Volatile DMNT directly protects plants against Plutella xylostella by disrupting the peritrophic matrix barrier in insect midgut

Insect pests negatively affect crop quality and yield; identifying new methods to protect crops against insects therefore has important agricultural applications. Our analysis of transgenic Arabidopsis thaliana plants showed that overexpression of pentacyclic triterpene synthase 1, encoding the key biosynthetic enzyme for the natural plant product (3E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), led to a significant resistance against a major insect pest, Plutella xylostella. DMNT treatment severely damaged the peritrophic matrix (PM), a physical barrier isolating food and pathogens from the midgut wall cells. DMNT repressed the expression of PxMucin in midgut cells, and knocking down PxMucin resulted in PM rupture and P. xylostella death. A 16S RNA survey revealed that DMNT significantly disrupted midgut microbiota populations and that midgut microbes were essential for DMNT-induced killing. Therefore, we propose that the midgut microbiota assists DMNT in killing P. xylostella. These findings may provide a novel approach for plant protection against P. xylostella.

Dissecting cholesterol and phytosterol biosynthesis via mutants and inhibitors

Plants stand out among eukaryotes due to the large variety of sterols and sterol derivatives that they can produce. These metabolites not only serve as critical determinants of membrane structures, but also act as signaling molecules, as growth-regulating hormones, or as modulators of enzyme activities. Therefore, it is critical to understand the wiring of the biosynthetic pathways by which plants generate these distinct sterols, to allow their manipulation and to dissect their precise physiological roles. Here, we review the complexity and variation of the biosynthetic routes of the most abundant phytosterols and cholesterol in the green lineage and how different enzymes in these pathways are conserved and diverged from humans, yeast, and even bacteria. Many enzymatic steps show a deep evolutionary conservation, while others are executed by completely different enzymes. This has important implications for the use and specificity of available human and yeast sterol biosynthesis inhibitors in plants, and argues for the development of plant-tailored inhibitors of sterol biosynthesis.

High-throughput cultivation and identification of bacteria from the plant root microbiota

Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called 'Culturome' ( https://github.com/YongxinLiu/Culturome ) and a graphical user interface web server ( http://bailab.genetics.ac.cn/culturome/ ). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8-9 weeks.

Root exudates drive soil-microbe-nutrient feedbacks in response to plant growth

Although interactions between plants and microbes at the plant-soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow- and fast-growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient-depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate-treated soils, with similar responses observed for slow-growing and fast-growing plant exudate treatments. The fast-growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow-growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth.

A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites

Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.

Enzymatic and non-enzymatic functional attributes of plant microbiome

Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.

Pinpointing secondary metabolites that shape the composition and function of the plant microbiome

One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.

Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity

Many plant specialized metabolites function in herbivore defense, and abrogating particular steps in their biosynthetic pathways frequently causes autotoxicity. However, the molecular mechanisms underlying their defense and autotoxicity remain unclear. Here, we show that silencing two cytochrome P450s involved in diterpene biosynthesis in the wild tobacco Nicotiana attenuata causes severe autotoxicity symptoms that result from the inhibition of sphingolipid biosynthesis by noncontrolled hydroxylated diterpene derivatives. Moreover, the diterpenes' defensive function is achieved by inhibiting herbivore sphingolipid biosynthesis through postingestive backbone hydroxylation products. Thus, by regulating metabolic modifications, tobacco plants avoid autotoxicity and gain herbivore defense. The postdigestive duet that occurs between plants and their insect herbivores can reflect the plant's solutions to the "toxic waste dump" problem of using potent chemical defenses.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

Characterization of a Pentacyclic Triterpene Acetyltransferase Involved in the Biosynthesis of Taraxasterol and ψ-Taraxasterol Acetates in Lettuce

