the iron content of plant products and iron assimilability represents a major issue for human nutrition and health. This is also a major challenge because iron is not readily available for plants in most cultivated soils despite its abundance in the Earth's crust. Iron biofortification is defined as the enhancement of the iron content in edible parts of plants. This biofortification aims to reach the objectives defined by world organizations for human nutrition and health while being environment friendly. A series of options has been proposed to enhance plant iron uptake and fight against hidden hunger, but they all show limitations. The present review addresses the potential of soil microorganisms to promote plant iron nutrition. Increasing knowledge on the plant microbiota and plant-microbe interactions related to the iron dynamics has highlighted a considerable contribution of microorganisms to plant iron uptake and homeostasis. The present overview of the state of the art sheds light on plant iron uptake and homeostasis, and on the contribution of plant-microorganism (plant-microbe and plant-plant-microbe) interactions to plant nutritition. It highlights the effects of microorganisms on the plant iron status and on the co-occurring mechanisms, and shows how this knowledge may be valued through genetic and agronomic approaches. We propose a change of paradigm based on a more holistic approach gathering plant and microbial traits mediating iron uptake. Then, we present the possible applications in plant breeding, based on plant traits mediating plant-microbe interactions involved in plant iron uptake and physiology.

Impact of Bacterial Siderophores on Iron Status and Ionome in Pea

Including more grain legumes in cropping systems is important for the development of agroecological practices and the diversification of protein sources for human and animal consumption. Grain legume yield and quality is impacted by abiotic stresses resulting from fluctuating availabilities in essential nutrients such as iron deficiency chlorosis (IDC). Promoting plant iron nutrition could mitigate IDC that currently impedes legume cultivation in calcareous soils, and increase the iron content of legume seeds and its bioavailability. There is growing evidence that plant microbiota contribute to plant iron nutrition and might account for variations in the sensitivity of pea cultivars to iron deficiency and in fine to seed nutritional quality. Pyoverdine (pvd) siderophores synthesized by pseudomonads have been shown to promote iron nutrition in various plant species (Arabidopsis, clover and grasses). This study aimed to investigate the impact of three distinct ferripyoverdines (Fe-pvds) on iron status and the ionome of two pea cultivars (cv.) differing in their tolerance to IDC, (cv. S) being susceptible and (cv. T) tolerant. One pvd came from a pseudomonad strain isolated from the rhizosphere of cv. T (pvd1T), one from cv. S (pvd2S), and the third from a reference strain C7R12 (pvdC7R12). The results indicated that Fe-pvds differently impacted pea iron status and ionome, and that this impact varied both according to the pvd and the cultivar. Plant iron concentration was more increased by Fe-pvds in cv. T than in cv. S. Iron allocation within the plant was impacted by Fe-pvds in cv. T. Furthermore, Fe-pvds had the greatest favorable impact on iron nutrition in the cultivar from which the producing strain originated. This study evidences the impact of bacterial siderophores on pea iron status and pea ionome composition, and shows that this impact varies with the siderophore and host-plant cultivar, thereby emphasizing the specificity of these plant-microorganisms interactions. Our results support the possible contribution of pyoverdine-producing pseudomonads to differences in tolerance to IDC between pea cultivars. Indeed, the tolerant cv. T, as compared to the susceptible cv. S, benefited from bacterial siderophores for its iron nutrition to a greater extent.

Let the Core Microbiota Be Functional

The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.

Beneficial rhizobacteria from rice rhizosphere confers high protection against biotic and abiotic stress inducing systemic resistance in rice seedlings

