Amino acids in the rhizosphere: from plants to microbes

Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption

Rhizosphere colonization by bacteria involves molecular and cellular mechanisms, such as motility and chemotaxis, biofilm formation, metabolic versatility, or biosynthesis of secondary metabolites, among others. Nonetheless, there is limited knowledge concerning the main regulatory factors that drive the rhizosphere colonization process. Here we show the importance of the AmrZ and FleQ transcription factors for adaption in the plant growth-promoting rhizobacterium (PGPR) and rhizosphere colonization model Pseudomonas ogarae F113. RNA-Seq analyses of P. ogarae F113 grown in liquid cultures either in exponential and stationary growth phase, and rhizosphere conditions, revealed that rhizosphere is a key driver of global changes in gene expression in this bacterium. Regarding the genetic background, this work has revealed that a mutation in fleQ causes considerably more alterations in the gene expression profile of this bacterium than a mutation in amrZ under rhizosphere conditions. The functional analysis has revealed that in P. ogarae F113, the transcription factors AmrZ and FleQ regulate genes involved in diverse bacterial functions. Notably, in the rhizosphere, these transcription factors antagonistically regulate genes related to motility, biofilm formation, nitrogen, sulfur, and amino acid metabolism, transport, signalling, and secretion, especially the type VI secretion systems. These results define the regulon of two important bifunctional transcriptional regulators in pseudomonads during the process of rhizosphere colonization.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.

Altitudinal Variation of Metabolites, Mineral Elements and Antioxidant Activities of Rhodiola crenulata (Hook.f. & Thomson) H.Ohba

Rhodiolacrenulata (Hook.f. & Thomson) H.Ohba is an alpine medicinal plant that can survive in extreme high altitude environments. However, its changes to extreme high altitude are not yet clear. In this study, the response of Rhodiola crenulata to differences in altitude gradients was investigated through chemical, ICP-MS and metabolomic methods. A targeted study of Rhodiola crenulata growing at three vertical altitudes revealed that the contents of seven elements Ca, Sr, B, Mn, Ni, Cu, and Cd, the phenolic components, the ascorbic acid, the ascorbic acid/dehydroascorbate ratio, and the antioxidant capacity were positively correlated with altitude, while the opposite was true for total ascorbic acid content. Furthermore, 1165 metabolites were identified: flavonoids (200), gallic acids (30), phenylpropanoids (237), amino acids (100), free fatty acids and glycerides (56), nucleotides (60), as well as other metabolites (482). The differential metabolite and biomarker analyses suggested that, with an increasing altitude: (1) the shikimic acid-phenylalanine-phenylpropanoids-flavonoids pathway was enhanced, with phenylpropanoids upregulating biomarkers much more than flavonoids; phenylpropanes and phenylmethanes upregulated, and phenylethanes downregulated; the upregulation of quercetin was especially significant in flavonoids; upregulation of condensed tannins and downregulation of hydrolyzed tannins; upregulation of shikimic acids and amino acids including phenylalanine. (2) significant upregulation of free fatty acids and downregulation of glycerides; and (3) upregulation of adenosine phosphates. Our findings provide new insights on the responses of Rhodiola crenulata to extreme high altitude adversity.

The Effects of Different Fertilization Practices in Combination with the Use of PGPR on the Sugar and Amino Acid Content of Asparagus officinalis

The present study examined the effects of different nitrogen (NH4NO3) and potassium (KNO3) fertilization levels in combination with a nitrogen-fixing, plant growth-promoting rhizobacteria (PGPR) inoculation on the carbohydrate (CHO), amino acid content, and nutrient concentrations (N, P, K) in the spears and the root system of asparagus plants. No significant differences were indicated between the different fertilization treatments regarding N, P, and K in the leaves and roots of asparagus. The inoculation of the asparagus fields with PGPR, no matter the type of the inorganic fertilizer, resulted in increased CHO and amino acid content of the foliage and roots of asparagus. The highest CHO content and amino acid content were recorded in the treatment that combined PGPR inoculation along with KNO3 fertilizer, indicating that higher K applications acted synergistically with the added PGPR.

Fluctuation in amino acids content in Triticum aestivum L. cultivars as an indicator on the impact of post-emergence herbicides in controlling weeds

This study was carried out in a demonstrated field in El-Sharkia Governorate, Egypt, during the winter of season 2020 to evaluate the leverage of four post-emergence herbicides i.e., tribenuron-methyl, clodinafop- propargyl, pyroxsulam and pinoxaden compared to control on total protein and amino acid contents in three wheat cultivars (Shandwel 1, Giza 171, and Sakha 95). Generally, the use of foliar herbicides led to a significant decrease in essential, non-essential amino acids and protein contents. However, tribenuran-methyl herbicide signifcantly increased the levels of proline, glycine, arginine, and histidine, but cystine and threonine not affected as compared to control. On the other hand, foliar herbicide application was significantly increased physiological , biochemical parameters and yield of Shandweel cultivar as compared to the other varieties. The physiological and biochemical models of dual-herbicide-tolerant wheat cultivars add to our understanding of the crop. In recent agricultural systems, herbicide tolerant plants are important for long-term weed management. Therefore, the study recommended the safely usage of Tribenuran-methyl as foliar herbicide in weed managment.