Triterpenoids exist in a free state and/or in conjugated states, such as triterpene glycosides (saponins) or triterpene esters. There is no information on the enzyme participating in the production of triterpene esters from free triterpenes. Lettuce (Lactuca sativa) contains various pentacyclic triterpene acetates (taraxasterol acetates, ψ-taraxasterol acetates, taraxerol acetates, lupeol acetates, α-amyrin acetates, β-amyrin acetates, and germanicol acetate). In this study, we report a novel triterpene acetyltransferase (LsTAT1) in lettuce involved in the biosynthesis of pentacyclic triterpene acetates from free triterpenes. The deduced amino acid sequences of LsTAT1 showed a phylogenetic relationship (43% identity) with those of sterol O-acyltransferase (AtSAT1) of Arabidopsis thaliana and had catalytic amino acid residues (Asn and His) that are typically conserved in membrane-bound O-acyltransferase (MBOAT) family proteins. An analysis of LsTAT1 enzyme activity in a cell-free system revealed that the enzyme exhibited activity for the acetylation of taraxasterol, ψ-taraxasterol, β-amyrin, α-amyrin, lupeol, and taraxerol using acetyl-CoA as an acyl donor but no activity for triterpene acylation using a fatty acyl donor. Lettuce oxidosqualene cyclase (LsOSC1) is a triterpene synthase that produces ψ-taraxasterol, taraxasterol, β-amyrin and α-amyrin. The ectopic expression of both the LsOSC1 and LsTAT1 genes in yeast and tobacco could produce taraxasterol acetate, ψ-taraxasterol acetate, β-amyrin acetate, and α-amyrin acetate. However, expression of the LsTAT1 gene in tobacco was unable to induce the conversion of intrinsic sterols (campesterol, stigmasterol, and β-sitosterol) to sterol acetates. The results demonstrate that the LsTAT1 enzyme is a new class of acetyltransferase belong to the MBOAT family that have a particular role in the acetylation of pentacyclic triterpenes and are thus functionally different from sterol acyltransferase conjugating fatty acyl esters.

Endophytic Fungi: From Symbiosis to Secondary Metabolite Communications or Vice Versa?

Endophytic fungi (EF) are a group of fascinating host-associated fungal communities that colonize the intercellular or intracellular spaces of host tissues, providing beneficial effects to their hosts while gaining advantages. In recent decades, accumulated research on endophytic fungi has revealed their biodiversity, wide-ranging ecological distribution, and multidimensional interactions with host plants and other microbiomes in the symbiotic continuum. In this review, we highlight the role of secondary metabolites (SMs) as effectors in these multidimensional interactions, and the biosynthesis of SMs in symbiosis via complex gene expression regulation mechanisms in the symbiotic continuum and via the mimicry or alteration of phytochemical production in host plants. Alternative biological applications of SMs in modern medicine, agriculture, and industry and their major classes are also discussed. This review recapitulates an introduction to the research background, progress, and prospects of endophytic biology, and discusses problems and substantive challenges that need further study.

Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance

Diterpenoids are the major group of antimicrobial phytoalexins in rice^1,2. Here, we report the discovery of a rice diterpenoid gene cluster on chromosome 7 (DGC7) encoding the entire biosynthetic pathway to 5,10-diketo-casbene, a member of the monocyclic casbene-derived diterpenoids. We revealed that DGC7 is regulated directly by JMJ705 through methyl jasmonate-mediated epigenetic control³. Functional characterization of pathway genes revealed OsCYP71Z21 to encode a casbene C10 oxidase, sought after for the biosynthesis of an array of medicinally important diterpenoids. We further show that DGC7 arose relatively recently in the Oryza genus, and that it was partly formed in Oryza rufipogon and positively selected for in japonica during domestication. Casbene-synthesizing enzymes that are functionally equivalent to OsTPS28 are present in several species of Euphorbiaceae but gene tree analysis shows that these and other casbene-modifying enzymes have evolved independently. As such, combining casbene-modifying enzymes from these different families of plants may prove effective in producing a diverse array of bioactive diterpenoid natural products.

A single bacterial genus maintains root growth in a complex microbiome

Plants grow within a complex web of species that interact with each other and with the plant^1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development^7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.

Getting to the roots of aeroponic indoor farming

Vertical farming is a type of indoor agriculture where plants are cultivated in stacked systems. It forms a rapidly growing sector with new emerging technologies. Indoor farms often use soil-free techniques such as hydroponics and aeroponics. Aeroponics involves the application to roots of a nutrient aerosol, which can lead to greater plant productivity than hydroponic cultivation. Aeroponics is thought to resolve a variety of plant physiological constraints that occur within hydroponic systems. We synthesize existing studies of the physiology and development of crops cultivated under aeroponic conditions and identify key knowledge gaps. We identify future research areas to accelerate the sustainable intensification of vertical farming using aeroponic systems.

