Amino acids in the rhizosphere: from plants to microbes

Root exudation under maize/soybean intercropping system mediates the arbuscular mycorrhizal fungi diversity and improves the plant growth

Introduction

Maize/soybean intercropping is a common cropping practice in Chinese agriculture, known to boost crop yield and enhance soil fertility. However, the role of below-ground interactions, particularly root exudates, in maintaining intercropping advantages in soybean/maize intercropping systems remains unclear.

Methods

This study aimed to investigate the differences in root exudates between intercropping and monocropping systems through two pot experiments using metabolomics methods. Multiple omics analyses were conducted to explore correlations between differential metabolites and the community of Arbuscular Mycorrhizal Fungi (AMF), shedding light on the mechanisms underlying the dominance of intercropping from the perspective of root exudates-soil microorganism interactions.

Results and discussion

The study revealed that intercropping significantly increased the types and contents of root exudates, lowered soil pH, increased the availability of nutrients like available nitrogen (AN) and available phosphorus (AP), and enhanced AMF colonization, resulting in improving the community composition of AMF. Besides, root exudates in intercropping systems differed significantly from those in monocropping, with 41 and 39 differential metabolites identified in the root exudates of soybean/maize, predominantly amino acids and organic acids. The total amount of amino acids in the root exudates of soybean intercropping was 3.61 times higher than in monocropping. Additionally, the addition of root exudates significantly improved the growth of soybean/maize and AMF colonization, with the mycorrhizal colonization rate in intercropping increased by 105.99% and 111.18% compared to monocropping, respectively. The identified metabolic pathways associated with root exudates were closely linked to plant growth, soil fertility improvement, and the formation of AMF. Correlation analysis revealed a significant relationship (P < 0.05) between certain metabolites such as tartaric acid, oxalic acid, malic acid, aspartic acid, alanine, and the AMF community. Notably, the photosynthetic carbon fixation pathway involving aspartic acid showed a strong association with the function of Glomus_f_Glomerace, the dominant genus of AMF. A combined analysis of metabolomics and high throughput sequencing revealed that the root exudates of soybean/maize intercropping have direct or indirect connections with AMF and soil nutrients.

Conclusion

This suggests that the increased root exudates of the soybean/maize intercropping system mediate an improvement in AMF community composition, thereby influencing soil fertility and maintaining the advantage of intercropping.

Genetic control of rhizosphere microbiome of the cotton plants under field conditions

Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.

Potential of amino acids-modified biochar in mitigating the soil Cu and Ni stresses - Targeting the tomato growth, physiology and fruit quality

Trace heavy metals (HMs) such as copper (Cu) and nickel (Ni) are toxic to plants, especially tomato at high levels. In this study, biochar (BC) was treated with amino acids (AA) to enhance amino functional groups, which effectively alleviated the adverse effects of heavy metals (HMs) on tomato growth. Hence, this study aimed to evaluate the effect of glycine and alanine modified BC (GBC/ABC) on various tomato growth parameters, its physiology, fruit yield and Cu/Ni uptake under Cu and Ni stresses. In a pot experiment, there was 21 treatments with three replications having two rates of simple BC and glycine/alanine enriched BC (0.5% and 1% (w/w). Cu and Ni stresses were added at 150 mg kg-1 respectively. Plants were harvested after 120 days of sowing and subjected to various analysis. Under Cu and Ni stresses, tomato roots accumulated more Cu and Ni than shoots and fruits, while GBC and ABC application significantly enhanced the root and shoot dry weight irrelevant to the stress conditions. Both rates of GBC decreased the malondialdehyde and hydrogen peroxide levels in plants. The addition of 0.5% GBC with Cu enhanced the tomato fruit dry weight by 1.3 folds in comparison to the control treatment; while tomato fruit juice content also increased (50%) in the presence of 0.5% GBC with Ni as compared to control. In summary, these results demonstrated that lower rate of GBC∼0.5% proved to be the best in mitigating the Cu and Ni stress on tomato plant growth by enhancing the fruit production.

Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

d-amino acids metabolism reflects the evolutionary origin of higher plants and their adaptation to the environment

d-amino acids are the d stereoisomers of the common l-amino acids found in proteins. Over the past two decades, the occurrence of d-amino acids in plants has been reported and circumstantial evidence for a role in various processes, including interaction with soil microorganisms or interference with cellular signalling, has been provided. However, examples are not numerous and d-amino acids can also be detrimental, some of them inhibiting growth and development. Thus, the persistence of d-amino acid metabolism in plants is rather surprising, and the evolutionary origins of d-amino acid metabolism are currently unclear. Systemic analysis of sequences associated with d-amino acid metabolism enzymes shows that they are not simply inherited from cyanobacterial metabolism. In fact, the history of plant d-amino acid metabolism enzymes likely involves multiple steps, cellular compartments, gene transfers and losses. Regardless of evolutionary steps, enzymes of d-amino acid metabolism, such as d-amino acid transferases or racemases, have been retained by higher plants and have not simply been eliminated, so it is likely that they fulfil important metabolic roles such as serine, folate or plastid peptidoglycan metabolism. We suggest that d-amino acid metabolism may have been critical to support metabolic functions required during the evolution of land plants.

Fulvic Acid Promotes Legume-Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

Drought Stress Amelioration Attributes of Plant-Associated Microbiome on Agricultural Plants

The future global food security depends on the availability of water for agriculture. Yet, the ongoing rise in nonagricultural uses for water, such as urban and industrial uses, and growing environmental quality concerns have increased pressure of irrigation water demand and posed danger to food security. Nevertheless, its severity and duration are predicted to rise shortly. Drought pressure causes stunted growth, severe damage to photosynthesis activity, loss in crop yield, reduced seed germination, and reduced nutrient intake by plants. To overcome the effects of a devastating drought on plants, it is essential to think about the causes, mechanisms of action, and long-term agronomy management and genetics. As a result, there is an urgent need for long-term medication to deal with the harmful effects of drought pressure. The review focuses on the adverse impact of drought on the plant, physiological, and biochemical aspects, and management measures to control the severity of drought conditions. This article reviews the role of genome editing (GE) technologies such as CRISPR 9 (CRISPR-Cas9) related spaces and short palindromic relapse between proteins in reducing the effects of phytohormones, osmolytes, external compounds, proteins, microbes (plant growth-promoting microorganism [PGPM]), approach omics, and drought on plants that support plant growth. This research is to examine the potential of using the microbiome associated with plants for drought resistance and sustainable agriculture. Researchers also advocate using a mix of biotechnology, agronomic, and advanced GE technologies to create drought-tolerant plant varieties.