Investigation of soil microbiome under the influence of different mulching treatments in northern highbush blueberry

Microbial communities on soil are fundamental for the long-term sustainability of agriculture ecosystems. Microbiota in soil would impact the yield and quality of blueberries since microbial communities in soil can interact with the rhizosphere of plant. This study was conducted to determine how different mulching treatments induce changes in soil microbial composition, diversity, and functional properties. A total of 150 soil samples were collected from 5 different mulch treatments (sawdust, green weed mat, sawdust topped with green weed mat, black weed mat, and sawdust topped with black weed mat) at 3 different depths (bottom, middle, and top region of 20 cm soil depth) from 2 different months (June and July 2018). A total of 8,583,839 sequencing reads and 480 operational taxonomic units (OTUs) of bacteria were identified at genus level. Eight different plant growth promoting rhizobacteria (PGPR) were detected, and the relative abundances of Bradyrhizobium, Bacillus, and Paenibacillus were more than 0.1% among all soil samples. Sampling depth and month of soil samples impacted the amount of PGPR, while there were no significant differences based on mulch type. Functional properties of bacteria were identified through PICRUSt2, which found that there is no significant difference between mulch treatment, depth, and month. The results indicated that sampling month and depth of soil impacted the relative abundance of PGPR in soil samples, but there were no significant differences of functional properties and beneficial microbial communities based on mulch type.

L-Canavanine, a Root Exudate From Hairy Vetch (Vicia villosa) Drastically Affecting the Soil Microbial Community and Metabolite Pathways

L-Canavanine, a conditionally essential non-proteinogenic amino acid analog to L-arginine, plays important roles in cell division, wound healing, immune function, the release of hormones, and a precursor for the synthesis of nitric oxide (NO). In this report, we found that the L-canavanine is released into the soil from the roots of hairy vetch (Vicia villosa) and declines several weeks after growth, while it was absent in bulk proxy. Hairy vetch root was able to exudate L-canavanine in both pots and in vitro conditions in an agar-based medium. The content of the L-canavanine in pots and agar conditions was higher than the field condition. It was also observed that the addition of L-canavanine significantly altered the microbial community composition and diversity in soil. Firmicutes and Actinobacteria became more abundant in the soil after the application of L-canavanine. In contrast, Proteobacteria and Acidobacteria populations were decreased by higher L-canavanine concentration (500 nmol/g soil). Prediction of the soil metabolic pathways using PICRUSt2 estimated that the L-arginine degradation pathway was enriched 1.3-fold when L-canavanine was added to the soil. Results indicated that carbon metabolism-related pathways were altered and the degradation of nitrogen-rich compounds (i.e., amino acids) enriched. The findings of this research showed that secretion of the allelochemical L-canavanine from the root of hairy vetch may alter the soil microbial community and soil metabolite pathways to increase the survival chance of hairy vetch seedlings. This is the first report that L-canavanine acts as an allelochemical that affects the biodiversity of soil microbial community.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Organic N compounds in plant nutrition: have methodologies based on stable isotopes provided unequivocal evidence of direct N uptake?

During the past two decades, interest has developed in regard to the possibility that plant roots can take up organic N compounds directly, a concept which challenges the conventional wisdom that soil inorganic N forms (NH4+ and NO3-) are the sole primary sources of N absorbed by plant roots. We reviewed the literature based on single or dual (¹⁵N, ¹³C) stable isotope labelling techniques to test the hypothesis of direct uptake. Both isotopically enriched and natural abundance approaches were reviewed. Of the methods examined, the dual enrichment technique, when combined with compound specific and position-specific stable isotope analysis, provided incontrovertible evidence for direct uptake of simple amino acids. We demonstrate that dual labelling lacks overall sensitivity due to the high C concentration in plant tissue relative to N, and the higher natural abundance of ¹³C cf. ¹⁵N, which limits the period of measurement due to isotope dilution, and hence an assessment of the long-term contribution of direct uptake to the N economy of plant communities.

Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata

Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.

Comparative assessment of amino acids composition in two types of marine fish silage

Fish silage is a brown liquefied product achieved by the action of enzymes when finely grounded whole/parts of either single or mixed fish types are subjected to acidification. This study made a comparative assessment of biochemical and nutritive properties, especially the amino acid composition in supernatant phase of formic acid silages prepared from two fish types, Indian mackerel (Rastrelliger kanagurta) and false travely (Lactarius lactarius) representing fat fish (FF, fat content > 5%) and lean fish (LF, fat content < 5%), respectively during 35 days of fermentation (DoF). Significantly higher content of total amino acid (TAA) and free amino acids (FAA) were recorded in FFS (TAA, 41.2 ± 0.03 mg/g; FAA, 31.3 ± 0.003 mg/g) compared to LFS (TAA, 35.8 ± 0.07 mg/g; FAA, 18.26 ± 0.003 mg/g; FAA, 31.3 ± 0.003 mg/g) (p < 0.05). At the end of 35 DoF, the concentrations of amino acids such as asparagine, histidine, isoleucine, valine, cysteine, serine, lysine and arginine were significantly higher in FFS as compared to LFS. The relative amino acid composition of FFS and LFS varied in accordance with DoF and the relationship was found to be highly significant (ANOVA, p < 0.00001). High concentrations of l-amino acids such as leucine, glutamic acid and arginine were recorded in both FFS and LFS. In conclusion, the analysis suggested that a fermentation period of 25–30 days showed a significant effect on the composition of amino acids in both types of ensilage compared to other fermentation periods (p < 0.05). Considering the role of amino acids in enhancing the plant growth and proliferation, the findings of the present study are quite useful.

Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

Metabolic interactions in beneficial microbe recruitment by plants

During millions of years of evolution, land plants and microorganisms have established elaborate partnerships. Microbes play essential roles in plant fitness and help plants cope with environmental challenges. Vice versa, plants provide the microbes with a niche and food. In the soil, a complex network of interactions mediated by metabolic signals drives the relationship between plants and microbes. Here, we review the roles of metabolic signaling in the plant-microbiome interaction. We discuss how plant-produced small molecules are involved in the recruitment of the microbiome. Also the microbial partners in this relationship use small molecules, such as quorum sensing molecules and volatiles for intra-species and inter-species communication. We give an overview of the regulation of the biosynthesis, secretion and perception of both plant and microbial small molecules and discuss the examples of biotechnological approaches to engineer the plant-microbiome interaction by targeting these metabolic dialogues. Ultimately, an improved understanding of the plant-microbiome interaction and engineering possibilities will pave the way to a more sustainable agriculture.

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome

BACKGROUND

Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.

RESULTS

Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not.

CONCLUSIONS

The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

Changes of fungal community and non-volatile metabolites during pile-fermentation of dark green tea

Fungal community and non-volatile metabolites changes during the pile-fermentation are key factors to organoleptic qualities of dark green tea. However, the correlation between fungal succession and non-volatile compounds has never been satisfactorily explained. The purpose of the present study was to investigate fungal succession and its correlation with flavor compounds by multi-omics. Illumina Miseq sequencing of ITS1 region was conducted to analyze the fungal succession, a total of 78 OTUs which consisted of one phyla, nine classes, 15 orders, 26 families, 37 genera were identified, with Ascomycota as dominant phyla. Cluster analysis and non-metric multidimensional scaling of samples demonstrated the distribution of OTUs in multi-dimensional space, the pile-fermentation process of dark green tea can be divided into four periods according to the generated trajectory of fungal population, S0, S1-S3, S4-S5, and S6. Aspergillus is the dominant genus. Penicillium, Cyberlindnera, Debaryomyces, Candida, Thermomyces, Rasamsonia, Thermoascus, and Byssochlamys appear in different periods. three alkaloids, seven catechins, nine amino acids, five organic acids, five flavones and flavonoid glycosides were identified by UPLC-QTOF-MS/MS, and the contents were all decreasing. Caffeine, EGC, EGCG, L-theanine, kaempferitrin, L-phenylalanine, gallic acid, and myricetin-3-O-galactoside are important ingredients which contribute to the flavor of dark green tea. This study demonstrated the fungal succession, non-volatile flavor compounds and their relationships during pile-fermentation of dark green tea, and provides new insights into evaluating pivotal role of fungal succession in the manufacturing process of dark green tea.

Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

Rhizobial Chemoattractants, the Taste and Preferences of Legume Symbionts

The development of host-microbe interactions between legumes and their cognate rhizobia requires localization of the bacteria to productive sites of initiation on the plant roots. This end is achieved by the motility apparatus that propels the bacterium and the chemotaxis system that guides it. Motility and chemotaxis aid rhizobia in their competitiveness for space, resources, and nodulation opportunities. Here, we examine studies on chemotaxis of three major model rhizobia, namely Sinorhizobium meliloti, Rhizobium leguminosarum, and Bradyrhizobium japonicum, cataloging their range of attractant molecules and correlating this in the context of root and seed exudate compositions. Current research areas will be summarized, gaps in knowledge discussed, and future directions described.

High-Throughput LC-ESI-MS/MS Metabolomics Approach Reveals Regulation of Metabolites Related to Diverse Functions in Mature Fruit of Grafted Watermelon

Grafting has been reported as a factor regulating the metabolome of a plant. Therefore, a comprehensive metabolic profile and comparative analysis of metabolites were conducted from fully mature fruit of pumpkin-grafted watermelon (PGW) and a self-rooted watermelon (SRW). Widely targeted LC-ESI-MS/MS metabolomics approach facilitated the simultaneous identification and quantification of 339 metabolites across PGW and SRW. Regardless of grafting, delta-aminolevulinic acid hydrochloride, sucrose, mannose-6-phosphate (carbohydrates), homocystine, 2-phenylglycine, s-adenosyl-L-homocysteine (amino acids and derivatives), malic, azelaic, H-butanoic acid ethyl ester-hexoside isomer 1, (organic acids), MAG (18:3) isomer1, LysoPC 16:0, LysoPC 18:2 2n isomer (lipids) p-coumaric acid, piperidine, and salicylic acid-o-glycoside (secondary metabolites) were among the dominant metabolite. Dulcitol, mono-, and disaccharide sugars were higher in PGW, while polysaccharides showed complex behavior. In PGW, most aromatic and nitrogen-rich amino acids accumulated greater than 1.5- and 1-fold, respectively. Intermediates of the tricarboxylic acid cycle (TCA), stress-related metabolites, vitamin B5, and several flavonoids were significantly more abundant in PGW. Most lipids were also significantly higher in grafted watermelon. This is the first report providing a comprehensive picture of watermelon metabolic profile and changes induced by grafting. Hence, the untargeted high-throughput LC-ESI-MS/MS metabolomics approach could be suitable to provide significant differences in metabolite contents between grafted and ungrafted plants.

Elucidating the effect of biofertilizers on bacterial diversity in maize rhizosphere soil