Enhancing Salix viminalis L.-mediated phytoremediation of polycyclic aromatic hydrocarbon-contaminated soil by inoculation with Crucibulum laeve (white-rot fungus)

Although plant-white-rot fungi (WRF) remediation is considered efficient in improving polycyclic aromatic hydrocarbon (PAH)-contaminated soil, the prospects for using it remain poorly known. Therefore, we evaluated whether the WRF Crucibulum laeve could improve the phytoremediation of PAH-contaminated soil by Salix viminalis L. A 60-day pot experiment was conducted to investigate the effects of C. laeve inoculation (using two inoculation treatments and a non-inoculated control) on the phytoremediation potential, growth, and antioxidant metabolism of S. viminalis cultivated in PAH-contaminated soil. The S. viminalis-C. laeve association synergistically caused the highest PAH removal rate. Under the S. viminalis-C. laeve treatment, 80% of the biological concentration and translocation factors for all tissues of S. viminalis were > 1, whereas only 20% of these factors were > 1 when S. viminalis was used alone. C. laeve inoculation remarkably enhanced phytoremediation by promoting S. viminalis-based phytoextraction of PAHs from soils. Furthermore, although C. laeve inoculation altered the antioxidant metabolism of S. viminalis by inducing oxidative stress, thereby inhibiting plant growth, the plant's hardiness enabled it to survive and grow normally for 60 days after treatment. Therefore, phytoremediation using S. viminalis inoculated with C. laeve can be considered a feasible approach for the phytoremediation of PAH-contaminated soil.

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins

During colonization of their hosts, pathogens secrete effector proteins to promote disease development through various mechanisms. Increasing evidence shows that the host microbiome plays a crucial role in health, and that hosts actively shape their microbiomes to suppress disease. We proposed that pathogens evolved to manipulate host microbiomes to their advantage in turn. Here, we show that the previously identified virulence effector VdAve1, secreted by the fungal plant pathogen Verticillium dahliae, displays antimicrobial activity and facilitates colonization of tomato and cotton through the manipulation of their microbiomes by suppressing antagonistic bacteria. Moreover, we show that VdAve1, and also the newly identified antimicrobial effector VdAMP2, are exploited for microbiome manipulation in the soil environment, where the fungus resides in absence of a host. In conclusion, we demonstrate that a fungal plant pathogen uses effector proteins to modulate microbiome compositions inside and outside the host, and propose that pathogen effector catalogues represent an untapped resource for new antibiotics.

Formation and diversification of a paradigm biosynthetic gene cluster in plants

Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between species for a paradigm BGC (the thalianol cluster), which has evolved recently in a common ancestor of the Arabidopsis genus. Comparisons at the species level reveal differences in BGC organization and involvement of auxiliary genes, resulting in production of species-specific triterpenes. Within species, the thalianol cluster is primarily fixed, showing a low frequency of deleterious haplotypes. We further identify chromosomal inversion as a molecular mechanism that may shuffle more distant genes into the cluster, so enabling cluster compaction. Antagonistic natural selection pressures are likely involved in shaping the occurrence and maintenance of this BGC. Our work sheds light on the birth, life and death of complex genetic and metabolic traits in plants.

Foliar Application of SiO2 Nanoparticles Alters Soil Metabolite Profiles and Microbial Community Composition in the Pakchoi (Brassica chinensis L.) Rhizosphere Grown in Contaminated Mine Soil

