Plant growth and phenolic compounds in the rhizosphere soil of wild oat (Avena fatua L.)

Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review

Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.

Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE

Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.

Transcriptome Sequencing and Analysis of Trichoderma polysporum Infection in Avena fatua L. Leaves before and after Infection

Biological control is a scientific management method used in modern agricultural production, and microbially derived biopesticides are one effective method with which to control weeds in agricultural fields. In order to determine the key genes for weed control by Trichoderma polysporum, transcriptome sequencing was carried out by high-throughput sequencing technology, and the strains of T. polysporum HZ-31 infesting Avena fatua L. at 24, 48, and 72 h were used as the experimental group, with 0 h as the control group. A total of 690,713,176 clean reads were obtained, and the sequencing results for each experimental group and the control group (0 h) were analyzed. In total, 3464 differentially expressed genes were found after 24 h of infection with the pathogen, including 1283 down-regulated genes and 2181 up-regulated genes. After 48 h of infection, the number of differentially expressed genes was 3885, of which 2242 were up-regulated and 1643 were down-regulated. The number of differentially expressed genes after 72 h of infection was the highest among all the groups, with 4594 differentially expressed genes, of which 2648 were up-regulated and 1946 were down-regulated. The up-regulated genes were analyzed by GO and KEGG, and the results showed that the up-regulated differentially expressed genes were mainly enriched in the biosynthesis of phenylalanine, tyrosine, and tryptophan; the degradation of aromatic compounds; methane metabolism; and other pathways. Among them, the PHA2, GDH, ADH2, and AROF genes were significantly enriched in the above-mentioned pathways, so they were hypothesized to play an important role in the synthesis of the herbicidally active substances of T. polysporum HZ-31. The results of this study can provide a theoretical basis for further studies on the pathogenicity of T. polysporum to A. fatua L., and accelerate the development and utilization of new and efficient bioherbicides.

Antioxidant capacity sources of soils under different land uses

Antioxidants (AOX) in soils originate mainly from secondary plant metabolites and are pivotal in many redox processes in environment, maintaining soil quality. Still, little is known about the influence of land uses on their accumulation in soil. The aim of the paper was to determine the content of these redox-active compounds in the extracts of A horizons of abandoned fallows, arable and woodland soils. Total antioxidant capacity (TAC) of soils under various uses and vegetation was evaluated in different soil extracts using Folin-Ciocâlteu method. The contribution of humic acids to TAC was determined and antioxidant profiles estimated using the chromatographic GC-MS method. Forest soils exhibited the highest TAC (15.5 mg g-1) and AOX contents (4.34 mg g-1), which were positively correlated with soil organic carbon content. It was estimated that humic acids contribute to over 50% of TAC in soils. The main phenolics in woodland A horizons were isovanillic and p-hydroxybenzoic acid (p-HA), while esculetin and p-HA predominated in the abandoned fallows due to the prevalence of herbaceous vegetation. Cultivated soils were the most abundant in p-HA (56.42%). In the studied topsoils, there were considerable amounts of aliphatic organic matter, which role in redox processes should be further evaluated.

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.

Nematocidal Potential of Phenolic Acids: A Phytochemical Seed-Coating Approach to Soybean Cyst Nematode Management

Soybeans, one of the most valuable crops worldwide, are annually decimated by the soybean cyst nematode (SCN), Heterodera glycines, resulting in massive losses in soybean yields and economic revenue. Conventional agricultural pesticides are generally effective in the short term; however, they pose growing threats to human and environmental health; therefore, alternative SCN management strategies are urgently needed. Preliminary findings show that phenolic acids are significantly induced during SCN infection and exhibit effective nematocidal activities in vitro. However, it is unclear whether these effects occur in planta or elicit any negative effects on plant growth traits. Here, we employed a phytochemical-based seed coating application on soybean seeds using phenolic acid derivatives (4HBD; 2,3DHBA) at variable concentrations and examined SCN inhibition against two SCN types. Moreover, we also examined plant growth traits under non-infected or SCN infected conditions. Notably, 2,3DHBA significantly inhibited SCN abundance in Race 2-infected plants with increasingly higher chemical doses. Interestingly, neither compound negatively affected soybean growth traits in control or SCN-infected plants. Our findings suggest that a phytochemical-based approach could offer an effective, more environmentally friendly solution to facilitate current SCN management strategies and fast-track the development of biopesticides to sustainably manage devastating pests such as SCN.

Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress

Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.

Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment

The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Explore the interaction between root metabolism and rhizosphere microbiota during the growth of Angelica sinensis

Angelica sinensis is a medicinal plant widely used to treat multiple diseases in Asia and Europe, which contains numerous active components with therapeutic value. The interaction between root and rhizosphere microorganisms is crucial for the growth and quality formation of medicinal plants. But the micro-plant-metabolite regulation patterns for A. sinensis remain largely undetermined. Here, we collected roots and rhizosphere soils from A. sinensis in seedling stage (M) and picking stage (G), respectively cultivated for one year and two years, generated metabolite for roots, microbiota data for rhizospheres, and conducted a comprehensive analysis. Changes in metabolic and microbial communities of A.sinensis over growth were distinct. The composition of rhizosphere microbes in G was dominated by proteobacteria, which had a strong correlation with the synthesis of organic acids, while in M was dominated by Actinobacteria, which had a strong correlation with the synthesis of phthalide and other organoheterocyclic compounds, flavonoids, amines, and fatty acid. Additionally, co-occurrence network analysis identified that Arthrobacter was found to be strongly correlated with the accumulation of senkyunolide A and n-butylidenephthalide. JGI 0001001.H03 was found to be strongly correlated with the accumulation of chlorogenic acid. Based on rhizosphere microorganisms, this study investigated the correlation between root metabolism and rhizosphere microbiota of A. sinensis at different growth stages in traditional geoherb region, which could provide references for exploring the quality formation mechanism of A. sinensis in the future.

Effect of Altitude on Volatile Organic and Phenolic Compounds of Artemisia brevifolia Wall ex Dc. From the Western Himalayas

Adaptation to changing environmental conditions is a driver of plant diversification. Elevational gradients offer a unique opportunity for investigating adaptation to a range of climatic conditions. The use of specialized metabolites as volatile and phenolic compounds is a major adaptation in plants, affecting their reproductive success and survival by attracting pollinators and protecting themselves from herbivores and other stressors. The wormseed Artemisia brevifolia can be found across multiple elevations in the Western Himalayas, a region that is considered a biodiversity hotspot and is highly impacted by climate change. This study aims at understanding the volatile and phenolic compounds produced by A. brevifolia in the high elevation cold deserts of the Western Himalayas with the view to understanding the survival strategies employed by plants under harsh conditions. Across four sampling sites with different elevations, polydimethylsiloxane (PDMS) sampling and subsequent GCMS analyses showed that the total number of volatile compounds in the plant headspace increased with elevation and that this trend was largely driven by an increase in compounds with low volatility, which might improve the plant’s resilience to abiotic stress. HPLC analyses showed no effect of elevation on the total number of phenolic compounds detected in both young and mature leaves. However, the concentration of the majority of phenolic compounds decreased with elevation. As the production of phenolic defense compounds is a costly trait, plants at higher elevations might face a trade-off between energy expenditure and protecting themselves from herbivores. This study can therefore help us understand how plants adjust secondary metabolite production to cope with harsh environments and reveal the climate adaptability of such species in highly threatened regions of our planet such as the Himalayas.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

Drought and Plant Community Composition Affect the Metabolic and Genotypic Diversity of Pseudomonas Strains in Grassland Soils

Climate and plant community composition (PCC) modulate the structure and function of microbial communities. In order to characterize how the functional traits of bacteria are affected, important plant growth-promoting rhizobacteria of grassland soil communities, pseudomonads, were isolated from a grassland experiment and phylogenetically and functionally characterized. The Miniplot experiment was implemented to examine the mechanisms underlying grassland ecosystem changes due to climate change, and it investigates the sole or combined impact of drought and PCC (plant species with their main distribution either in SW or NE Europe, and a mixture of these species). We observed that the proportion and phylogenetic composition of nutrient-releasing populations of the Pseudomonas community are affected by prolonged drought periods, and to a minor extent by changes in plant community composition, and that these changes underlie seasonality effects. Our data also partly showed concordance between the metabolic activities and 16S phylogeny. The drought-induced shifts in functional Pseudomonas community traits, phosphate and potassium solubilization and siderophore production did not follow a unique pattern. Whereas decreased soil moisture induced a highly active phosphate-solubilizing community, the siderophore-producing community showed the opposite response. In spite of this, no effect on potassium solubilization was detected. These results suggest that the Pseudomonas community quickly responds to drought in terms of structure and function, the direction of the functional response is trait-specific, and the extent of the response is affected by plant community composition.

