Composition Of Root Exudates Research Articles

Single and Combined Fe and S Deficiency Differentially Modulate Root Exudate Composition in Tomato: A Double Strategy for Fe Acquisition?

Fe chlorosis is considered as one of the major constraints on crop growth and yield worldwide, being particularly worse when associated with S shortage, due to the tight link between Fe and S. Plant adaptation to inadequate nutrient availabilities often relies on the release of root exudates that enhance nutrients, mobilization from soil colloids and favour their uptake by roots. This work aims at characterizing the exudomic profile of hydroponically grown tomato plants subjected to either single or combined Fe and S deficiency, as well as at shedding light on the regulation mechanisms underlying Fe and S acquisition processes by plants. Root exudates have been analysed by untargeted metabolomics, through liquid chromatography–mass spectrometry as well as gas chromatography–mass spectrometry following derivatization. More than 200 metabolites could be putatively annotated. Venn diagrams show that 23%, 10% and 21% of differential metabolites are distinctively modulated by single Fe deficiency, single S deficiency or combined Fe–S deficiency, respectively. Interestingly, for the first time, a mugineic acid derivative is detected in dicot plants root exudates. The results seem to support the hypothesis of the co-existence of the two Fe acquisition strategies in tomato plants.

Selective metal leaching from technosols based on synthetic root exudate composition

This study focused on metal release from technosols induced by synthetic root exudate (SRE). The effect of SRE composition on metal release was studied using six technosols. This was done by treating the technosols with SRE solutions having varying concentrations of low molecular weight organic acids (LMWOAs), namely oxalic, citric, and malic acids. Consequently, the physico-chemical parameters (pH and electric conductivity), Ca, Mg, Fe, Zn, and Cu release (by atomic absorption spectroscopy, AAS), chemical changes (by Fourier transform infrared, FT-IR), and organic parameters (by fluorescence) were investigated. Metal release showed to be dependent on the SRE composition and technosol characteristics. Citric acid selectively released Ca, Mg, Zn, and Cu from technosols in a concentration-dependent manner; oxalic acid showed a significant role in the release of Mg and Fe. Under relatively high LMWOA concentrations, particulate organo-mineral complexes precipitated. Additionally, technosol weathering was seen by the dissolution of humic substances and ferriallophanes, which in turn caused metal release. However, re-precipitation of these phases showed to re-sorb metals, thus underestimating the role of LMWOAs in metal release. Therefore, the selective metal leaching was highly dependent on the SRE composition and LMWOA concentrations on one hand, and on the mineral, organic, and organo-mineral components of the technosols on the other. The understanding of such processes is crucial for proposing and implementing environmental management strategies to reduce metal leaching or for the beneficial re-usage of metals (e.g., for agromining) from technosols.

Agrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere.

The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the interaction occurring in the rhizosphere between the beneficial and the pathogenic microbes is thus interesting for the development of effective biopesticides for the management of crown gall disease. However, very little is still known about the influence of these complex interactions on the biocontrol determinants of beneficial bacteria, especially Bacillus strains. This study aimed to evaluate the effect of the soil borne pathogen Agrobacterium tumefaciens C58 on root colonization and lipopeptide production by Bacillus velezensis strain 32a during interaction with tomato plants. Results show that the presence of A. tumefaciens C58 positively impacted the root colonization level of the Bacillus strain. However, negative impact on surfactin production was observed in Agrobacterium-treated seedling, compared with control. Further investigation suggests that these modulations are due to a modified tomato root exudate composition during the tripartite interaction. Thus, this work contributes to enhance the knowledge on the impact of interspecies interaction on the ecological fitness of Bacillus cells living in the rhizosphere.

Aromatic Carboxylic Acids in Barley-Root Exudates and Their Influence on the Growth of Fusarium culmorum and Pseudomonas fluorescens

An ultraperformance liquid chromatography system was used to establish the presence of seven aromatic carboxylic acids, known as antimicrobial substances, in root exudates of barley colonized by the phytopathogenic fungus Fusarium culmorum and the antagonistic bacterium Pseudomonas fluorescens. It was established that barley produced fewer antimicrobial components in exudates in response to the colonization of P. fluorescens than after colonization by F. culmorum. All aromatic carboxylic acids inhibited the growth of F. culmorum, but only two of them inhibited the growth of P. fluorescens and only at the highest concentration. The obtained data demonstrate the ability of the plant to create favorable conditions for the development of beneficial rhizobacteria and to create unfavorable conditions for the growth of the phytopathogenic fungus via the composition of root exudates. In the future, it will be possible to select varieties of grain crops with a specific composition of antimicrobial components in root exudates.