The present study reports a screening for PGPR in a highly selective environment, the rhizosphere of rice plants, in southwestern of Spain. Among the 900 isolates, only 38% were positive for at least one of the biochemical activities to detect putative PGPR. The best 80 isolates were selected and identified by 16S rRNA partial sequencing. Among these, 13 strains were selected for growth promotion assays. Only one strain (BaC1-38) was able to significantly increase height, while nine strains significantly inhibited it. Five strains significantly increased dry weight, and only BaC1-21 significantly decreased it. Based on significant modifications in growth, three bacteria (BaC1-13, BaC1-21 and BaC1-38) were tested for systemic induction of resistance against stress challenge (salt and Xanthomonas campestris infection). Protection against salt stress and pathogen infection was similar; BaC1-38 protected by 80%, BaC1-13 by 50% and BaC1-21 only by 20%. Toxicity of salt stress to the plants was evaluated by photosynthetic efficiency of seedlings. Fv/Fm only decreased significantly in plants inoculated with BaC1-13. ΦPSII also decreased significantly in plants inoculated with BaC1-21, but increased significantly with BaC1-38. NPQ decreased significantly in plants inoculated with BaC1-21. The two strains able to induce systemic resistance against Xanthomonas campestris seem to work by different pathways. BaC1-13 primed enzymes related with the detoxification of reactive oxygen species (ROS). However, BaC1-38 primed pathogenesis-related proteins (PRs), and this pathway was more effective, both improved chlorophyll index confirming the priming state of the plant.

An underground tale: contribution of microbial activity to plant iron acquisition via ecological processes

BACKGROUND

Iron (Fe) deficiency in crops is a worldwide agricultural problem. Plants have evolved several strategies to enhance Fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid Fe deficiency in Fe-limited soils. Soil micro-organisms also play a critical role in plant Fe acquisition; however, the mechanisms behind their promotion of Fe acquisition remain largely unknown.

SCOPE

This review focuses on the possible mechanisms underlying the promotion of plant Fe acquisition by soil micro-organisms.

CONCLUSIONS

Fe-deficiency-induced root exudates alter the microbial community in the rhizosphere by modifying the physicochemical properties of soil, and/or by their antimicrobial and/or growth-promoting effects. The altered microbial community may in turn benefit plant Fe acquisition via production of siderophores and protons, both of which improve Fe bioavailability in soil, and via hormone generation that triggers the enhancement of Fe uptake capacity in plants. In addition, symbiotic interactions between micro-organisms and host plants could also enhance plant Fe acquisition, possibly including: rhizobium nodulation enhancing plant Fe uptake capacity and mycorrhizal fungal infection enhancing root length and the nutrient acquisition area of the root system, as well as increasing the production of Fe(3+) chelators and protons.

The composition of root exudates from two different resistant peanut cultivars and their effects on the growth of soil-borne pathogen

The high incidence of various soil-borne diseases in the monoculture field of peanut is a major production constraint in the red soil regions of southern China. The peanut root exudates are generally thought to play an important role in regulating soil-borne pathogens. The responses of the soil-borne pathogens, Fusarium oxysporum and F. solani to the peanut root exudates were studied using one susceptible cultivar Ganhua-5 (GH) and one mid-resistant cultivar Quanhua-7 (QH) as the test materials. The components and contents of the amino acids, sugars and phenolic acids in the peanut root exudates were determined. The results demonstrated that the root exudates from both susceptible and mid-resistant cultivars significantly promoted the spore germination, sporulation and mycelial growth of soil-borne pathogens, F. oxysporum, F. solani compared with the control. The extent of the stimulation was depended on the strains of the Fusarium tested, and gradually increased with the increased concentrations of peanut root exudates. HPLC analysis showed that the contents of sugars, alanine, total amino acids in the root exudates of GH were significantly higher than that in QH, whereas the contents of p-hydroxybenzoic acid, benzoic acid, p-coumaric acid and total phenolic acids were significantly lower than that in QH. Results of the study suggested that the differences in the root exudates from the different peanut cultivars were considered to regulate the wilt-resistance mechanism in the rhizosphere of peanut. The results are therefore crucial important to illustrate the mechanism of peanut replanted obstacle, and to develop its control techniques in the red soil regions of southern China.