Evaluation of Phenolic Root Exudates as Stimulants of Saptrophic Fungi in the Rhizosphere

The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.

Application of biochar and inorganic phosphorus fertilizer influenced rhizosphere soil characteristics, nodule formation and phytoconstituents of cowpea grown on tropical soil

The effect of biochar alone or co-applied with triple superphosphate on rhizosphere soil characteristics, nodule formation, phytoconstituents and antioxidant property of cowpea (Vigna uguiculata) is yet to be adequately examined in sub Saharan Africa. A field experiment was conducted where cowpea (Vigna unguiculata) was grown in a tropical sandy loam soil amended with biochar at 1.5 t ha⁻¹ and 2.5 t ha⁻¹ solely or together with inorganic phosphate fertilizer (Triple superphosphate), applied at a rate of 60 kg P ha ⁻¹. At 50% flowering, changes in selected rhizosphere soil properties (pH, total nitrogen, available phosphorus, soil organic carbon, cation exchange capacity), nodule count, phytochemicals (phenols, flavonoids, alkaloids, tannins, saponins) and antioxidant property of cowpea roots and leaves were determined by standard laboratory procedures. Differences between means of the measured parameters were established using ANOVA, and relationships among the parameters were explored using Pearson correlation (p < 0.05). Addition of biochar solely or in combination with TSP significantly (p < 0.05) increased soil pH, total nitrogen, available phosphorus, soil organic carbon, cation exchange capacity and root nodule count. Flavonoids, phenols, alkaloids, saponin, tannin contents and antioxidant activity in the roots and leaves were significantly (p < 0.05) higher in the amended soils compared with the unamended soil. Similarly, soil flavonoids, phenols, alkaloids and antioxidant activity were significantly higher in amended soils compared with control. Significant, positive inter and intra correlation with varying strength was found between soil properties, nodule number and phytoconstituents. This is an indication that biochar can be co-applied with triple superphosphate to sustain soil fertility, improve nodulation and enhance concentrations of phytoconstituents in soil, cowpea roots and leaves.

Metabolic Profiling Provides Unique Insights to Accumulation and Biosynthesis of Key Secondary Metabolites in Annual Pasture Legumes of Mediterranean Origin

Annual legumes from the Mediterranean region are receiving attention in Australia as alternatives to traditional pasture species. The current study employed novel metabolic profiling approaches to quantify key secondary metabolites including phytoestrogens to better understand their biosynthetic regulation in a range of field-grown annual pasture legumes. In addition, total polyphenol and proanthocyanidins were quantified using Folin-Ciocalteu and vanillin assays, respectively. Metabolic profiling coupled with biochemical assay results demonstrated marked differences in the abundance of coumestans, flavonoids, polyphenols, and proanthocyanidins in annual pasture legume species. Genetically related pasture legumes segregated similarly from a chemotaxonomic perspective. A strong and positive association was observed between the concentration of phytoestrogens and upregulation of the flavonoid biosynthetic pathway in annual pasture legumes. Our findings suggest that evolutionary differences in metabolic dynamics and biosynthetic regulation of secondary metabolites have logically occurred over time in various species of annual pasture legumes resulting in enhanced plant defense.

Constitutive and Induced Expression of Total Phenol and Phenol Oxidases in Wheat Genotypes Ranging in Resistance/Susceptibility to the Root-Lesion Nematode Pratylenchus thornei

Plant-derived phenolic compounds contribute to the defense against various pathogens, including root-lesion nematodes (Pratylenchus spp.). However, there are no reports on the role of phenolic compounds in wheat (Triticum aestivum) against Pratylenchus thornei. In this study, wheat genotypes ranging from resistant to very susceptible to P. thornei were used to investigate the level of total phenols and phenol oxidases, polyphenol oxidase (PPO), and peroxidase (POD) expressed in root tissues when grown in the presence and absence of P. thornei over time (2–8 weeks). Higher constitutive levels of total phenols were found in resistant synthetic hexaploid wheats CPI133872 (576 µg gallic acid equivalent (GAE)/g root) and CPI133859 (518 µg GAE/g root) at 8 weeks after sowing, compared with moderately resistant and susceptible genotypes (192 to 390 µg GAE/g root). The activity of PPO was induced in resistant (CPI133872) and moderately resistant (GS50a and its derivate QT8343) genotypes, becoming maximal at 4 weeks after P. thornei inoculation. The activity of POD was induced in CPI133872 at 6 weeks after P. thornei inoculation. Different genetic sources of resistance to P. thornei showed diverse defense mechanisms and differences in timing responses. The combined effects of total phenols and oxidative enzymes could be important for defense against P. thornei in some resistant wheat genotypes.