Colonization by multi-potential Pseudomonas aeruginosa P4 stimulates peanut (Arachis hypogaea L.) growth, defence physiology and root system functioning to benefit the root-rhizobacterial interface

The beneficial associations between Arachis hypogaea L. (peanut) and fluorescent Pseudomonas species have been poorly explored despite their predominance in the peanut rhizosphere. The present study explores the mutually beneficial interactions between peanut roots and P. aeruginosa P4 (P4) in terms of their impact on plant growth, defence physiology and the root-rhizobacterial interface. The efficient phosphate solubilizer P4 exhibited biocontrol abilities, including the production of siderophores, pyocyanin, indole-3-acetic acid and hydrogen cyanide. The bacterization of peanut seeds with multi-potential P4 significantly enhanced in vitro seed germination and seedling vigour. Under sand-based gnotobiotic (10 days post-inoculation) and sterile soil-based cultivation systems (30 days post-inoculation), sustained P4 colonization enhanced the peanut root length and dry plant biomass. The subsequent increase in catalase, polyphenol oxidase and phenylalanine ammonia lyase activities with increased phenolic contents in the peanut roots and shoots suggested the systemic priming of defences. Consequently, the altered root exudate composition caused enhanced chemo-attraction towards P4 itself and the symbiotic N2-fixing Bradyrhizobium strain. Co-inoculating peanuts with P4 and Bradyrhizobium confirmed the improved total bacterial colonization (∼2 fold) of the root tip, with the successful co-localization of both, as substantiated by scanning electron microscopy. Collectively, the peanut-P4 association could potentially model the beneficial Pseudomonas-driven multi-trophic rhizosphere benefits, emphasizing the plausible role of non-rhizobium PGPR in promoting N2 fixation.

The effect of pre-sowing seed treatment on seedlings growth rate and their excretory activity

The importance of studying pre-sowing seed treatment lies in the possibility of regulating the rate of seed germination, the intensity of their growth and obtaining root exudates in biotechnology. The effect of three pre-sowing treatment methods was examined (control – washing with running water; the first method – washing with 0.05% sodium permanganate solution; the second method – 30 se­conds in 70% ethyl alcohol (C2H5OH) and 30 minutes in 5% sodium hypochlorite (NaOCl); the third method – 5 minutes in 70% C2H5OH and 40 minutes in 5% NaOCl) on the growth rate, germination rate, excretion rate of seeds of wheat and peas and composition (of protein, carbohydrate, amino acid content) of root exudates from the first to the third day of growth in order to obtain root exudates. It was revealed that the same pre-sowing treatment of wheat and pea seeds has a different effect on the rate and variability of seedling growth from the first to the third day, as well as on the qualitative and quantitative composition of root exudates. It was shown that pre-sowing treatment of wheat and pea seeds for 5 minutes with 70% ethanol followed by treatment with sodium hypochlorite (a “hard” treatment method) accelerates seedling growth and seed germination. This method of treatment reduces the intensity of excretion of root exudates and composition in wheat, but it increases the intensity of excretion in peas. The discovered effects can be explained by hormesis. Additionally, the third method of pre-sowing seed treatment can be used in root technologies for obtaining root exudates.

Short-Term Effects of Salt Stress on the Amino Acids of Phragmites australis Root Exudates in Constructed Wetlands

In this study, the short-term effects of NaCl stress on the free amino acid content and composition of root exudates of Phragmites australis were evaluated. Nineteen amino acid types were detected in all samples. The results indicated that NaCl significantly influenced the total amino acid (TotAA) content. The TotAA content at 6‰ salinity (1098.79 μM g−1 DW) was up to 24 times higher than that in the control group (45.97 μM g−1 DW) but decreased to 106.32 μM g−1 DW at 6‰ salinity in the first hour. The stress period also significantly affected the TotAA content. After 4 h of stress, the TotAA content of the control and 1‰ salinity groups increased by approximately 30- and 14-fold, and those of the 3‰ and 6‰ groups decreased to 60% and 37%, respectively. The increase in TotAA content was primarily caused by the increase in proline content; the proportion of proline accounted for 58.05% of the TotAA content at 3‰ salinity level in 2 h. Most amino acids showed a significant positive correlation with each other, but proline and methionine showed a different trend. Therefore, the proline level is a useful indicator of salt stress in Phragmites australis, especially in saltwater wetlands.