Silica nanoparticles (SiO₂-NPs) are promising in nanoenabled agriculture due to their large surface area and biocompatible properties. Understanding the fundamental interaction between SiO₂-NPs and plants is important for their sustainable use. Here, 3 week-old pakchoi (Brassica chinensis L.) plants were sprayed with SiO₂-NPs every 3 days for 15 days (5 mg of SiO₂-NPs per plant), after which the phenotypes, biochemical properties, and molecular responses of the plants were evaluated. The changes in rhizosphere metabolites were characterized by gas chromatography-mass spectrometry (GC-MS)-based metabolomics, and the response of soil microorganisms to the SiO₂-NPs were characterized by high-throughput bacterial 16S rRNA and fungal internal transcribed spacer (ITS) gene sequencing. The results showed that the SiO₂-NP spray had no adverse effects on photosynthesis of pakchoi plants nor on their biomass. However, the rhizosphere metabolite profile was remarkably altered upon foliar exposure to SiO₂-NPs. Significant increases in the relative abundance of several metabolites, including sugars and sugar alcohols (1.3-9.3-fold), fatty acids (1.5-18.0-fold), and small organic acids (1.5-66.9-fold), and significant decreases in the amino acid levels (60-100%) indicated the altered carbon and nitrogen pool in the rhizosphere. Although the community structure was unchanged, several bacterial (Rhodobacteraceae and Paenibacillus) and fungal (Chaetomium) genera in the rhizosphere involved in carbon and nitrogen cycles were increased. Our results provide novel insights into the environmental effects of SiO₂-NPs and point out that foliar application of NPs can alter the soil metabolite profile.

The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.

Pseudomonas fluorescens accelerates a reverse and long-distance transport of cadmium and sucrose in the hyperaccumulator plant Sedum alfredii

Plant growth-promoting bacteria (PGPB) can promote root uptake and shoot accumulation of cadmium (Cd) in hyperaccumulator plants, but the mechanisms by which PGPB accelerate root-to-shoot transport of Cd is still unknown. A better understanding of these mechanisms is necessary to develop the strategies that can promote the practical phytoextraction of Cd-polluted soils. In this study, we found that Pseudomonas fluorescens accelerates a reversed and a long-distance transport of Cd and sucrose in Sedum alfredii, by examining the xylem and phloem sap and by quantifying the concentrations of Cd and sucrose in shoot and root. The transcriptome sequencing has revealed the up-regulated expressions of starch metabolism and sucrose biosynthesis related genes in the shoots of Cd hyperaccumulator plant S. alfredii that was inoculated with PGPB P. fluorescens. In addition, the genes of sugar, cation and anion transporters were also up-regulated by bacterial treatment, showing a complicated co-expression network with sucrose biosynthesis related genes. The expression levels of Cd transporter genes, such as ZIP1, ZIP2, HMA2, HMA3 and CAX2, were elevated after PGPB inoculation. As a result, the PGPB successfully colonized the root, and promoted the sucrose shoot-to-root transport and Cd root-to-shoot transport in S. alfredii. Since non-photosynthetic root-associated bacteria usually obtain sugars from photosynthetic plants, our results highlight the importance of PGPB-induced changes in hyperaccumlator plants for both the host and the PGPB.

Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be "cultured" by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

Secretion dynamics of soyasaponins in soybean roots and effects to modify the bacterial composition

Soyasaponins are triterpenoid saponins widely found in legume plants. These compounds have drawn considerable attention because they have various activities beneficial for human health, and their biosynthesis has been actively studied. In our previous study, we found that legume plants including soybean secrete soyasaponins from the roots in hydroponic culture throughout the growth period, but the physiological roles of soyasaponins in the rhizosphere and their fate in soil after exudation have remained unknown. This study demonstrates that soyasaponins are secreted from the roots of field-grown soybean, and soyasaponin Bb is the major soyasaponin detected in the rhizosphere. In vitro analysis of the distribution coefficient suggested that soyasaponin Bb can diffuse over longer distances in the soil in comparison with daidzein, which is a typical isoflavone secreted from soybean roots. The degradation rate of soyasaponin Bb in soil was slightly faster than that of daidzein, whereas no soyasaponin Bb degradation was observed in autoclaved soil, suggesting that microbes utilize soyasaponins in the rhizosphere. Bacterial community composition was clearly influenced by soyasaponin Bb, and potential plant growth-promoting rhizobacteria such as Novosphingobium were significantly enriched in both soyasaponin Bb-treated soil and the soybean rhizosphere. These results strongly suggest that soyasaponin Bb plays an important role in the enrichment of certain microbes in the soybean rhizosphere.