This study was conducted to investigate the effect of biofertilizers on the structure and diversity of the rhizosphere bacterial community of maize. Different biofertilizers were applied to maize. The physical and chemical properties of rhizosphere soil samples were analyzed and the rhizosphere bacteria were analyzed by 16S amplicon sequencing. The results showed that treatment with Bacillus licheniformis and B. amyloliquefaciens as biofertilizers increased the soil organic matter (SOM), total nitrogen, total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents, indicating that the plant growth-promoting rhizobacteria in the biofertilizers might help the host plant to produce root exudates that, in return, recruit beneficial communities due to available sugars, amino acids, organic acids, vitamins, and polymers. The rhizosphere of maize treated with B. subtilis biofertilizer had the highest diversity and richness. However, the rhizosphere treated with the combined bacterial strains had the lowest diversity and richness, which might be due to the directional increase of the abundance of some bacteria with special functions, but the decrease of the overall bacterial community diversity in the soil. The dominant bacterial phyla were Proteobacteria (32.2%–34.6%), Acidobacteria (15.0%–21.0%), Actinobacteria (13.1%–17.2%), and Gemmatimonadetes (9.0%–10.8%), and the dominant bacterial species were Aciditerrimonas ferrireducens JCM 15389 (4.3%–5.2%), Gemmatimonas aurantiaca (3.2%–4.1%), and Pyrinomonas methylaliphatogenes (2.1%–4.8%). The significantly enriched bacterial functions were associated with amino acid metabolism, sugar metabolism, and energy metabolism pathways. The results of a redundancy analysis showed that SOM, TP, and AK were the main factors affecting the microbial community structure in the maize rhizosphere. In conclusion, the application of biofertilizers increased the diversity and richness of the bacterial community in the maize rhizosphere soil. However, combined strain treatment was failed and not an ideal strategy due to the lowest abundance and diversity.

Effect of neonicotinoid dinotefuran on root exudates of Brassica rapa var. chinensis

Root exudates are released by plant roots and are important carrier substances for material exchange and information transmission among plants and the rhizosphere. In the present study, the effect of dinotefuran on root exudates of Chinese cabbage (Brassica rapa var. chinensis) was investigated. The physiological activities revealed that dinotefuran uptake caused oxidative stress in vegetable tissues even at low dinotefuran exposure levels. The metabolic profile of plant root exudates acquired by LC-QTOF/MS was clearly changed by dinotefuran, where the numbers of both up- and down-regulated MS peaks increased with increasing dinotefuran concentration. Under dinotefuran stress, some osmotic adjustment substances (proline and betaine) and defence-related metabolites (spermidine, phenylalanine and some phenolic acids) were significantly upregulated, which may help plants adapt to adverse environmental conditions. Specifically, the contents of some phenylalanine-derived secondary metabolites increased with increasing dinotefuran concentration, which may increase the external detoxification ability of plants. Moreover, respiration metabolism was significantly affected, where some intermediates in the TCA cycle (succinic acid and malic acid) were upregulated with low-level dinotefuran exposure; however, anaerobic respiration products (lactic acid and 3-phenyllactic acid) were accumulated at high exposure levels. In addition, the release of glucosinolates was significantly inhibited in both dinotefuran treatment groups.

Induced secretion system mutation alters rhizosphere bacterial composition in Sorghum bicolor (L.) Moench

A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Favorable plant-microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.

Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria

There is growing interest in the use of associative, plant growth-promoting bacteria (PGPB) as biofertilizers to serve as a sustainable alternative for agriculture application. While a variety of mechanisms have been proposed to explain bacterial plant growth promotion, the molecular details of this process remain unclear.

The plant rhizosphere harbors a diverse population of microorganisms, including beneficial plant growth-promoting bacteria (PGPB), that colonize plant roots and enhance growth and productivity. In order to specifically define bacterial traits that contribute to this beneficial interaction, we used high-throughput transposon mutagenesis sequencing (TnSeq) in two model root-bacterium systems associated with Setaria viridis: Azoarcus olearius DQS4^T and Herbaspirillum seropedicae SmR1. This approach identified ∼100 significant genes for each bacterium that appeared to confer a competitive advantage for root colonization. Most of the genes identified specifically in A. olearius encoded metabolism functions, whereas genes identified in H. seropedicae were motility related, suggesting that each strain requires unique functions for competitive root colonization. Genes were experimentally validated by site-directed mutagenesis, followed by inoculation of the mutated bacteria onto S. viridis roots individually, as well as in competition with the wild-type strain. The results identify key bacterial functions involved in iron uptake, polyhydroxybutyrate metabolism, and regulation of aromatic metabolism as important for root colonization. The hope is that by improving our understanding of the molecular mechanisms used by PGPB to colonize plants, we can increase the adoption of these bacteria in agriculture to improve the sustainability of modern cropping systems.

Volatile-Mediated Inhibitory Activity of Rhizobacteria as a Result of Multiple Factors Interaction: The Case of Lysobacter capsici AZ78

Plant beneficial rhizobacteria may antagonize soilborne plant pathogens by producing a vast array of volatile organic compounds (VOCs). The production of these compounds depends on the medium composition used for bacterial cell growth. Accordingly, Lysobacter capsici AZ78 (AZ78) grown on a protein-rich medium was previously found to emit volatile pyrazines with toxic activity against soilborne phypathogenic fungi and oomycetes. However, the discrepancy between the quantity of pyrazines in the gaseous phase and the minimum quantity needed to achieve inhibition of plant pathogens observed, lead us to further investigate the volatile-mediated inhibitory activity of AZ78. Here, we show that, besides VOCs, AZ78 cells produce ammonia in increased amounts when a protein-rich medium is used for bacterial growth. The production of this volatile compound caused the alkalinization of the physically separated culture medium where Rhizoctonia solani was inoculated subsequently. Results achieved in this work clearly demonstrate that VOC, ammonia and the growth medium alkalinization contribute to the overall inhibitory activity of AZ78 against R. solani. Thus, our findings suggest that the volatile-mediated inhibitory activity of rhizobacteria in protein-rich substrates can be regarded as a result of multiple factors interaction, rather than exclusively VOCs production.