Intercropping with wheat suppressed Fusarium wilt in faba bean and modulated the composition of root exudates

The causal agent of Fusarium wilt in faba bean is Fusarium oxysporum f. sp. fabae (FOF), which significantly reduces the yield in continuous cropping systems. We aimed to evaluate the role of wheat in alleviating Fusarium wilt in faba bean. We assessed the effect of wheat on the occurrence of Fusarium wilt in faba bean and analyzed the differences in the root exudates produced by faba bean in monocropping and intercropping systems before and after infection by FOF. Treatment with FOF increased the incidence and disease index of Fusarium wilt and significantly increased the number of rhizosphere pathogens. Phenolic acids, organic acids, amino acids and sugars exuded from the roots of faba bean increased by 39.1%, 329.0%, 921.7% and 1195.7%, respectively, while intercropping reduced them by 28.04%, 55.69%, 79.10% and 78.75%, respectively. The rhizosphere pathogens of faba bean decreased significantly following intercropping, and the incidence of Fusarium wilt dropped to tolerable levels. This study suggests that the inoculation with FOF stimulated the exudation of phenolic acids, organic acids, amino acids and sugars from faba bean roots. These compounds were closely related to the changes in the disease resistance of faba bean and could also be used as nutrients to promote pathogen proliferation. After intercropping with wheat, the exudates of faba bean decreased significantly, which may imply that the faba bean recovered from stress, reduced the amount of nutrients needed for pathogen growth, limited the proliferation of pathogens and contributed to the alleviation of Fusarium wilt.

МОНИТОРИНГ КОНСОРТОВ В ЭКОСИСТЕМЕ: РАСТЕНИЕ – ФИТОПАТОГЕНЫ – САПРОФЫ ПОЧВЫ

Monitoring studies were carried out according to generally accepted methods in the northern forest-steppe of West Siberia in 2019–2020, using the varieties collection of the Institute of Cytology and Genetics SB RAS. Studies have shown that the genotypes of spring wheat varieties had a significant impact on the functioning of the “plant-phytopathogensaprotrophs” system. The parasitic activity of phytopathogens (Bipolaris sorokiniana Sacc. Shoem., Fusarium spp. Link.) differed in the varietal groups to 43.6 %. Varieties of Asian origin (China, India, Kazakhstan, Syria) were most affected by the root infections, Australian varieties were least affected by phytopathogens, due to the chemical composition of root exudates, which suppressed the number of parasitic and saprotrophic microorganisms. Varietal secretions of the wheat plants roots regulated the number of saprotrophic rhizospheric microorganisms. The share of the influence of the “variety” factor on the number of saprotrophic soil microorganisms was 24.3 % and was reliable at a 1 % level. The most sensitive to the composition and number of root exudates of wheat plants turned out to be bacteria of various trophic groups, the most resistant were micromycetes. In comparison with the background indices of non-rhizospheric soil, the number of cellulosolytic bacteria increased up to 3 times (West European varieties), bacteria consuming organic nitrogen – up to 5.6 times (Asian varieties), consumers of organic nitrogen forms – up to 2.9 times (West European varieties), oligonitrophilic bacteria – up to 12.7 times (Siberian varieties). Varieties far from the region of the study (Australia, Africa, America) exerted a repressive effect on the trophic groups of microorganisms, reducing their number in comparison with indicators of non-rhizospheric soil.

Taxonomic Diversity of Micromycete Complexes in the Root Zone of a Perennial Wild Species of Sunflower Helianthus Grosseserratus