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae

Plants produce an array of specialized metabolites with important ecological functions. The mechanisms underpinning the evolution of new biosynthetic pathways are not well-understood. Here, we exploit available genome sequence resources to investigate triterpene biosynthesis across the Brassicaceae. Oxidosqualene cyclases (OSCs) catalyze the first committed step in triterpene biosynthesis. Systematic analysis of 13 sequenced Brassicaceae genomes was performed to identify all OSC genes. The genome neighbourhoods (GNs) around a total of 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions. All-vs-all comparisons of OSC neighbourhoods and phylogenomic analysis were used to investigate the sequence similarity and evolutionary relationships of the numerous candidate triterpene biosynthetic gene clusters (BGCs) observed. Functional analysis of three representative BGCs was carried out and their triterpene pathway products were elucidated. Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene-diversifying enzymes, presumably in response to strong environmental selection pressure. These results illuminate a genomic basis for diversification of plant-specialized metabolism through natural combinatorics of enzyme families, which can be mimicked using synthetic biology to engineer diverse bioactive molecules.

DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

Root-associated soil bacteria can strongly influence plant fitness. DNA methylation is an epigenetic mark important to many fundamental biological processes; however, its roles in plant interactions with beneficial microbes remain elusive. Here, we report that active DNA demethylation in Arabidopsis controls root secretion of myo-inositol and consequently plant growth promotion triggered by Bacillus megaterium strain YC4. Root-secreted myo-inositol is critical for YC4 colonization and preferentially attracts B. megaterium among the examined bacteria species. Active DNA demethylation antagonizes RNA-directed DNA methylation in controlling myo-inositol homeostasis. Importantly, we demonstrate that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and Solanum lycopersicum, thus suggesting a conserved nature of this epigenetic regulatory mechanism.

Microbiome-Mediated Stress Resistance in Plants

Plants are subjected to diverse biotic and abiotic stresses in life. These can induce changes in transcriptomics and metabolomics, resulting in changes to root and leaf exudates and, in turn, altering the plant-associated microbial community. Emerging evidence demonstrates that changes, especially the increased abundance of commensal microbes following stresses, can be beneficial for plant survival and act as a legacy, enhancing offspring fitness. However, outstanding questions remain regarding the microbial role in plant defense, many of which may now be answered utilizing a novel synthetic community approach. In this article, building on our current understanding on stress-induced changes in plant microbiomes, we propose a 'DefenseBiome' concept that informs the design and construction of beneficial microbial synthetic communities for improving fundamental understanding of plant-microbial interactions and the development of plant probiotics.

Phenolic Acids Released in Maize Rhizosphere During Maize-Soybean Intercropping Inhibit Phytophthora Blight of Soybean

Interspecies interactions play a key role in soil-borne disease suppression in intercropping systems. However, there are limited data on the underlying mechanisms of soil-borne Phytophthora disease suppression. Here, a field experiment confirmed the effects of maize and soybean intercropping on Phytophthora blight of soybean caused by Phytophthora sojae. Experimentally, the roots and root exudates of maize were found to attract P. sojae zoospores and inhibit their motility and the germination of cystospores. Furthermore, five phenolic acids (p-coumaric acid, cinnamic acid, p-hydroxybenzoic acid, vanillic acid, and ferulic acid) that were consistently identified in the root exudates and rhizosphere soil of maize were found to interfere with the infection behavior of P. sojae. Among them, cinnamic acid was associated with significant chemotaxis in zoospores, and p-coumaric acid and cinnamic acid showed strong antimicrobial activity against P. sojae. However, in the rhizosphere soil of soybean, only p-hydroxybenzoic acid, low concentrations of vanillic acid, and ferulic acid were identified. Importantly, the coexistence of five phenolic acids in the maize rhizosphere compared with three phenolic acids in the soybean rhizosphere showed strong synergistic antimicrobial activity against the infection behavior of P. sojae. In summary, the types and concentrations of phenolic acids in maize and soybean rhizosphere soils were found to be crucial factors for Phytophthora disease suppression in this intercropping system.

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history

As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species' average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences

Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.

The Plant Microbiome: From Ecology to Reductionism and Beyond

Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.

Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield

In 1840, Justus von Liebig proposed the theory of mineral plant nutrition, through the invention of the Haber–Bosch process, leading to the industrialization of chemical fertilizer (inorganic nitrogen) to feed the human population. Because the excessive use of chemical fertilizer has led to numerous environmental problems, understanding the agroecosystem that contains plants, microbes, and soils is necessary for sustainable agriculture. We revealed the network structure of an agroecosystem established with different management practices and identified that organic nitrogen is a key component contributing to crop yield under the condition of soil solarization, even in the presence of inorganic nitrogen. Our finding provides a potential solution to make crop production more sustainable by utilizing organic nitrogen induced by soil solarization.