Exploring the Metabolic Response of Pseudomonas putida to L-arginine

Beyond their role as protein-building units, amino acids are modulators of multiple behaviours in different microorganisms. In the root-colonizing beneficial bacterium Pseudomonas putida (recently proposed to be reclassified as alloputida) KT2440, current evidence suggests that arginine functions both as a metabolic indicator and as an environmental signal molecule, modulating processes such as chemotactic responses, siderophore-mediated iron uptake or the levels of the intracellular second messenger cyclic diguanylate (c-di-GMP). Using microcalorimetry and extracellular flux analysis, in this work we have studied the metabolic adaptation of P. putida KT2440 to the presence of L-arginine in the growth medium, and the influence of mutations related to arginine metabolism. Arginine causes rapid changes in the respiratory activity of P. putida, particularly magnified in a mutant lacking the transcriptional regulator ArgR. The metabolic activity of mutants affected in arginine transport and metabolism is also altered during biofilm formation in the presence of the amino acid. The results obtained here further support the role of arginine as a metabolic signal in P. putida and the relevance of ArgR in the adaptation to the amino acid. They also serve as proof of concept on the use of calorimetric and extracellular flux techniques to analyse metabolic responses in bacteria and the impact of different mutant backgrounds on such responses.

Chemical structures, biological activities, and medicinal potentials of amine compounds detected from Aloe species

Unrestricted interest in Aloe species has grown rapidly, and a lot of research is currently being done to learn more about the properties of the various Aloe constituents. Organic compounds containing amine as functional group are present in a vivid variety of compounds, namely, amino acids, hormones, neurotransmitters, DNA, alkaloids, dyes, etc. These compounds have amine functional groups that have various biological activities, which make them responsible for medicinal potential in the form of pharmaceutical, nutraceutical, and cosmeceutical applications. Consequently, the present review work provides an indication of the amines investigated in Aloe species and their therapeutic uses. Various amine compounds of the Aloe species have effective biological properties to treat diseases. Generally, the genus Aloe has various active amine-containing compounds to combat diseases when humans use them in various forms.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Genetic evidence for algal auxin production in Chlamydomonas and its role in algal-bacterial mutualism

Interactions between algae and bacteria are ubiquitous and play fundamental roles in nutrient cycling and biomass production. Recent studies have shown that the plant auxin indole acetic acid (IAA) can mediate chemical crosstalk between algae and bacteria, resembling its role in plant-bacterial associations. Here, we report a mechanism for algal extracellular IAA production from L-tryptophan mediated by the enzyme L-amino acid oxidase (LAO1) in the model Chlamydomonas reinhardtii. High levels of IAA inhibit algal cell multiplication and chlorophyll degradation, and these inhibitory effects can be relieved by the presence of the plant-growth-promoting bacterium (PGPB) Methylobacterium aquaticum, whose growth is mutualistically enhanced by the presence of the alga. These findings reveal a complex interplay of microbial auxin production and degradation by algal-bacterial consortia and draws attention to potential ecophysiological roles of terrestrial microalgae and PGPB in association with land plants.

Signaling in Legume-Rhizobia Symbiosis

Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb

IMPORTANCE

Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction

BACKGROUND

Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.

RESULTS

We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.

CONCLUSION

Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

Data-driven identification of major axes of functional variation in bacteria

The discovery of major axes of correlated functional variation among species and habitats has revealed the fundamental trade-offs structuring both functional and taxonomic diversity in eukaryotes such as plants. Whether such functional axes exist in the bacterial realm and whether they could explain bacterial taxonomic turnover among ecosystems remains unknown. Here, we use a data-driven approach to leverage global genomic and metagenomic datasets to reveal the existence of major axes of functional variation explaining both evolutionary differentiation within Bacteria and their ecological sorting across diverse habitats. We show that metagenomic variation among bacterial communities from various ecosystems is structured along a few axes of correlated functional pathways. Similar clusters of traits explained phylogenetic trait variation among >16,000 bacterial genomes, suggesting that functional turnover among bacterial communities from distinct habitats does not only result from the differential filtering of similar functions among communities, but also from phylogenetic correlations among these functions. Concordantly, functional pathways associated with trait clusters that were most important for defining functional turnover among bacterial communities were also those that had the highest phylogenetic signal in the bacterial genomic phylogeny. This study overall underlines the important role of evolutionary history in shaping contemporary distributions of bacteria across ecosystems.

Metabolomic and transcriptomic analyses reveal comparisons against liquid-state fermentation of primary dark tea, green tea and white tea by Aspergillus cristatus

Liquid-state fermentation (LSF) of tea leaves is a promising way to obtain tea-based nutraceutical products rich in various bioactive compounds. In the study, the changes of bioactive compounds, tea pigments and complex metabolites from LSF of primary dark tea, green tea and white tea infusions with Aspergillus cristatus were determined. Chemical analyses revealed that soluble sugars, monosaccharide composition, total polyphenols, total flavonoids, free amino acids, soluble proteins and tea pigments were changed in different ways. An untargeted metabolomic analysis and ribonucleic acid sequencing (RNA-seq) based transcriptomic analysis were performed to investigate the metabolic differentiation and clarify the key differentially expressed genes (DEGs, fold change >2 and p < 0.05), showing that amino acid metabolism, carbohydrate metabolism and lipid metabolism were the most enriched pathways during A. cristatus fermentation of primary dark tea, green tea and white tea infusions. In addition, glycerophospholipid metabolism, linoleic acid metabolism and phenylalanine metabolism were greatly accumulated in the fermentation of primary dark tea and white tea infusions; Pyruvate metabolism, glycolysis/gluconeogenesis, fatty acid degradation, tyrosine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and valine and leucine, isoleucine degradation were greatly accumulated in the fermentation of primary dark tea and green tea infusions; Starch and sucrose metabolism was greatly accumulated in the fermentation of green tea and white tea infusions; Galactose metabolism was significantly enhanced in the fermentation of primary dark tea infusion; Amino sugar and nucleotide sugar metabolism, sphingolipid metabolism and alanine, aspartate and glutamate metabolism were significantly enhanced in the fermentation of green tea infusion. Besides, some other pathways involving aminobenzoate degradation, biosynthesis of cofactors, pyrimidine metabolism, benzoxazinoid biosynthesis and phenazine biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis and flavone and flavonol biosynthesis also differed from each other. These findings support that A. cristatus plays a vital role in the biochemical and genetic regulation of metabolite profile, and could be considered a potential prospect for better use of A. cristatus on different kinds of tea materials.