The aim of our research was to determine the peculiarities of the formation of the taxonomic structure of micromycete complexes in the root zone of the perennial wild species of sunflower Helianthus grosseserratus when grown in the South of Ukraine. Soil samples taken from the root zone of two samples of perennial wild sunflower Helianthus grosseserratus 1630 and H. grosseserratus 1201, which were grown for more than 20 years in one place in the collection nursery of the Institute of Oilseed Crops of NAAS of Ukraine, were studied. Areas where plants are grown have not been treated with herbicides. Samples of fallow soil served as a control. Soil - chernozem ordinary low-humus leached. Soil samples for analysis were taken at the end of the growing season. To isolate microscopic fungi from the soil, the generally accepted method of serial dilutions was used, followed by sowing of the soil suspension on a dense nutrient medium Chapek-Dox. The method of sowing - deep, dilution of the suspension - 1: 1000. Duration of fungi cultivation - 7-14 days in a thermostat at a temperature of 28оС. The experiment was repeated five times. The complex of fungi-micromycetes in soil samples was determined using determinants and original works. The similarity of the species composition of the soil mycobiota of the fallow and the root zone of wild sunflower was determined by the Sorensen coefficient. Reliable indicators of similarity when comparing the species composition of two different associations were considered those in which the Sorensen coefficient was more than 50%.The analysis of the taxonomic structure of the studied mycocenoses revealed qualitative differences in the genus and species composition of micromycete fungi in the rhizosphere of wild sunflower species and fallow soil. In total, of the 29 species of micromycetes we isolated, 11 were found only in the soil of the fallow. According to our data, only 4 species (A. alliaceus, Paecilomyces lilacinus, F. oxysporum var. orthoceras, M. racemosus) were common species in the soil samples of fallow and root zone Helianthus grosseserratus 1630 and H. grosseserratus 1201. The species diversity of micromycetes of the root zone of H. grosseserratus 1201 was wider, and, accordingly, more similar to the soil of the fallow - 15 common species. Micromycetes that were typical for both fallow soil and sunflower are saprotrophs of A. niveus, P. canescens, P. crustosum, P. nigricans, P. thomii, as well as opportunistic species Verticillium album and V. lateritium. A comparative analysis of the lists of species composition of micromycete complexes revealed significant differences between the mycocenoses of the root zone of wild sunflower and fallow soil, as evidenced by the calculated Sorensen coefficients. The data indicated that the similarity of the species composition of the mycobiota H. grosseserratus 1201 with fallow was 66.7% (Cs = 0.67), and Helianthus grosseserratus 1630 - only 35.8% (Cs = 0, 35). The coefficient of similarity of the species composition of the mycobiota of the root zone of wild sunflower was 0.47, which is apparently due to the peculiarities of the composition of the root exudates of plants and their selection zones, which affect the formation of microbial complexes of the rhizosphere and edaphosphere.

ABC transporter genes ABC-C6 and ABC-G33 alter plant-microbe-parasite interactions in the rhizosphere

Plants are master regulators of rhizosphere ecology, secreting a complex mixture of compounds into the soil, collectively termed plant root exudate. Root exudate composition is highly dynamic and functional, mediating economically important interactions between plants and a wide range of soil organisms. Currently we know very little about the molecular basis of root exudate composition, which is a key hurdle to functional exploitation of root exudates for crop improvement. Root expressed transporters modulate exudate composition and could be manipulated to develop beneficial plant root exudate traits. Using Virus Induced Gene silencing (VIGS), we demonstrate that knockdown of two root-expressed ABC transporter genes in tomato cv. Moneymaker, ABC-C6 and ABC-G33, alters the composition of semi-volatile compounds in collected root exudates. Root exudate chemotaxis assays demonstrate that knockdown of each transporter gene triggers the repulsion of economically relevant Meloidogyne and Globodera spp. plant parasitic nematodes, which are attracted to control treatment root exudates. Knockdown of ABC-C6 inhibits egg hatching of Meloidogyne and Globodera spp., relative to controls. Knockdown of ABC-G33 has no impact on egg hatching of Meloidogyne spp. but has a substantial inhibitory impact on egg hatching of G. pallida. ABC-C6 knockdown has no impact on the attraction of the plant pathogen Agrobacterium tumefaciens, or the plant growth promoting Bacillus subtilis, relative to controls. Silencing ABC-G33 induces a statistically significant reduction in attraction of B. subtilis, with no impact on attraction of A. tumefaciens. By inoculating selected differentially exuded compounds into control root exudates, we demonstrate that hexadecaonic acid and pentadecane are biologically relevant parasite repellents. ABC-C6 represents a promising target for breeding or biotechnology intervention strategies as gene knockdown leads to the repulsion of economically important plant parasites and retains attraction of the beneficial rhizobacterium B. subtilis. This study exposes the link between ABC transporters, root exudate composition, and ex planta interactions with agriculturally and economically relevant rhizosphere organisms, paving the way for new approaches to rhizosphere engineering and crop protection.