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent increase in the pollution of water bodies due to nitrogen leaching from soils. Designing agroecosystems that are environmentally friendly is urgently required. Since agroecosystems are highly complex and consist of entangled webs of interactions between plants, microbes, and soils, identifying critical components in crop production remain elusive. To understand the network structure in agroecosystems engineered by several farming methods, including environmentally friendly soil solarization, we utilized a multiomics approach on a field planted with Brassica rapa. We found that the soil solarization increased plant shoot biomass irrespective of the type of fertilizer applied. Our multiomics and integrated informatics revealed complex interactions in the agroecosystem showing multiple network modules represented by plant traits heterogeneously associated with soil metabolites, minerals, and microbes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as one of the key components to increase crop yield. A germ-free plant in vitro assay and a pot experiment using arable soils confirmed that specific organic nitrogen, namely alanine and choline, directly increased plant biomass by acting as a nitrogen source and a biologically active compound. Thus, our study provides evidence at the agroecosystem level that organic nitrogen plays a key role in plant growth.

Pea (Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India

Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter, and Sphingomonas were significantly higher in the rhizosphere. At the same time, Massilia, Paenibacillus, and Planomicrobium were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes in Arabidopsis thaliana Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.

Higher dimensional metabolomics using stable isotope labeling for identifying the missing specialized metabolism in plants

The exact mechanics of specialized metabolism and its importance throughout plant evolution remain mysterious. Specialized metabolites and their corresponding biosynthetic genes are crucial to understand the reason for the prevalence of certain metabolism. Even though mass spectrometry-based metabolomics has enabled us to acquire data about the structural properties of unknown specialized metabolites as well as known metabolites and their corresponding isomers/analogs, extensive analytical approaches are still required. Herein, we review the most advanced analytical approaches using stable isotope labeling that can be used to identify the unknown specialized metabolites.

Towards a functional understanding of the plant metabolome

Plants are true organic chemists-the chemical diversity of plant metabolomes goes hand in hand with functional diversity. New, often unexpected roles are being reported for both evolutionarily conserved and well-characterised central metabolites such as amino acids, nucleotides, and sugars, and for specialized/secondary metabolites such as carotenoids, glucosinolates, and terpenoids. Our review aims to highlight recent studies reporting novel roles of metabolites and to emphasize the importance of cell-wide identification of metabolite-protein complexes for the comprehensive, functional understanding of the plant metabolome.

Bacterial endophytes from Lycoris radiata promote the accumulation of Amaryllidaceae alkaloids

Lycoris radiata is the major source of Amaryllidaceae alkaloids, having various medicinal activities. However, the low content of these alkaloids in planta limits their pharmaceutical development and utilization. In this study, the ability of bacterial endophytes to enhance the accumulation of five important Amaryllidaceae alkaloids was investigated. A total of 188 bacterial endophytes were isolated from L. radiata and their composition and diversity were analyzed. Fourteen ones were demonstrated to significantly increase the concentration of the alkaloids of interest in different organs, up to 11.1-fold over the control level, with no adverse influence on the plant growth. An additional 3 bacterial endophytes were found to significantly increase the dry weight of L. radiata with no adverse influence on the concentration of the alkaloids in planta, so the total yield of alkaloids in planta was increased up to 2.4-fold over the control level. Considering the plant growth-promoting abilities of these bacterial endophytes, it is speculated that the indole-3-acetic acid and siderophore secreted by them, combined with their nitrogen fixation ability, may contribute to the enhanced plant growth and the increased alkaloid accumulation in L. radiata. To our knowledge, this work is firstly defining the diversity of culturable bacterial endophytes in L. radiata and determining which species promoted the accumulation of Amaryllidaceae alkaloids. It provides several valuable bacterial inoculants that can be further applied to improve alkaloid production in L. radiata and broadens our understanding of the interactions between a medicinal plant and the bacterial endophytes.