Organic amendments alter microbiota assembly to stimulate soil metabolism for improving soil quality in wheat-maize rotation system

Straw retention (SR) and organic fertilizer (OF) application contribute to improve soil quality, but it is unclear how the soil microbial assemblage under organic amendments mediate soil biochemical metabolism pathways to perform it. This study collected soil samples from wheat field under different application of fertilizer (chemical fertilizer, as control; SR, and OF) in North China Plain, and systematically investigated the interlinkages among microbe assemblages, metabolites, and physicochemical properties. Results showed that the soil organic carbon (SOC) and permanganate oxidizable organic carbon (LOC) in soil samples followed the trend as OF > SR > control, and the activity of C-acquiring enzymes presented significantly positive correlation with SOC and LOC. In organic amendments, bacteria and fungi community were respectively dominated by deterministic and stochastic processes, while OF exerted more selective pressure on soil microbe. Compared with SR, OF had greater potential to boost the microbial community robustness through increasing the natural connectivity and stimulating fungal taxa activities in inter-kingdom microbial networks. Altogether 67 soil metabolites were significantly affected by organic amendments, most of them belonged to benzenoids (Ben), lipids and lipid-like molecules (LL), and organic acids and derivatives (OA). These metabolites were mainly derived from lipid and amino acid metabolism pathways. A list of keystone genera such as stachybotrys and phytohabitans were identified as important to soil metabolites, SOC, and C-acquiring enzyme activity. Structural equation modeling showed that soil quality properties were closely associated with LL, OA, and PP drove by microbial community assembly and keystone genera. Overall, these findings suggested that straw and organic fertilizer might drive keystone genera dominated by determinism to mediate soil lipid and amino acid metabolism for improving soil quality, which provided new insights into understanding the microbial-mediated biological process in amending soil quality.

CsBPC2 is a key regulator of root growth and development

BASIC PENTACYSTEINE (BPCs) transcription factors are important regulators of plant growth and development. However, the regulatory mechanism of BPC2 in roots remains unclear. In our previous study, we created Csbpc2 cucumber mutants by the CRISPR/Cas9 system, and our studies on the phenotype of Csbpc2 mutants showed that the root growth was inhibited compared with wide-type (WT). Moreover, the surface area, volume and number of roots decreased significantly, with root system architecture changing from dichotomous branching to herringbone branching. Compared with WT, the leaf growth of the Csbpc2 mutants was not affected. However, the palisade and spongy tissue were significantly thinner, which was not beneficial for photosynthesis. The metabolome of root exudates showed that compared with WT, amino acids and their derivatives were significantly decreased, and the enriched pathways were mainly regulated by amino acids and their derivatives, indicating that knockout of CsBPC2 mainly affected the amino acid content in root exudates. Importantly, transcriptome analysis showed that knockout of CsBPC2 mainly affected root gene expression. Knockout of CsBPC2 significantly reduced the gene expression of gibberellins synthesis. However, the expression of genes related to amino acid synthesis, nitrogen fixation and PSII-related photosynthesis increased significantly, which may be due to the effect of knocking out CsBPC2 on gibberellins synthesis, resulting in the inhibition of seedling growth, thus forming negative feedback regulation. Generally, we showed for the first time that BPC2 is a key regulator gene of root growth and development, laying the foundation for future mechanisms of BPC2 regulation in roots.

Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress

Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.

L-amino acids affect the hydrogenase activity and growth of Ralstonia eutropha H16

Ralstonia eutropha H16 is a chemolithoautotrophic bacterium with O₂-tolerant hydrogenase (Hyds) enzymes. Hyds are expressed in the presence of gas mixtures (H₂, O₂, CO₂) or under energy limitation and stress conditions. O₂-tolerant Hyds are promising candidates as anode biocatalysts in enzymatic fuel cells (EFCs). Supplementation of 0.5% (w/v) yeast extract to the fructose-nitrogen (FN) growth medium enhanced H₂-oxidizing Hyd activity ~ sixfold. Our study aimed to identify key metabolites (L-amino acids (L-AAs) and vitamins) in yeast extract that are necessary for the increased synthesis and activity of Hyds. A decrease in pH and a reduction in ORP (from + 240 ± 5 mV to - 180 mV ± 10 mV values) after 24 h of growth in the presence of AAs were observed. Compared to the FN-medium control, supplementation of 7.0 μmol/ml of the L-AA mixture stimulated the growth of bacteria ~ 1.9 to 2.9 fold, after 72 h. The whole cells' H₂-oxidizing Hyd activity was not observed in control samples, whereas the addition of L-AAs, mainly glycine resulted in a maximum of ~ 22 ± 0.5 and 15 ± 0.3 U, g CDW^-1 activity after 24 h and 72 h, respectively. Our results suggest a correlation between ORP, pH, and function of Hyds in R. eutropha H16 in the presence of key L-AAs. L-AAs used in small amounts can be proposed as signaling molecules or key components of Hyd maturation. These results are important for the optimization of O₂-tolerant Hyds production as anode biocatalysts.