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.)

Domestication has induced major genetic changes in crop plants to satisfy human needs and as a consequence of adaptation to agroecosystems. This adaptation might have affected root exudate composition, which can influence the interactions in the rhizosphere. Here, using two different soil types (sand, soil), we provide an original example of the impact of domestication and crop evolution on root exudate composition through metabolite profiling of root exudates for a panel of 10 wheat genotypes that correspond to the key steps in domestication of tetraploid wheat (wild emmer, emmer, durum wheat). Our data show that soil type can dramatically affect the composition of root exudates in the rhizosphere. Moreover, the composition of the rhizosphere metabolites is associated with differences among the genotypes of the wheat domestication groups, as seen by the high heritability of some of the metabolites. Overall, we show that domestication and breeding have had major effects on root exudates in the rhizosphere, which suggests the adaptive nature of these changes.

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure

Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.

Transformation of the Herbicide Sulcotrione into a Root Growth Enhancer Compound by Sequential Photolysis and Hydrolysis

Xanthene-1,9-dione-3,4-dihydro-6-methylsulfonyl (1), the main product of sulcotrione phototransformation on plant leaves, was slowly hydrolyzed into 2-hydroxy-4-methylsulfonylbenzoic acid (2) and 1,3-cyclohexanedione (3) in aqueous solution. Interestingly, the rate of hydrolysis was significantly enhanced in the presence of roots of monocotyledonous plants, while the same treatment showed adverse effects on broadleaf weeds. Root growth enhancement varied according to the plant species and concentrations of compound 2, as shown with Zea mays roots. Compound 2 is a derivative of salicylic acid that is known to be a plant signaling messenger. Compound 2 was, therefore, able to mimic some known effects of this phytohormone. This work showed that a pesticide like sulcotrione was transformed into a compound exhibiting a positive impact on plant growth. This study exemplified a rarely reported situation where chemical and biological chain reactions transformed a xenobiotic into a compound exhibiting potential beneficial effects.

Research Progress on the use of Plant Allelopathy in Agriculture and the Physiological and Ecological Mechanisms of Allelopathy

Allelopathy is a common biological phenomenon by which one organism produces biochemicals that influence the growth, survival, development, and reproduction of other organisms. These biochemicals are known as allelochemicals and have beneficial or detrimental effects on target organisms. Plant allelopathy is one of the modes of interaction between receptor and donor plants and may exert either positive effects (e.g., for agricultural management, such as weed control, crop protection, or crop re-establishment) or negative effects (e.g., autotoxicity, soil sickness, or biological invasion). To ensure sustainable agricultural development, it is important to exploit cultivation systems that take advantage of the stimulatory/inhibitory influence of allelopathic plants to regulate plant growth and development and to avoid allelopathic autotoxicity. Allelochemicals can potentially be used as growth regulators, herbicides, insecticides, and antimicrobial crop protection products. Here, we reviewed the plant allelopathy management practices applied in agriculture and the underlying allelopathic mechanisms described in the literature. The major points addressed are as follows: (1) Description of management practices related to allelopathy and allelochemicals in agriculture. (2) Discussion of the progress regarding the mode of action of allelochemicals and the physiological mechanisms of allelopathy, consisting of the influence on cell micro- and ultra-structure, cell division and elongation, membrane permeability, oxidative and antioxidant systems, growth regulation systems, respiration, enzyme synthesis and metabolism, photosynthesis, mineral ion uptake, protein and nucleic acid synthesis. (3) Evaluation of the effect of ecological mechanisms exerted by allelopathy on microorganisms and the ecological environment. (4) Discussion of existing problems and proposal for future research directions in this field to provide a useful reference for future studies on plant allelopathy.

Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134

Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.