Molecular Characterization of Mycobiota and Aspergillus Species from Eupolyphaga sinensis Walker Based on High-Throughput Sequencing of ITS1 and CaM

Eupolyphaga sinensis Walker is a valuable traditional Chinese animal medicine first recorded in Shennong Bencao. Previous research has shown that E. sinensis is easily contaminated by aflatoxins (AFs), which are highly toxic mycotoxins, during harvest, storage, and transport, thereby posing a considerable threat to consumer health. Most often, these AFs are produced by Aspergillus species. In this study, we contrast the traditional culture-based dilution plating method to the high-throughput sequencing (HTS) technology for fungal identification in TCM E. sinensis. Both of the methods used internal transcribed spacer 1 (ITS1) and calmodulin (CaM) sequencing for fungal molecular identification. The new CaM primer we designed in the study is suitable for MiSeq PE300 sequencing used for identification of Aspergillus species in community DNA samples. More fungal species were found in the E. sinensis samples based on HTS than those found using the culture-based dilution plating method. Overall, combining the sequencing power of ITS1 and CaM is an effective method for the detection and monitoring of potential toxigenic Aspergillus species in E. sinensis. In conclusion, HTS can be used to obtain a large amount of sequencing data about fungi contaminating animal medicine, allowing earlier detection of potential toxigenic fungi and ensuring the efficient production and safety of E. sinensis.

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Plant roots nurture a wide variety of microbes via exudation of metabolites, shaping the rhizosphere's microbial community. Despite the importance of plant specialized metabolites in the assemblage and function of microbial communities in the rhizosphere, little is known of how far the effects of these metabolites extend through the soil. We employed a fluid model to simulate the spatiotemporal distribution of daidzein, an isoflavone secreted from soybean roots, and validated using soybeans grown in a rhizobox. We then analysed how daidzein affects bacterial communities using soils artificially treated with daidzein. Simulation of daidzein distribution showed that it was only present within a few millimetres of root surfaces. After 14 days in a rhizobox, daidzein was only present within 2 mm of root surfaces. Soils with different concentrations of daidzein showed different community composition, with reduced α-diversity in daidzein-treated soils. Bacterial communities of daidzein-treated soils were closer to those of the soybean rhizosphere than those of bulk soils. This study highlighted the limited distribution of daidzein within a few millimetres of root surfaces and demonstrated a novel role of daidzein in assembling bacterial communities in the rhizosphere by acting as more of a repellant than an attractant.

Plant abiotic stress response and nutrient use efficiency

Abiotic stresses and soil nutrient limitations are major environmental conditions that reduce plant growth, productivity and quality. Plants have evolved mechanisms to perceive these environmental challenges, transmit the stress signals within cells as well as between cells and tissues, and make appropriate adjustments in their growth and development in order to survive and reproduce. In recent years, significant progress has been made on many fronts of the stress signaling research, particularly in understanding the downstream signaling events that culminate at the activation of stress- and nutrient limitation-responsive genes, cellular ion homeostasis, and growth adjustment. However, the revelation of the early events of stress signaling, particularly the identification of primary stress sensors, still lags behind. In this review, we summarize recent work on the genetic and molecular mechanisms of plant abiotic stress and nutrient limitation sensing and signaling and discuss new directions for future studies.

Metabolome Analysis Identified Okaramines in the Soybean Rhizosphere as a Legacy of Hairy Vetch

Inter-organismal communications below ground, such as plant-microbe interactions in the rhizosphere, affect plant growth. Metabolites are shown to play important roles in biological communication, but there still remain a large number of metabolites in soil to be uncovered. Metabolomics, a technique for the comprehensive analysis of metabolites in samples, may uncover the molecules that intermediate these interactions. We conducted a multivariate analysis using liquid chromatography (LC)-mass spectrometry (MS)-based untargeted metabolomics in several soil samples and also targeted metabolome analysis for the identification of the candidate compounds in soil. We identified okaramine A, B, and C in the rhizosphere soil of hairy vetch. Okaramines are indole alkaloids first identified in soybean pulp (okara) inoculated with Penicillium simplicissimum AK-40 and are insecticidal. Okaramine B was detected in the rhizosphere from an open field growing hairy vetch. Okaramine B was also detected in both bulk and rhizosphere soils of soybean grown following hairy vetch, but not detected in soils of soybean without hairy vetch growth. These results suggested that okaramines might be involved in indirect defense of plants against insects. To our knowledge, this is the first report of okaramines in the natural environment. Untargeted and targeted metabolomics would be useful to uncover the chemistry of the rhizosphere.