Root exudate-derived compounds stimulate the phosphorus solubilizing ability of bacteria

Low phosphorus (P) availability in soils is a major challenge for sustainable food production, as most soil P is often unavailable for plant uptake and effective strategies to access this P are limited. Certain soil occurring bacteria and root exudate-derived compounds that release P are in combination promising tools to develop applications that increase phosphorus use efficiency in crops. Here, we studied the ability of root exudate compounds (galactinol, threonine, and 4-hydroxybutyric acid) induced under low P conditions to stimulate the ability of bacteria to solubilize P. Galactinol, threonine, and 4-hydroxybutyric acid were incubated with the P solubilizing bacterial strains Enterobacter cloacae, Pseudomonas pseudoalcaligenes, and Bacillus thuringiensis under either inorganic (calcium phosphate) or organic (phytin) forms of plant-unavailable P. Overall, we found that the addition of individual root exudate compounds did not support bacterial growth rates. However, root exudates supplemented to the different bacterial appeared to enhance P solubilizing activity and overall P availability. Threonine and 4-hydroxybutyric acid induced P solubilization in all three bacterial strains. Subsequent exogenous application of threonine to soils improved the root growth of corn, enhanced nitrogen and P concentrations in roots and increased available levels of potassium, calcium and magnesium in soils. Thus, it appears that threonine might promote the bacterial solubilization and plant-uptake of a variety of nutrients. Altogether, these findings expand on the function of exuded specialized compounds and propose alternative approaches to unlock existing phosphorus reservoirs of P in crop lands.

L-DOPA functions as a plant pheromone for belowground anti-herbivory communication

While mechanisms of plant-plant communication for alerting neighbouring plants of an imminent insect herbivore attack have been described aboveground via the production of volatile organic compounds (VOCs), we are yet to decipher the specific components of plant-plant signalling belowground. Using bioassay-guided fractionation, we isolated and identified the non-protein amino acid l-DOPA, released from roots of Acyrtosiphon pisum aphid-infested Vicia faba plants, as an active compound in triggering the production of VOCs released aboveground in uninfested plants. In behavioural assays, we show that after contact with l-DOPA, healthy plants become highly attractive to the aphid parasitoid (Aphidius ervi), as if they were infested by aphids. We conclude that l-DOPA, originally described as a brain neurotransmitter precursor, can also enhance immunity in plants.

Influence of chicken feather waste derived protein hydrolysate on the growth of tea plants under different application methods and fertilizer rates

Modern agriculture prioritizes eco-friendly and sustainable strategies to enhance crop growth and productivity. The utilization of protein hydrolysate extracted from chicken feather waste as a plant biostimulant paves the path to waste recycling. A greenhouse experiment was performed to evaluate the implications of different doses (0, 1, 2, and 3 g L-1) of chicken feather protein hydrolysate (CFPH), application method (soil and foliar), and fertilizer rate (50% and 100%) on the growth performance of tea nursery plants. The highest dose of CFPH (3 g L-1) increased the shoot and root dry weights by 43% and 70%, respectively over control. However, no significant differences were observed between 2 and 3 g L-1 doses in plant dry weight, biometric, and root morphological parameters. Foliar application of CFPH significantly increased all the growth parameters compared to soil drenching except N, P, and K concentrations in leaves and roots. Plants grown under 100% fertilizer rate showed better growth performance than 50% fertilizer rate. Tea nursery plants treated with foliar 2 g L-1 dose and grown under full fertilizer rate recorded the highest plant dry weight, root length, and root surface area. However, tea plants under 50% fertilizer rate and treated with foliar 2 and 3 g L-1 doses sustained the growth similar to untreated plants under 100% fertilizer rate. The significantly higher N, P, and K concentrations in leaves were observed in plants treated with soil drenching of 2 and 3 g L-1 CFPH doses under 100% fertilizer rate. Our results indicate that the application of CFPH as a foliar spray is highly effective in producing vigorous tea nursery plants suitable for field planting, eventually capable of withstanding stress and higher yield.

β-Cyclocitral-Mediated Metabolic Changes Optimize Growth and Defense Responses in Solanum lycopersicum L

β-cyclocitral (βCC) is one of the significant oxidative products of β-carotene. It primes plants for multiple stress acclimation without compromising plant growth. Metabolic reorganization is necessary to maintain a balance between growth and defense. However, the βCC-mediated changes in a plant’s metabolic network are unknown. Here, we demonstrate how βCC-induced metabolic changes enable Solanum lycopersicum L. (tomato) plants to promote defense and maintain growth under stress. An analysis of early (0–240 min) and late (72 h) changes in the tomato metabolome after βCC-treatment using liquid chromatography and tandem mass spectrometry identified 57 compounds. A principal coordinate analysis suggested that βCC treatment significantly changes the metabolite profile. A variable importance in projection (VIP) analysis revealed 16 and 19 discriminant metabolites from early and late samples, respectively (VIP ≥ 1.0). Upregulated metabolites were mainly amino acids and phytophenols. Pathway enrichment analysis showed that βCC treatment influenced amino acid metabolism at early and later times; however, phenylpropanoid and isoquinoline biosynthesis were influenced only at the later time. A 66.6% similarity in the upregulated metabolites of βCC- and simulated-herbivory-treated plants confirmed βCC’s role against herbivores. We conclude that βCC steers a temporal separation in amino acids and defense metabolite accumulation that optimizes resource allocation to growth and defense.

The Arabidopsis LHT1 Amino Acid Transporter Contributes to Pseudomonas simiae-Mediated Plant Growth Promotion by Modulating Bacterial Metabolism in the Rhizosphere

The root microbiome structure ensures optimal plant host health and fitness, and it is, at least in part, defined by the plant genotype. It is well documented that root-secreted amino acids promote microbial chemotaxis and growth in the rhizosphere. However, whether the plant-mediated re-uptake of amino acids contributes to maintaining optimal levels of amino acids in the root exudates, and, in turn, microbial growth and metabolism, remains to be established. Here, we show that Lysine-Histidine Transporter-1 (LHT1), an amino acid inward transporter expressed in Arabidopsis thaliana roots, limits the growth of the plant-growth-promoting bacteria Pseudomonas simiae WCS417r (Ps WCS417r). The amino acid profiling of the lht1 mutant root exudates showed increased levels of glutamine, among other amino acids. Interestingly, lht1 exudates or Gln-supplemented wild-type exudates enhance Ps WCS417r growth. However, despite promoting bacterial growth and robust root colonization, lht1 exudates and Gln-supplemented wild-type exudates inhibited plant growth in a Ps WCS417r-dependent manner. The transcriptional analysis of defense and growth marker genes revealed that plant growth inhibition was not linked to the elicitation of plant defense but likely to the impact of Ps WCS417r amino acids metabolism on auxin signaling. These data suggest that an excess of amino acids in the rhizosphere impacts Ps WCS417r metabolism, which, in turn, inhibits plant growth. Together, these results show that LHT1 regulates the amino-acid-mediated interaction between plants and Ps WCS417r and suggest a complex relationship between root-exuded amino acids, root colonization by beneficial bacteria, bacterial metabolism, and plant growth promotion.

Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.

Enhancing Mechanisms of the Plant Growth-Promoting Bacterial Strain Brevibacillus sp. SR-9 on Cadmium Enrichment in Sweet Sorghum by Metagenomic and Transcriptomic Analysis

To explore the mechanism by which the plant growth-promoting bacterium Brevibacillus sp. SR-9 improves sweet sorghum tolerance and enriches soil cadmium (Cd) under pot conditions, the effect of strain SR-9 inoculation on the microbial community of sorghum rhizosphere soil was analyzed by metagenomics. Gene expression in sweet sorghum roots was analyzed using transcriptomics. The results showed that strain SR-9 promoted the growth of sweet sorghum and improved the absorption and enrichment of Cd in the plants. Compared with the uninoculated treatment, the aboveground part and root dry weight in strain SR-9 inoculated with sorghum increased by 21.09% and 17.37%, respectively, and the accumulation of Cd increased by 135% and 53.41%, respectively. High-throughput sequencing showed that strain SR-9 inoculation altered the rhizosphere bacterial community, significantly increasing the relative abundance of Actinobacteria and Firmicutes. Metagenomic analysis showed that after inoculation with strain SR-9, the abundance of genes involved in amino acid transport metabolism, energy generation and conversion, and carbohydrate transport metabolism increased. KEGG functional classification showed that inoculation with strain SR-9 increased the abundance of genes involved in soil microbial metabolic pathways in the rhizosphere soil of sweet sorghum and the activity of soil bacteria. Transcriptome analysis identified 198 upregulated differentially expressed genes in sweet sorghum inoculated with strain SR-9, including those involved in genetic information processing, biological system, metabolism, environmental information processing, cellular process, and human disease. Most of the annotated differentially expressed genes were enriched in the metabolic category and were related to pathways such as signal transduction, carbohydrate metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. This study showed that plant growth-promoting bacteria can alter the rhizosphere bacterial community composition, increasing the activity of soil bacteria and upregulating gene expression in sweet sorghum roots. The findings enhance our understanding of the microbiological and botanical mechanisms by which plant growth-promoting bacterial inoculation improves the remediation of heavy metals by sorghum.

Genome-wide association studies of five free amino acid levels in rice

Rice (Oryza sativa L.) is one of the important staple foods for human consumption and livestock use. As a complex quality trait, free amino acid (FAA) content in rice is of nutritional importance. To dissect the genetic mechanism of FAA level, five amino acids' (Val, Leu, Ile, Arg, and Trp) content and 4,325,832 high-quality SNPs of 448 rice accessions were used to conduct genome-wide association studies (GWAS) with nine different methods. Of these methods, one single-locus method (GEMMA), seven multi-locus methods (mrMLM, pLARmEB, FASTmrEMMA, pKWmEB, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU), and the recent released 3VmrMLM were adopted for methodological comparison of quantitative trait nucleotide (QTN) detection and identification of stable quantitative trait nucleotide loci (QTLs). As a result, 987 QTNs were identified by eight multi-locus GWAS methods; FASTmrEMMA detected the most QTNs (245), followed by 3VmrMLM (160), and GEMMA detected the least QTNs (0). Among 88 stable QTLs identified by the above methods, 3VmrMLM has some advantages, such as the most common QTNs, the highest LOD score, and the highest proportion of all detected stable QTLs. Around these stable QTLs, candidate genes were found in the GO classification to be involved in the primary metabolic process, biosynthetic process, and catalytic activity, and shown in KEGG analysis to have participated in metabolic pathways, biosynthesis of amino acids, and tryptophan metabolism. Natural variations of candidate genes resulting in the content alteration of five FAAs were identified in this association panel. In addition, 95 QTN-by-environment interactions (QEIs) of five FAA levels were detected by 3VmrMLM only. GO classification showed that the candidate genes got involved in the primary metabolic process, transport, and catalytic activity. Candidate genes of QEIs played important roles in valine, leucine, and isoleucine degradation (QEI_09_03978551 and candidate gene LOC_Os09g07830 in the Leu dataset), tryptophan metabolism (QEI_01_00617184 and candidate gene LOC_Os01g02020 in the Trp dataset), and glutathione metabolism (QEI_12_09153839 and candidate gene LOC_Os12g16200 in the Arg dataset) pathways through KEGG analysis. As an alternative of the multi-locus GWAS method, these findings suggested that the application of 3VmrMLM may provide new insights into better understanding FAA accumulation and facilitate the molecular breeding of rice with high FAA level.

Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.

Rhizobacteria Mitigate the Negative Effect of Aluminum on Pea Growth by Immobilizing the Toxicant and Modulating Root Exudation

High soil acidity is one of the main unfavorable soil factors that inhibit the growth and mineral nutrition of plants. This is largely due to the toxicity of aluminum (Al), the mobility of which increases significantly in acidic soils. Symbiotic microorganisms have a wide range of beneficial properties for plants, protecting them against abiotic stress factors. This report describes the mechanisms of positive effects of plant growth-promoting rhizobacteria Pseudomonas fluorescens SPB2137 on four pea (Pisum sativum L.) genotypes grown in hydroponics and treated with 80 µM AlCl3. In batch culture, the bacteria produced auxins, possessed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, alkalized the medium and immobilized Al, forming biofilm-like structures and insoluble phosphates. Inoculation with Ps. fluorescens SPB2137 increased root and/or shoot biomass of Al-treated plants. The bacteria alkalized the nutrient solution and transferred Al from the solution to the residue, which contained phosphorus that was exuded by roots. As a result, the Al concentration in roots decreased, while the amount of precipitated Al correlated negatively with its concentration in the solution, positively with the solution pH and negatively with Al concentration in roots and shoots. Treatment with Al induced root exudation of organic acids, amino acids and sugars. The bacteria modulated root exudation via utilization and/or stimulation processes. The effects of Al and bacteria on plants varied depending on pea genotype, but all the effects had a positive direction and the variability was mostly quantitative. Thus, Ps. fluorescens SPB2137 improved the Al tolerance of pea due to immobilization and exclusion of toxicants from the root zone.