Changes in physiological activities and root exudation profile of two grapevine rootstocks reveal common and specific strategies for Fe acquisition

In several cultivation areas, grapevine can suffer from Fe chlorosis due to the calcareous and alkaline nature of soils. This plant species has been described to cope with Fe deficiency by activating Strategy I mechanisms, hence increasing root H⁺ extrusion and ferric-chelate reductase activity. The degree of tolerance exhibited by the rootstocks has been reported to depend on both reactions, but to date, little emphasis has been given to the role played by root exudate extrusion. We studied the behaviour of two hydroponically-grown, tolerant grapevine rootstocks (Ramsey and 140R) in response to Fe deficiency. Under these experimental conditions, the two varieties displayed differences in their ability to modulate morpho-physiological parameters, root acidification and ferric chelate reductase activity. The metabolic profiling of root exudates revealed common strategies for Fe acquisition, including ones targeted at reducing microbial competition for this micronutrient by limiting the exudation of amino acids and sugars and increasing instead that of Fe(III)-reducing compounds. Other modifications in exudate composition hint that the two rootstocks cope with Fe shortage via specific adjustments of their exudation patterns. Furthermore, the presence of 3-hydroxymugenic acid in these compounds suggests that the responses of grapevine to Fe availability are rather diverse and much more complex than those usually described for Strategy I plants.

High accumulation of phenolics and amino acids confers tolerance to the combined stress of cobalt and copper in barley (Hordeum vulagare)

Cobalt (Co) and copper (Cu) co-exist in the metal contaminated soils and cause the serious toxicity to crops, while their interactive effect on plant growth and development is still poorly understood. In this work, a hydroponic experiment was carried out to reveal the interactive effect of Co and Cu on photosynthesis and metabolite profiles of two barley genotypes differing in metal tolerance. The results showed that both single and combined treatments of Co and Cu caused a significant reduction in chlorophyll content and photosynthetic rate of the two barley (Hordeum vulgare) genotypes, with the effect being greater for the combined treatment and the sensitive genotype (Ea52) being more affected than the tolerant genotype (Yan66). Compared to Cu or Co treatment alone, the combined treatment significantly increased the levels of phenolic components, including cinnamic derivatives (caffeic, chlorogenic, ferullic, p-coumaric); benzoic derivatives (p-hydroxybenzoic, vanillic, syringic, sallicilic, protocatechuic acid) as well as free amino acids, with Yan66 having more accumulation than Ea52. Meanwhile, under the combined treatment, the phenylalanine ammonialyase-related gene (HvPAL) was highly regulated along with the genes involved in the synthesis of malate (HvMDH) and citrate (HvCSY), with Ya66 showing the higher expression of these genes than Ea52. It can be concluded that higher Cu and Co stress tolerance in Yan66 is attributed to more accumulation of the metabolites including phenolics and amino acids.

Root exudate composition of grass and forb species in natural grasslands

Plants exude a diverse cocktail of metabolites into the soil as response to exogenous and endogenous factors. So far, root exudates have mainly been studied under artificial conditions due to methodological difficulties. In this study, each five perennial grass and forb species were investigated for polar and semi-polar metabolites in exudates under field conditions. Metabolite collection and untargeted profiling approaches combined with a novel classification method allowed the designation of 182 metabolites. The composition of exuded polar metabolites depended mainly on the local environment, especially soil conditions, whereas the pattern of semi-polar metabolites was primarily affected by the species identity. The profiles of both polar and semi-polar metabolites differed between growth forms, with grass species being generally more similar to each other and more responsive to the abiotic environment than forb species. This study demonstrated the feasibility of investigating exudates under field conditions and to identify the driving factors of exudate composition.

Bacillus subtilis and Bacillus velezensis population dynamics and quantification of spores after inoculation on ornamental plants

Bacillus subtilis and Bacillus velezensis are used in organic agriculture as an alternative to chemical pesticides to fight against phytopathogen organisms. These Gram-positive soil-dwelling bacteria are able to resist harsh conditions and survive by differentiating into endospores. Few studies have examined how bacterial populations change on plants over time, and whether they remain active or enter a dormant state. Nonetheless, these characteristics are strikingly important to determine the usage of B. subtilis and B. velezensis and their efficacy in environmental conditions. Here, we investigated the population dynamics of B. subtilis NCIB3610 and B. velezensis QST713 when applied as spores on different ornamental plants. We report that on all the plants studied (Echinacea purpurea 'Salsa red', Echinacea purpurea 'Fatal attraction', and Lavandula angustifolia 'Hidecote blue'), spores rapidly germinated and colonized the rhizoplane, maintaining a relatively low proportion of spores in the population over time, whereas the bacterial population on the leaves rapidly declined. Bacteria in the surrounding soil did not germinate and persisted as spores. Taken together, these results suggest that only cells found at the rhizosphere remain metabolically active to allow the formation of a lasting relationship with the plant, making possible beneficial effects from the inoculated bacteria.

Inoculation with Indole-3-Acetic Acid-Producing Rhizospheric Rhodobacter sphaeroides KE149 Augments Growth of Adzuki Bean Plants Under Water Stress

The use of plant growth-promoting rhizobacteria is economically viable and environmentally safe for mitigating various plant stresses. Abiotic stresses such as flood and drought are a serious threat to present day agriculture. In the present study, the indole-3-acetic acid-producing rhizobacterium R. sphaeroides KE149 was selected, and its effect on the growth of adzuki bean plants was investigated under flood stress (FS) and drought stress (DS). IAA quantification of bacterial pure culture revealed that KE149 produced significant amount of IAA. KE149 inoculation significantly decreased stress-responsive endogenous abscisic acid and jasmonic acid and increased salicylic acid in plants under DS and FS. KE149 inoculation also increased proline under DS and methionine under FS. Moreover, KE149 inoculation significantly increased the calcium (Ca), magnesium (Mg), and potassium (K) content and lowered the sodium (Na) content in the plant shoot under stress. KE149-treated plants had significantly higher root length, shoot length, stem diameter, biomass, and chlorophyll content under both normal and stressed conditions. These results suggest that KE149 could be an efficient biofertilizer for mitigating water stress.