Ethylene Response Factor (ERF) genes modulate plant root exudate composition and the attraction of plant parasitic nematodes

Plant root exudates are compositionally diverse, plastic and adaptive. Ethylene signalling influences the attraction of plant parasitic nematodes, presumably through the modulation of root exudate composition. Understanding this pathway could lead to new sources of crop parasite resistance. Here we used Virus-Induced Gene Silencing to knock down the expression of two Ethylene Response Factor (ERF) genes, ERF-E2 and ERF-E3, in tomato. Root exudates were significantly more attractive to the PPNs Meloidogyne incognita and Globodera pallida following knockdown of ERF-E2, which had no impact on the attraction of Meloidogyne javanica. Knockdown of ERF-E3 had no impact on the attraction of Meloidogyne or Globodera spp. Gas Chromatography Mass Spectrometry analysis revealed major changes in root exudate composition relative to controls. However, these changes did not alter the attraction of rhizosphere microbes Bacillus subtilis or Agrobacterium tumefaciens. This study further supports the potential of engineering plant root exudate for parasite control, through the modulation of plant genes.

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

Effect of root exudates of Eucalyptus urophylla and Acacia mearnsii on soil microbes under simulated warming climate conditions

BackgroundRecent studies demonstrated that warming and elevated carbon dioxide (CO2) indirectly affect the soil microbial community structure via plant root exudates. However, there is no direct evidence for how the root exudates affect soil microbes and how the compositions of root exudates respond to climate change.ResultsThe results showed that warming directly decreased biomass of soil-borne bacteria and fungi for Acacia mearnsii De Willd but it did not impact soil microbial community for Eucalyptus urophylla S.T. Blake. In contrast, elevated CO2 had strong direct effect on increasing soil microbial biomass for both plant species. However, plant roots could significantly increase the secretion of antibacterial chemicals (most probable organic acids), which inhibited the growth of bacteria and fungi in elevated CO2 environment. This inhibitory effect neutralized the facilitation from increasing CO2 concentration on microbial growth.ConclusionsWe concluded that climate change can directly affect microorganisms, and indirectly affect the soil microbial community structure by changes in composition and content of plant root exudates.

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity

Root-derived compounds can change rates of soil organic matter decomposition (rhizosphere priming effects) through microbial production of extracellular enzymes. Such soil priming can be affected by plant identity and soil nutrient status. However, the effect of plant-plant competition on the temporal dynamics of soil organic matter turnover processes is not well understood. This study used zymography to detect the spatial and temporal pattern of cellulase and leucine aminopeptidase activity, two enzyme classes involved in soil organic matter turnover. The effect of plant-plant competition on enzyme activity was examined using barley (Hordeum vulgare) plants grown in i) isolation, ii) intra- and iii) inter-cultivar competition. The enzyme activities of leucine aminopeptidase and cellulase were measured from portions of the root system at 18, 25 and 33 days after planting, both along the root axis and in the root associated area with detectable enzyme activity. The activities of cellulase and leucine aminopeptidase were both strongly associated with plant roots, and increased over time. An increase in the area of cellulase activity around roots was delayed when plants were in competition compared to in isolation. A similar response was found for leucine aminopeptidase activity, but only when in intra-cultivar competition, and not when in inter-cultivar competition. Therefore, plant-plant competition had a differential effect on enzyme classes, which was potentially mediated through root exudate composition. This study demonstrates the influence of plant-plant competition on soil microbial activity and provides a potential mechanism by which temporal dynamism in plant resource capture can be mediated.

Restrictive water condition modifies the root exudates composition during peanut-PGPR interaction and conditions early events, reversing the negative effects on plant growth