Reconciling concepts of black queen and tragedy of the commons in simulated bulk soil and rhizosphere prokaryote communities

The Black Queen hypothesis describes the evolutionary strategy to lose costly functions in favour of improving growth efficiency. This results in mutants (cheaters) becoming obligately dependent upon a provider (black queen) to produce a necessary resource. Previous analyses demonstrate black queens and cheaters reach a state of equilibrium in pair-wise systems. However, in complex communities, accumulation of cheaters likely poses a serious burden on shared resources. This should result in a Tragedy of the Commons (ToC), whereby over-utilisation of public resources risks making them growth-limiting. With a collection of differential equations, microbial communities composed of twenty prokaryote ‘species’ either from rhizosphere, characterised by abundant carbon and energy sources, or bulk soil, with limited carbon and energy supply, were simulated. Functional trait groups differed based on combinations of cellulase and amino acid production, growth and resource uptake. Randomly generated communities were thus composed of species that acted as cellulolytic prototrophic black queens, groups that were either cellulolytic or prototrophic, or non-cellulolytic auxotrophic cheaters. Groups could evolve to lose functions over time. Biomass production and biodiversity were tracked in 8,000 Monte Carlo simulations over 500 generations. Bulk soil favoured oligotrophic co-operative communities where biodiversity was positively associated with growth. Rhizosphere favoured copiotrophic cheaters. The most successful functional group across both environments was neither black queens nor cheaters, but those that balanced providing an essential growth-limiting function at a relatively low maintenance cost. Accumulation of loss of function mutants in bulk soil risked resulting in loss of cumulative growth by ToC, while cumulative growth increased in the rhizosphere. In the bulk soil, oligotrophic adaptations assisted species in avoiding extinction. This demonstrated that loss of function by mutation is a successful evolutionary strategy in host-associated and/or resource-rich environments, but poses a risk to communities that must co-operate with each other for mutual co-existence. It was concluded that microbial communities must follow different evolutionary and community assembly strategies in bulk soil versus rhizosphere, with bulk soil communities more dependent on traits that promote co-operative interactions between microbial species.

In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry

The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.

The power of seaweeds as plant biostimulants to boost crop production under abiotic stress

Abiotic stresses like drought and salinity are major factors resulting in crop yield losses and soil degradation worldwide. To meet increasing food demands, we must improve crop productivity, especially under increasing abiotic stresses due to climate change. Recent studies suggest that seaweed-based biostimulants could be a solution to this problem. Here, we summarize the current findings of using these biostimulants and highlight current knowledge gaps. Seaweed extracts were shown to enhance nutrient uptake and improve growth performance in crops under stressed and normal conditions. Seaweed extracts contain several active compounds, for example, polysaccharides, polyphenols and phytohormones. Although some of these compounds have growth-promoting properties on plants, the molecular mechanisms that underly seaweed extract action remain understudied. In this paper, we review the role of these extracts and their bioactive compounds as plant biostimulants. The targeted application of seaweed extract to improve crop performance and protein accumulation is also discussed.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Plant-microbe interactions in the rhizosphere via a circular metabolic economy

Chemical exchange often serves as the first step in plant-microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome-root-shoot-environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon "Systemically Induced Root Exudation of Metabolites" in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands.

Antihyperlipidemic effect and increased antioxidant enzyme levels of aqueous extracts from Liupao tea and green tea in vivo

Liupao tea (fermented dark tea) may improve the active function of hyperlipidemia. Utilizing a hyperlipidemia Sprague-Dawley model and UPLC-MS/MS metabolomics, we examined how the effect of Liupao and green tea extracts on hyperlipidemia and antoxidant enzyme levels and compared their constituents. The results showed that the two types of tea could reduce the levels of total cholesterol (TC), total triglyceride, and low-density lipoprotein cholesterol (LDL-C); increase the contents of bile acids and cholesterol in feces; and improve catalase and glutathione peroxidase (GSH-Px) activities. Compared with the model control group, Liupao tea effectively reduced TC and LDL-C levels by 39.53% and 58.55% and increased GSH-Px activity in the liver by 67.07%, which was better than the effect of green tea. A total of 93 compounds were identified from two samples; the amounts of alkaloids and fatty acids increased compared with green tea, and ellagic acid, hypoxanthine, and theophylline with relatively high contents in Liupao tea had a significantly positive correlation with antihyperlipidemic and antioxidant effects. Therefore, Liupao tea had better antihyperlipidemic and antioxidant activities in vivo than green tea, which might be related to the relatively high content of some active substances.

Integrated metabolomic and transcriptomic analyses of two peanut (Arachis hypogaea L.) cultivars differing in amino acid metabolism of the seeds

Peanut is an important economic crop worldwide. The content of amino acids, especially essential amino acids, is an important nutritional quality trait of peanut seeds. However, the regulation of amino acid metabolism in peanut seeds is poorly understood. Here, two peanut cultivars, Zhonghuahei 1 and Zhongkaihua 151, with high and low free amino acids in mature seeds, respectively, were selected to investigate the regulatory mechanisms of amino acids during seed development. Zhonghuahei 1 is composed of significantly higher arginine (Arg), asparagine (Asn), and glutamate (Glu) contents than Zhongkaihua 151. However, the metabolomic analyses indicated that the contents of most amino acids were significantly lower in Zhonghuahei 1 at the early developmental stage, while they were reverse at the middle and late stages. Transcriptomic analyses also revealed that the differentially expressed genes between the two cultivars during different stages were enriched in multiple pathways associated with amino acid metabolism. Among them, the Arg biosynthesis pathway showed different regulatory profiles between the two cultivars according to the temporal analysis of gene expression patterns. Subsequent gene co-expression network analysis showed that the gene module darkorange was significantly correlated with Arg content, with an enriched Arg biosynthesis pathway. Accordingly, a gene regulatory network for Arg biosynthesis and metabolism, including key genes (ALDH, ASS1, OTC, and GAD) and transcription factors (GATA, HEX, and ATF), was constructed. These findings provide insights into the regulatory network of amino acid metabolism in peanuts and provide candidate genes that can be applied to facilitate peanut breeding with desirable seeds.