Nitrogen Substrate Utilization in Three Rhizosphere Bacterial Strains Investigated Using Proteomics

Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilizers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilize diverse nitrogen substrates. Here we investigate nitrogen substrate utilization in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces, and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results vs. computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilization being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine, and urea. The proteomic response to these nitrogen sources was strongly strain-dependent, with lysine nutrition eliciting widespread protein-level changes in Pseudomonas sp. Root9, whereas Rhizobium sp. Root491 showed relatively stable proteome composition across different nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilize organic nitrogen substrates.

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

Assessment of the effects of metribuzin, glyphosate, and their mixtures on the metabolism of the model plant Lemna minor L. applying metabolomics

Chemical plant protection products (PPPs) is a major group of xenobiotics that are being released in the environment. Although the effects of individual active ingredients (a.i.) on organisms have been studied, information on those of mixtures, is fragmented. Aquatic environments are being polluted by PPPs, posing serious risks for the environment, human, and other organisms. Based on the potential of the model aquatic plant Lemna minor L. in the assessment of PPPs-caused stresses, we have undertaken the task of developing a metabolomics approach for the study of the effects of metribuzin and glyphosate, and their mixtures. Bioassays revealed that metribuzin exhibit higher toxicity than glyphosate and metabolomics highlighted corresponding changes in its metabolome. Treatments had a substantial impact on plants' amino acid pool, resulting in elevated levels of the majority of the identified amino acids. Results indicate that the increased proteolytic activity is a common effect of the a.i. and their mixtures. Additionally, the activation of salicylate-signaling pathways was recorded as a response to the toxicity caused by mixtures. Among the identified metabolites that were discovered as biomarkers were γ-aminobutyric acid (GABA), salicylate, caffeate, α,α-trehalose, and squalene, which play multiple roles in plants' metabolism such as, signaling, antioxidant, and structure protection. No reports exist on the combined effects of PPPs on Lemna and results confirm the applicability of Lemna metabolomics in the study of the combined effects of herbicides and its potential in the monitoring of the environmental health of aquatic environments based on fluctuations of the plant's metabolism.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

Insights into physiological responses of mosses Physcomitrella patens and Pohlia drummondii to lichen secondary metabolites

It is widely accepted that allelopathy among mosses and lichens do exist due to its similar ecological needs, though it is rarely documented. With an aim to test whether there is an effect of allelochemicals to mosses, we grow axenically two moss species (namely Physcomitrella patens and Pohlia drummondii) in controlled conditions and use them to test the effect of lichen Pseudevernia furfuracea acetone extracts containing active compounds: atranorin, chloratranorin, and physodic acid. The photosynthesis value and the biochemical parameters were measured to detect changes in moss organisms upon application of different concentration of lichen extract. The results obtained clearly showed that both moss species reacted to allelochemicals applied in test but to different extent. This suggests that tested moss species have various patterns on reaction to allelochemicals, and that the process of allelopathy is rather a recently coevolving one, than pre-defined. The lichen secondary metabolites are allelochemicals effective also to moss species that are not selected lichen cohabitants.

RNA-Seq analysis reveals an essential role of tyrosine metabolism pathway in response to root-rot infection in Gerbera hybrida

Gerbera hybrida is one of the top five cut flowers across the world, it is host for the root rot causing parasite called Phytophthora cryptogea. In this study, plantlets of healthy and root-rot pathogen-infected G. hybrida were used as plant materials for transcriptome analyis using high-throughput Illumina sequencing technique. A total 108,135 unigenes were generated with an average length of 727 nt and N50 equal to 1274 nt out of which 611 genes were identified as DEGs by DESeq analyses. Among DEGs, 228 genes were up-regulated and 383 were down-regulated. Through this annotated data and Kyoto encyclopedia of genes and genomes (KEGG), molecular interaction network, transcripts accompanying with tyrosine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction pathways were thoroughly observed considering expression pattern. The involvement of DEGs in tyrosine metabolism pathway was validated by real-time qPCR. We found that genes related with tyrosine metabolism were activated and up-regulated against stress response. The expression of GhTAT, GhAAT, GhHPD, GhHGD and GhFAH genes was significantly increased in the leaves and petioles at four and six dpi (days post inoculation) as compared with control. The study predicts the gene sequences responsible for the tyrosine metabolism pathway and its responses against root-rot resistance in gerbera plant. In future, identification of such genes is necessary for the better understanding of rot resistance mechanism and to develop a root rot resistance strategy for ornamental plants.

Shedding light on the presymbiontic phase of C. arietinum

A complex network of symbiotic events between plants and bacteria allows the biosphere to exploit the atmospheric reservoir of molecular nitrogen. In seeds, a series of presymbiotic steps are already identified during imbibition, while interactions between the host and its symbiont begin in the early stages of germination. In the present study, a detailed analysis of the substances' complex delivered by Cicer arietinum seeds during imbibition showed a relevant presence of proteins and amino acids, which, except for cysteine, occurred with the whole proteinogenic pool. The imbibing solution was found to provide essential probiotic properties able to sustain the growth of the specific chickpea symbiont Mesorhizobium ciceri. Moreover, the imbibing solution, behaving as a complete medium, was found to be critically important for the symbiont's attraction, a fact this that is strictly related to the presence of the amino acids glycine, serine, and threonine. Here, the presence of these amino acids is constantly supported by the presence of the enzymes serine hydroxymethyltransferase and formyltetrahydrofolate deformylase, which are both involved in their biosynthesis. The reported findings are discussed in the light of the pivotal role played by the imbibing solution in attracting and sustaining symbiosis between the host and its symbiont.

Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome

The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.

Phytobiome metabolism: beneficial soil microbes steer crop plants' secondary metabolism

Crops are negatively affected by abiotic and biotic stresses, however, plant-microbe cooperation allows prompt buffering of these environmental changes. Microorganisms exhibit an extensive metabolic capability to assist plants in reducing these burdens. Interestingly, beneficial microbes may also trigger, at the host side, a sequence of events from signal perception to metabolic responses leading to stress tolerance or protection against biotic threats. Although plants are well known for their vast chemical diversity, plant-microbial interactions often stimulate the production of a rich and different repertoire of metabolites in plants. The targeted microbial-plant interactions reprogramming plant metabolism represent potential means to foster various pest managements. However, the molecular mechanisms of microbial modulation of plant metabolic plasticity are still poorly understood. Here, we review an increasing amount of reports providing evidence for alterations to plant metabolism caused by beneficial microbial colonization. In addition, we highlight the vital importance of these metabolic reprograms for plants under stress erratic conditions. © 2019 Society of Chemical Industry.

Glycine transformation induces repartition of cadmium and lead in soil constituents

Heavy metal stress in soil accelerates the plant root exudation of organic ligands. The degradation of exudate ligands can be fundamental to controlling the complexation of heavy metals. However, this process remains poorly understood. Here, we investigated the relationship between the transformation of glycine, a representative amino acid exudate, and cadmium/lead mobility in soils. Two 48-h incubation experiments were conducted after glycine addition to the soils. Parameters related to glycine distribution and degradation, Cd/Pb mobility, and the formation of glycine-Cd complex were analyzed. Glycine addition gradually decreased the Cd and Pb mobility throughout the 48-h incubation. By the end of the experiment, the CaCl₂-extracted Cd and Pb concentrations decreased by 63.5% and 43.6%, respectively. The glycine mineralization was strong in the first 6 h, as indicated by a sharp decrease in CO₂ efflux rates from 10.04 ± 0.62 to 3.51 ± 0.07 mg C-CO₂ kg^-1 soil h^-1. The mineralization rates notably decreased after 6 h. The comparisons of dissolved organic carbon and hydrolyzable amino acid contents indicated that glycine mineralization in solution (95.6%) was much stronger than that in soil solids (49.3%). At the end of incubation, 0.22 mmol kg^-1 glycine remained in soil solids. The remaining glycine provided sufficient sorption sites for Cd²⁺ and Pb²⁺, resulting in enhanced metal fixation via complexation. Comparisons of zeta potentials supported the formation of the glycine-Cd complex. The Cd and Pb immobilization processes could be attributed to metal-glycine complex formation, sorption re-equilibrium, and glycine degradation. These findings emphasize that the biogeochemical processes of glycine, derived from root exudates or protein degradation products, increased the sorption of heavy metals to soils and thus reduced their toxicity to plants.

A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2)

Bacteria from the genus Streptomyces have been long exploited as the most prolific producers of antibiotics, other secondary metabolites and enzymes. They are important members of soil microbial communities that can adapt to changing conditions thank to the fine regulation of gene expression in response to environmental signals. Streptomyces coelicolor A3(2) is a model organism for molecular studies with the most deeply recognized interactions within the complex metabolic and regulatory network. However, details about molecular signals recognized by specialized regulatory proteins as well as their direct targets are often missing. We describe here a zinc-binding protein HypR (SCO6294) which belongs to FadR subfamily of GntR-like regulators. The DNA sequence 5'-TACAATGTCAC-3' recognized by the HypR protein in its own promoter region was identified by DNase I footprinting. Binding of six DNA fragments containing similar sequences located in other promoter regions were confirmed by the electrophoretic mobility shift assay (EMSA). The sequences of 7 in vitro-determined binding sites were assembled to generate a logo of the HypR binding motif, 5'-CTNTGC(A/C)ATGTCAC-3'. Comparison of luciferase reporter genes expression under the control of cloned promoter regions in S. coelicolor A3(2) wild type and deletion mutant strains revealed, that the HypR protein acts as a repressor of its target genes. Genes belonging to the regulon of HypR code for enzymes putatively involved in collagen degradation and utilization of L-hydroxyproline (L-Hyp) as concluded from predicted structure and conserved domains. Their transcription is induced in the wild type strain by the addition of L-Hyp to the culture medium. Moreover, knockout of one of the genes from the predicted L-Hyp utilization operon abolished the ability of the strain to grow on L-Hyp as a sole source of carbon. To our knowledge, this work is the first indication of the existence of the pathway of L-hydroxyproline catabolism in Streptomycetes.

1-Aminocyclopropane-1-Carboxylate: A Novel and Strong Chemoattractant for the Plant Beneficial Rhizobacterium Pseudomonas putida UW4

Plant growth-promoting rhizobacteria (PGPR) and fungi-bacterial biofilms are both important biofertilizer inoculants for sustainable agriculture. However, the strongest chemoattractant for bacteria to colonize the rhizosphere and mycelia is not clear. Coincidentally, almost all the PGPRs possess 1-aminocyclopropane-1-carboxylate (ACC) deaminase (AcdS) and can utilize ACC as the sole nitrogen source. Here, we found that ACC was a novel, metabolic dependent and methyl-accepting chemoreceptor-involved chemoattractant for Pseudomonas putida UW4. The chemotactic response of UW4 to ACC is significantly greater than that to the amino acids and organic acids identified in the plant root and fungal hyphal exudates. The colonization counts of the UW4 acdS or cheR deletion mutants in the wheat rhizosphere and on Agaricus bisporus mycelia were reduced one magnitude compared with those of UW4. The colonization counts of UW4 on A. bisporus antisense ACC oxidase mycelia with a high ACC production significantly increased compared with A. bisporus, followed by the UW4 cheR complementary strain and the ethylene chemoreceptor gene-deletion mutant. The colonization counts of the UW4 strains on A. bisporus acdS⁺ mycelia with a low ACC production decreased significantly compared with A. bisporus wild type. These results suggested that ACC and not ethylene should be the strongest chemoattractant for the PGPR that contain AcdS.