Identification of traits shared by rhizosphere-competent strains of fluorescent pseudomonads

Rhizosphere competence of fluorescent pseudomonads is a prerequisite for the expression of their beneficial effects on plant growth and health. To date, knowledge on bacterial traits involved in rhizosphere competence is fragmented and derived mostly from studies with model strains. Here, a population approach was taken by investigating a representative collection of 23 Pseudomonas species and strains from different origins for their ability to colonize the rhizosphere of tomato plants grown in natural soil. Rhizosphere competence of these strains was related to phenotypic traits including: (1) their carbon and energetic metabolism represented by the ability to use a wide range of organic compounds, as electron donors, and iron and nitrogen oxides, as electron acceptors, and (2) their ability to produce antibiotic compounds and N-acylhomoserine lactones (N-AHSL). All these data including origin of the strains (soil/rhizosphere), taxonomic identification, phenotypic cluster based on catabolic profiles, nitrogen dissimilating ability, siderovars, susceptibility to iron starvation, antibiotic and N-AHSL production, and rhizosphere competence were submitted to multiple correspondence analyses. Colonization assays revealed a significant diversity in rhizosphere competence with survival rates ranging from approximately 0.1 % to 61 %. Multiple correspondence analyses indicated that rhizosphere competence was associated with siderophore-mediated iron acquisition, substrate utilization, and denitrification. However, the catabolic profile of one rhizosphere-competent strain differed from the others and its competence was associated with its ability to produce antibiotics phenazines and N-AHSL. Taken together, these data suggest that competitive strains have developed two types of strategies to survive in the rhizosphere.

Plant Fe status affects the composition of siderophore-secreting microbes in the rhizosphere

BACKGROUND AND AIMS

Soil microbes have been demonstrated to play an important role in favouring plant iron (Fe) uptake under Fe-limiting conditions. However, the mechanisms involved are still unclear. This present study reported the effects of plant Fe status on the composition of siderophore-secreting microbes in the rhizosphere, and their potential function in improving plant Fe nutrition.

METHODS

An Fe-efficient plant, red clover (Trifolium pratense 'Kenland') was cultured in a calcareous soil to obtain rhizosphere soils with (Fe-sufficient) or without (Fe-stressed) foliar FeEDTA spraying. The siderophore-producing ability of rhizospheric microbes was measured. The bioavailability of the siderophore-solubilized Fe from iron oxides/hydroxides was tested in hydroponic culture.

KEY RESULTS

In rhizosphere soil, the number of microbes that secreted siderophores quickly was more in the Fe-stressed treatment than in the Fe-sufficient one, while the number of microbes that did not secret siderophores was the opposite. A significantly higher concentration of phenolics was detected in the rhizosphere soil of Fe-stressed plants. Moreover, after the soil was incubated with phenolic root exudates, the composition of the siderophore-secreting microbial community was similar with that of the rhizosphere of Fe-stressed plant. Additionally, the siderophores produced by a rhizospheric microbe isolated from the Fe-stressed treatment can well solubilize iron oxides/hydroxides, and the utilization of the siderophore-solubilized Fe by plant was even more efficient than EDTA-Fe.

CONCLUSIONS

Iron-deficiency stress of red clover would alter the composition of siderophore-secreting microbes in the rhizosphere, which is probably due to the phenolics secretion of the root, and may in turn help to improve the solubility of Fe in soils and plant Fe nutrition via elevated microbial siderophore secretion.

Do transgenic plants affect rhizobacteria populations?

Plant genetic manipulation has led to the development of genetically modified plants (GMPs) expressing various traits. Since their first commercial use in 1996, GMPs have been increasingly used, reaching a global cultivating production area of 114.3 million hectares in 2007. The rapid development of agricultural biotechnology and release of GMPs have provided many agronomic and economic benefits, but has also raised concerns over the potential impact these plants might have on the environment. Among these environmental concerns, the unintentional impact that GMPs might have on soil‐associated microbes, especially rhizosphere‐inhabiting bacteria or rhizobacteria, represents one of the least studied and understood areas. As rhizobacteria are responsible for numerous key functions including nutrient cycling and decomposition, they have been defined as good indicator organisms to assess the general impact that GMPs might have on the soil environment. This minireview summarizes the results of various experiments that have been conducted to date on the impact of GMPs on rhizobacteria. Both biological and technical parameters are discussed and an attempt is made to determine if specific rhizobacterial responses exist for the different categories of GMPs developed to date.