Multiomics analysis reveals that peach gum colouring reflects plant defense responses against pathogenic fungi

In the present study, the differences in the antioxidant capability, metabolite composition and fungal diversity in peach gum with various colours were investigated. Metabolomics revealed that peach gum comprised many small-molecule metabolites (including primary and secondary metabolites), and most polyphenols (such as flavonoids and phenolic acids) showed a significantly positive relationship with the colour deepening, total phenol content and antioxidant capability. Using fungal diversity analysis, the abundance of five fungi at the genus level increased with peach gum colour deepening, and these fungi demonstrated a significantly positive relationship with two defense hormones (salicylic acid and abscisic acid) and most polyphenols (particularly flavonoids). The gummosis pathogenic fungus Botryosphaeria was among the five fungi, suggesting that peach gum colouring may reflect plant defense responses against pathogenic fungi. Additionally, the concentrations of 12 flavonoids in peach gum samples were detected based on LC-QQQ/MS, among which hesperetin, naringenin and eriodictyol were the most abundant.

Perspectives on Converting Keratin-Containing Wastes Into Biofertilizers for Sustainable Agriculture

Keratin-containing wastes become pollution to the environment if they are not treated properly. On the other hand, these wastes can be converted into value-added products applicable to many fields. Organic fertilizers and biofertilizers are important for sustainable agriculture by providing nutrients to enhance the growth speed of the plant and production. Keratin-containing wastes, therefore, will be an important resource to produce organic fertilizers. Many microorganisms exhibit capabilities to degrade keratins making them attractive to convert keratin-containing wastes into valuable products. In this review, the progress in microbial degradation of keratins is summarized. In addition, perspectives in converting keratin into bio- and organic fertilizers for agriculture are described. With proper treatment, feather wastes which are rich in keratin can be converted into high-value fertilizers to serve as nutrients for plants, reduce environmental pressure and improve the quality of the soil for sustainable agriculture.

Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB

Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.

Nitrogen Enrichment during Soil Organic Matter Burning and Molecular Evidence of Maillard Reactions

Wildfires in forested watersheds dramatically alter stored and labile soil organic matter (SOM) pools and the export of dissolved organic matter (DOM). Ecosystem recovery after wildfires depends on soil microbial communities and revegetation and therefore is limited by the availability of nutrients, such as nitrogen-containing and labile, water-soluble compounds. However, SOM byproducts produced at different wildfire intensities are poorly understood, leading to difficulties in assessing wildfire severity and predicting ecosystem recovery. In this work, water-extractable organic matter (WEOM) from laboratory microcosms of soil burned at discrete temperatures was characterized by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry to study the impacts of fire temperature on SOM and DOM composition. The molecular composition derived from different burn temperatures indicated that nitrogen-containing byproducts were enriched with heating and composed of a wide range of aromatic features and oxidation states. Mass difference-based analysis also suggested that products formed during heating could be modeled using transformations along the Maillard reaction pathway. The enrichment of N-containing SOM and DOM at different soil burning intensities has important implications for ecosystem recovery and downstream water quality.

The Rhizosphere Microbiomes of Five Species of Coffee Trees

Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health.

IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.

A glass bead semi-hydroponic system for intact maize root exudate analysis and phenotyping

BACKGROUND

Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage.

RESULTS

This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl₂, and to measure root phenotype data using standard methods and the Digital imaging of root traits (DIRT) software. LC-MS/MS (Liquid Chromatography-Tandem Mass Spectrometry) and GC-MS (Gas Chromatography-Mass Spectrometry) targeted metabolomics platforms were used to detect and quantify metabolites in the root exudates. Phytohormones, some of which are reported in maize root exudates for the first time, the benzoxazinoid DIMBOA (2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one), amino acids, and sugars were detected and quantified. After validating the methodology using known concentrations of standards for the targeted compounds, we found that the choice of the exudate collection solution affected the exudation and analysis of a subset of analyzed metabolites. No differences between collection in water or CaCl₂ were found for phytohormones and sugars. In contrast, the amino acids were more concentrated when water was used as the exudate collection solution. The collection in CaCl₂ required a clean-up step before MS analysis which was found to interfere with the detection of a subset of the amino acids. Finally, using the phenotypic measurements and the metabolite data, significant differences between genotypes were found and correlations between metabolites and phenotypic traits were identified.

CONCLUSIONS

A new plant growth system combining glass beads supported hydroponics with semi-automated drip irrigation of sterile solutions was implemented to grow maize plants and collect root exudates without disturbing or damaging the roots. The validated targeted exudate metabolomics platform combined with root phenotyping provides a powerful tool to link plant root and exudate phenotypes to genotype and study the natural variation of plant populations.

Substrate Composition Influences Amino Acid Carbon Isotope Profiles of Fungi: Implications for Tracing Fungal Contributions to Food Webs

Fungi link detrital resources and metazoan consumers through their role as decomposers. However, fungal contributions to metazoans may be misestimated in amino acid isotope studies because fungi are capable of both synthesizing amino acids (AAs) de novo and absorbing AAs from their environment. While fungi cultured in AA-free media have been used to represent fungi in studies of natural environments, fungi likely gain energetic benefits by taking up substrate AAs directly in situ. Consequently, fungi cultured on AA-free media may not be representative of the true variability of natural fungal δ¹³ C_AA profiles. Therefore, the objective of this experiment was to determine the effect of substrate AA availability on yeast δ¹³ C_AA profiles. We found that yeasts cultured in media of relatively higher AA content had different δ¹³ C_AA profiles than fungi grown in AA-free media, in part because yeasts utilized two essential AAs (Leu and Val) directly from media substrates when available in sufficient amounts. Furthermore, these differences among yeast δ¹³ C_AA profiles remained after normalization of δ¹³ C_AA values. We recommend further characterization of the variation in fungal δ¹³ C_AA profiles and the incorporation of this potential variability into interpretations of basal resource use by metazoans. This article is protected by copyright. All rights reserved.