Effect of water availability on changes in root amino acids and associated rhizosphere on root exudation of amino acids in Pisum sativum L

Root exudation is considered to regulate the abundance of the microbial community. It may vary both qualitatively and quantitatively in response to the environment in which the plant is growing. A part of exuded N derives from amino acids (AAs). This, in turn, may help plants to cope with abiotic stresses by favouring positive interactions with the rhizosphere environment, thus playing a potential role in maintaining healthy plants. In this respect, an under-investigated area is the effect of stress due to water deficit (WD). It is proposed that the AA profile in the rhizosphere may be altered by WD, reflecting a modulation of root AA exudation linked to a physiological response of the plant to water stress. To investigate this, Pisum sativum L. plants, grown in unsterilised Rhizobium leguminosarum-enriched soil, were stem-labelled with 15N-urea for 96 h, and then subjected/not subjected to 72 h of WD. The concentrations and abundance of 15N-labelling in individual AAs were determined in both roots and the associated rhizosphere at 24, 48 and 72 h after stress application. It was found that both AAs metabolism in the pea root and AAs exudation were strongly modified in WD conditions. After 24 h of WD, the concentrations of all measured AAs increased in the roots, accompanied by a dramatic stress-related increase in the 15N-labelling of some AAs. Furthermore, after 48-72 h of WD, the concentrations of Pro, Ala and Glu increased significantly within the rhizosphere, notably with a concomitant increase in 15N-enrichment in Pro, Ser, Asn, Asp, Thr and Ile. These results support the concept that, in response to WD, substantial amounts of recently assimilated N are rapidly translocated from the shoots to the roots, a portion of which is exuded as AAs. This leads to the rhizosphere being relatively augmented by specific AAs (notably HSer, Pro and Ala) in WD conditions, with a potential impact on soil water retention.

Comparative metabolomic profiling in the roots and leaves in contrasting genotypes reveals complex mechanisms involved in post-anthesis drought tolerance in wheat

Understanding the contrasting biochemical changes in different plant parts in response to drought can help to formulate smart strategies to develop drought tolerant genotypes. The current study used metabolomics and physiological approaches to understand the differential biochemical changes coupled with physiological adjustments in leaves and roots to cope with drought stress in two wheat genotypes, LA754 (drought tolerant) and AGS2038 (drought sensitive). The gas chromatography-mass spectrometry (GC-MS) analysis and physiological trait estimation were performed in the roots and leaves after drought imposition. Drought induced reduction was observed in all physiological and yield related traits. In LA754, higher numbers of metabolites were altered in leaves (45) compared to roots (20) which indicates that plants allocated more resources to leaves in tolerant genotype. In addition, the metabolic components of the root were less affected by the stress which supports the idea that the roots are more drought tolerant than the leaf or shoot. In AGS2038, thirty and twenty eight metabolites were altered in the leaves and roots, respectively. This indicates that the sensitive genotype compromised resource allocation to leaves, rather allocated more towards roots. Tryptophan, valine, citric acid, fumaric acid, and malic acid showed higher accumulation in leaf in LA754, but decreased in the root, while glyceric acid was highly accumulated in the root, but not in the leaf. The results demonstrated that the roots and shoots have a different metabolic composition, and shoot metabolome is more variable than the root metabolome. Though the present study demonstrated that the metabolic response of shoots to drought contrasts with that of roots, some growth metabolites (protein, sugar, etc) showed a mirror increase in both parts. Protein synthesis and energy cycle was active in both organs, and the organs were metabolically activated to enhance water uptake and maintain growth to mitigate the effect of drought.

Plant health: feedback effect of root exudates-rhizobiome interactions

The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.

Non-Targeted Metabolomics Reveals Sorghum Rhizosphere-Associated Exudates are Influenced by the Belowground Interaction of Substrate and Sorghum Genotype

Root exudation is an important plant process by which roots release small molecules into the rhizosphere that serve in overall plant functioning. Yet, there is a major gap in our knowledge in translating plant root exudation in artificial systems (i.e., hydroponics, sterile media) to crops, specifically for soils expected in field conditions. Sorghum (Sorghum bicolor L. Moench) root exudation was determined using both ultra-performance liquid chromatography and gas chromatography mass spectrometry-based non-targeted metabolomics to evaluate variation in exudate composition of two sorghum genotypes among three substrates (sand, clay, and soil). Above and belowground plant traits were measured to determine the interaction between sorghum genotype and belowground substrate. Plant growth and quantitative exudate composition were found to vary largely by substrate. Two types of changes to rhizosphere metabolites were observed: rhizosphere-enhanced metabolites (REMs) and rhizosphere-abated metabolites (RAMs). More REMs and RAMs were detected in sand and clay substrates compared to the soil substrate. This study demonstrates that belowground substrate influences the root exudate profile in sorghum, and that two sorghum genotypes exuded metabolites at different magnitudes. However, metabolite identification remains a major bottleneck in non-targeted metabolite profiling of the rhizosphere.

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO₂ emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.