Water deficit is one of the most serious environmental factors that affect the productivity of crops in the world. Arachis hypogaea is a legume with a high nutritional value and 70% is cultivated in semi-arid regions. This research aimed to study the effect of water deficit on peanut root exudates composition, analyzing the importance of exudates on peanut-PGPR interaction under restrictive water condition.Peanut seedlings were subjected to six treatments: 0 and 15 mM PEG, in combination with non-inoculated, Bradyrhizobium sp. and Bradyrhizobium-Azospirillum brasilense inoculated treatments. We analyzed the 7-day peanut root exudate in response to a water restrictive condition and the presence of bacterial inocula. Molecular analysis was performed by HPLC, UPLC and GC. Bacteria motility, chemotaxis, bacterial adhesion to peanut roots and peanut growth parameters were analyzed.Restrictive water condition modified the pattern of molecules exuded by roots, increasing the exudation of Naringenin, oleic FA, citric and lactic acid, and stimulation the release of terpenes of known antioxidant and antimicrobial activity. The presence of microorganisms modified the composition of root exudates. Water deficit affected the first events of peanut-PGPR interaction and the root exudates favored bacterial mobility, the chemotaxis and attachment of bacteria to peanut roots.Changes in the profile of molecules exuded by roots allowed A. hypogaea-Bradyrhizobium and A.hypogaea–Bradyrhizobium-Azospirillum interaction thus reversing the negative effects of restrictive water condition on peanut growth. These findings have a future potential application to improve plant-PGPR interactions under water deficit by formulating inoculants containing key molecules exuded during stress.

Culturing Simpler and Bacterial Wilt Suppressive Microbial Communities from Tomato Rhizosphere.

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 1st transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 1st transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.

Small-Scale Bioreactor for Sterile Hydroponics and Hairy Roots: Metabolic Diversity and Salicylic Acid Exudation by Hairy Roots of Hyoscyamus niger

The volume and complexity of commercial bioreactors for sterile hydroponics and hairy roots are too large for comparative analysis of many cultures. Here a small-scale bioreactor fabricated from standard glass materials and suitable for both airlift and bubble aeration mode is described. The performance of the bioreactor was tested by growing oilseed rape (Brassica napus L.) and rose plants (Rosa canina L.) in sterile hydroponics and by cultivating hairy roots of henbane (Hyoscyamus niger L.) and sesame (Hyoscyamus niger L.). Plants grown in hydroponics for up to six weeks did not show chloroses or necroses. Hairy roots grew faster or comparably fast in bioreactors as compared to shaking flasks. Root exudates of roses and exudates of hairy roots of henbane were subjected to targeted and nontargeted analysis by HPLC coupled with optical and mass spectrometric detectors. The diversity and concentration of hairy root exudates were higher in bioreactors than in shaking flasks. The composition of hairy root exudates of three accessions of H. niger did not match the genetic relatedness among the accessions. Hairy roots of Hyoscyamus niger exuded salicylic acid in amounts varying among plant accessions and between bioreactors and shaking flask cultures.

Metagenomic Functional Shifts to Plant Induced Environmental Changes.

The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the environment surrounding the plant to intensify plant propagation and to improve fruit yield, and therefore is an advantageous model to study the interaction between soil microorganisms and plant–host interactions. We studied this system to address the question of a trade-off between microbial adaptation to a plant-influenced environment and its general metabolic capabilities. We found that many basic metabolic functions were similarly represented in bulk soil and rhizosphere microbiomes overall. However, we identified a niche-specific difference in functions potentially beneficial for microbial survival in the rhizosphere but that might also reduce the ability of microbes to withstand stresses in bulk soils. These functions could provide the microbiome with additional capabilities to respond to environmental fluctuations in the rhizosphere triggered by changes in the composition of root exudates. Based on our analysis we hypothesize that the rhizosphere-specific pathways involved in xenobiotics biodegradation could provide the microbiome with functional flexibility to respond to plant stress status.

Root exudates: from plant to rhizosphere and beyond.

This article describes the composition of root exudates, how these metabolites are released to the rhizosphere and their importance in the recruitment of beneficial microbiota that alleviate plant stress. Metabolites secreted to the rhizosphere by roots are involved in several processes. By modulating the composition of the root exudates, plants can modify soil properties to adapt and ensure their survival under adverse conditions. They use several strategies such as (1) changing soil pH to solubilize nutrients into assimilable forms, (2) chelating toxic compounds, (3) attracting beneficial microbiota, or (4) releasing toxic substances for pathogens, etc. In this work, the composition of root exudates as well as the different mechanisms of root exudation have been reviewed. Existing methodologies to collect root exudates, indicating their advantages and disadvantages, are also described. Factors affecting root exudation have been exposed, including physical, chemical, and biological agents which can produce qualitative and quantitative changes in exudate composition. Finally, since root exudates play an important role in the recruitment of mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR), the mechanisms of interaction between plants and the beneficial microbiota have been highlighted.