Combined Bioremediation of Bensulfuron-Methyl Contaminated Soils With Arbuscular Mycorrhizal Fungus and Hansschlegelia zhihuaiae S113

Over the past decades, because of large-scale bensulfuron-methyl (BSM) application, environmental residues of BSM have massively increased, causing severe toxicity in rotation-sensitive crops. The removal of BSM from the environment has become essential. In this study, the combined bioremediation of the arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices and BSM-degrading strain Hansschlegelia zhihuaiae S113 of BSM-polluted soil was investigated. BSM degradation by S113 in the maize rhizosphere could better promote AMF infection in the roots of maize, achieving an infection rate of 86.70% on the 36th day in the AMF + S113 + BSM group. Similarly, AMF enhanced the colonization and survival of S113 in maize rhizosphere, contributing 4.65 × 105 cells/g soil on the 15th day and 3.78 × 104 cells/g soil on the 20th day to a population of colonized-S113 (based possibly on the strong root system established by promoting plant-growth AMF). Both S113 and AMF coexisted in rhizosphere soil. The BSM-degrading strain S113 could completely remove BSM at 3 mg/kg from the maize rhizosphere soil within 12 days. AMF also promoted the growth of maize seedlings. When planted in BSM-contaminated soil, maize roots had a fresh weight of 2.59 ± 0.26 g in group S113 + AMF, 2.54 ± 0.20 g in group S113 + AMF + BSM, 2.02 ± 0.16 g in group S113 + BSM, and 2.61 ± 0.25 g in the AMF group, all of which exceeded weights of the control group on the 36th day except for the S113 + BSM group. Additionally, high-throughput sequencing results indicated that simultaneous inoculation with AMF and strain S113 of BSM-polluted maize root-soil almost left the indigenous bacterial community diversity and richness in maize rhizosphere soil unaltered. This represents a major advantage of bioremediation approaches resulting from the existing vital interactions among local microorganisms and plants in the soil. These findings may provide theoretical guidance for utilizing novel joint-bioremediation technologies, and constitute an important contribution to environmental pollution bioremediation while simultaneously ensuring crop safety and yield.

Thermal Hydrolysis Pretreatment-Anaerobic Digestion Promotes Plant-Growth Biostimulants Production from Sewage Sludge by Upregulating Aromatic Amino Acids Transformation and Quinones Supply

Micromolecular plant-growth biostimulants (micro-PBs) production from sewage sludge is attracting increasing interest, as it is expected to enhance the fertilizing effect of sludge for land application. This study attempted to promote effective micro-PBs production from sewage sludge through thermal hydrolysis pretreatment-anaerobic digestion (THP-AD) and explore the underpinning regulation mechanisms. Results showed that the highest effective micro-PB production in digested sludge was achieved in THP(160 °C)-AD by day 12, with 80.73 mg/kg volatile solid (VS) of phytohormones and 417.75 mg/kg VS of allelochemicals, and these effective micro-PBs all originated from aromatic amino acids (AAAs). The metabolomic and metagenomic results revealed that, as compared with THP(120 °C)-AD and AD without THP, THP(160°C)-AD uniquely upregulated AAAs biosynthesis and consequently improved AAAs metabolism toward effective micro-PBs production. Further exploration of related microbial pathways and metabolites suggested that the upregulated AAAs biosynthesis in THP(160 °C)-AD in the early stage was partially attributed to the enhanced carbohydrate release. More importantly, the results showed that the amount of quinones, which probably facilitate energy generation via acting as electron-transfer mediators, was significantly positively correlated with the abundance of AAAs biosynthesis genes (R² = 0.93). Hence, the improved initial release and biosynthesis of quinones are critical in enhancing the AAAs biosynthesis in THP(160 °C)-AD. Moreover, the enhanced quinones supply and the consequent active AAAs transformation in THP(160 °C)-AD reinforced the humification process, highly supporting effective micro-PBs stabilization. The important roles of quinones in effective micro-PBs production and stabilization in sludge anaerobic digestion should be considered in technology development for micro-PBs recovery.

The Potential of Fermented Food from Southeast Asia as Biofertiliser

The intensive amount of chemical usage in agricultural practices could contribute to a significant impact on food safety issues and environmental health. Over-usage of chemical fertilisers may alter soil characteristics and contaminate water sources, leading to several human and animal health issues. Recently, there have been efforts to use microbial biofertilisers as a more sustainable and environmentally friendly agricultural practice in the common household of Southeast Asia. Traditionally, this method tends to utilise leftover food materials and readily available bacterial cultures, such as yoghurt drinks, and ferment them under a specific period in either solid or liquid form. So far, most of the testimonial-based feedbacks from local communities have been positive, but only limited information is available in the literature regarding the usage of biofertiliser fermented food (BFF). Previously, raw food waste has been used in the agriculture system to promote plant growth, however, the functional role of fermented food in enhancing plant growth have yet to be discovered. An understanding of the symbiotic relationship between fermented food and plants could be exploited to improve agricultural plant production more sustainably. Fermented food is known to be rich in good microbial flora (especially lactic acid bacteria (LAB)). LAB exist in different sources of fermented food and can act as a plant growth-promoting agent, improving the nutrient availability of food waste and other organic materials. Therefore, in this review, the potential use of seafood-based, plant-based, and animal-based fermented food as biofertiliser, especially from Southeast Asia, will be discussed based on their types and microbial and nutritional contents. The different types of fermented food provide a wide range of microbial flora for the enrichment of proteins, amino acids, vitamins, and minerals content in enhancing plant growth and overall development of the plant. The current advances of biofertiliser and practices of BFF will also be discussed in this review.