Glycoside-specific glycosyltransferases catalyze regio-selective sequential glucosylations for a sesame lignan, sesaminol triglucoside

Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside]. We previously reported that the 2-O-glucosylation of (+)-sesaminol aglycon and β1→6-O-glucosylation of (+)-sesaminol 2-O-β-d-glucoside (SMG) are mediated by UDP-sugar-dependent glucosyltransferases (UGT), UGT71A9 and UGT94D1, respectively. Here we identified a distinct UGT, UGT94AG1, that specifically catalyzes the β1→2-O-glucosylation of SMG and (+)-sesaminol 2-O-β-d-glucosyl-(1→6)-O-β-d-glucoside [termed SDG(β1→6)]. UGT94AG1 was phylogenetically related to glycoside-specific glycosyltransferases (GGTs) and co-ordinately expressed with UGT71A9 and UGT94D1 in the seeds. The role of UGT94AG1 in STG biosynthesis was further confirmed by identification of a STG-deficient sesame mutant that predominantly accumulates SDG(β1→6) due to a destructive insertion in the coding sequence of UGT94AG1. We also identified UGT94AA2 as an alternative UGT potentially involved in sugar-sugar β1→6-O-glucosylation, in addition to UGT94D1, during STG biosynthesis. Yeast two-hybrid assays showed that UGT71A9, UGT94AG1, and UGT94AA2 were found to interact with a membrane-associated P450 enzyme, CYP81Q1 (piperitol/sesamin synthase), suggesting that these UGTs are components of a membrane-bound metabolon for STG biosynthesis. A comparison of kinetic parameters of these UGTs further suggested that the main β-O-glucosylation sequence of STG biosynthesis is β1→2-O-glucosylation of SMG by UGT94AG1 followed by UGT94AA2-mediated β1→6-O-glucosylation. These findings together establish the complete biosynthetic pathway of STG and shed light on the evolvability of regio-selectivity of sequential glucosylations catalyzed by GGTs.

Transcriptome analysis and functional characterization of oxidosqualene cyclases of the arjuna triterpene saponin pathway

Arjuna (Terminalia arjuna) tree has been popular in Indian traditional medicine to treat cardiovascular ailments. The tree accumulates bioactive triterpene glycosides (saponins) and aglycones (sapogenins), in a tissue-preferential manner. Oleanane triterpenes/saponins (derived from β-amyrin) with potential cardioprotective function predominantly accumulate in the bark. However, arjuna triterpene saponin pathway enzymes remain to be identified and biochemically characterized. Here, we employed a combined transcriptomics, metabolomics and biochemical approach to functionally define a suite of oxidosqualene cyclases (OSCs) that catalyzed key reactions towards triterpene scaffold diversification. De novo assembly of 131 millions Illumina NextSeq500 sequencing reads obtained from leaf and stem bark samples led to a total of 156,650 reference transcripts. Four distinct OSCs (TaOSC1-4) with 54-71 % sequence identities were identified and functionally characterized. TaOSC1, TaOSC3 and TaOSC4 were biochemically characterized as β-amyrin synthase, cycloartenol synthase and lupeol synthase, respectively. However, TaOSC2 was found to be a multifunctional OSC producing both α-amyrin and β-amyrin, but showed a preference for α-amyrin product. Both TaOSC1 and TaOSC2 produced β-amyrin, the direct precursor for oleanane triterpene/saponin biosynthesis; but, TaOSC1 transcript expressed preferentially in bark, suggesting a major role of TaOSC1 in the biosynthesis of oleanane triterpenes/saponins in bark.

Recent advances in the role of plant metabolites in shaping the root microbiome

The last decade brought great progress in describing the repertoire of microbes associated with plants and identifying principles of their interactions. Metabolites exuded by plant roots have been considered candidates for the mechanisms by which plants shape their root microbiome. Here, we review the evidence for several plant metabolites affecting plant interaction with microbes belowground. We also discuss the development of new approaches to study the mechanisms of such interaction that will help to elucidate the metabolic networks in the rhizosphere.