An ancestral function of strigolactones as symbiotic rhizosphere signals

Hub metabolites at the root-microbiome interface: unlocking plant drought resilience

Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.

CYP722A1-mediated 16-hydroxylation of carlactonoic acid regulates the floral transition in Arabidopsis

Strigolactones (SLs) are multifunctional plant hormones and rhizosphere signals with diverse structures, roughly classified into two categories: canonical and noncanonical SLs. In Arabidopsis thaliana, SL biosynthesis mutants exhibit increased shoot branching and early flowering, underscoring their roles in developmental regulation. Shoot branching inhibition in Arabidopsis is associated with the methylation of a noncanonical SL, carlactonoic acid (CLA), catalyzed by CLA methyltransferase (CLAMT). Canonical SLs primarily function as rhizosphere signals, with their biosynthesis in dicots mediated by CYP722C enzymes. It is hypothesized that Arabidopsis does not produce canonical SL because of the lack of the CYP722C genes in its genome. Instead, Arabidopsis possesses CYP722A1, a member of the previously uncharacterized CYP722A subfamily, distinct from the CYP722C subfamily. This study demonstrates that Arabidopsis cyp722a1 mutants exhibit an earlier floral transition without excessive shoot branching. Biochemical analysis revealed that CYP722A1 catalyzes the hydroxylation of CLA to produce 16-hydroxy-CLA (16-HO-CLA), which is subsequently methylated by CLAMT to form 16-HO-MeCLA. 16-HO-CLA and 16-HO-MeCLA were detected in the wildtype; however, these compounds were absent in max1-4 mutant, deficient in CLA synthesis, and in cyp722a1 mutant. These findings show CYP722A1-dependent 16-hydroxylation activity of CLA in Arabidopsis. Moreover, they suggest that hydroxylated CLA specifically regulates floral transition, distinct from branching inhibition. Through the identification of CYP722A1 affecting floral transition, which is the distinct role of the CYP722A subfamily, this work provides insights into the structural diversification of SLs for specialized biological functions in plant development.

Transcriptional regulation of development by SMAX1-LIKE proteins - targets of strigolactone and karrikin/KAI2 ligand signaling

SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE (SMXL) proteins comprise a family of plant growth regulators that includes downstream targets of the karrikin (KAR)/KAI2 ligand (KL) and strigolactone (SL) signaling pathways. Following the perception of KAR/KL or SL signals by α/β hydrolases, some types of SMXL proteins are polyubiquitinated by an E3 ubiquitin ligase complex containing the F-box protein MORE AXILLARY GROWTH2 (MAX2)/DWARF3 (D3), and proteolyzed. Because SMXL proteins interact with TOPLESS (TPL) and TPL-related (TPR) transcriptional co-repressors, SMXL degradation initiates changes in gene expression. This simplified model of SMXL regulation and function in plants must now be revised in light of recent discoveries. It has become apparent that SMXL abundance is not regulated by KAR/KL or SL alone, and that some SMXL proteins are not regulated by MAX2/D3 at all. Therefore, SMXL proteins should be considered as signaling hubs that integrate multiple cues. Here we review the current knowledge of how SMXL proteins impose transcriptional regulation of plant development and environmental responses. SMXL proteins can bind DNA directly and interact with transcriptional regulators from several protein families. Multiple mechanisms of downstream genetic control by SMXL proteins have been identified recently that do not involve the recruitment of TPL/TPR, expanding the paradigm of SMXL function.

Omics approaches to investigate pre-symbiotic responses of the mycorrhizal fungus Tulasnella sp. SV6 to the orchid host Serapias vomeracea

Like other plant-microbe symbioses, the establishment of orchid mycorrhiza (ORM) is likely to require specific communication and metabolic adjustments between the two partners. However, while modulation of plant and fungal metabolism has been investigated in fully established mycorrhizal tissues, the molecular changes occurring during the pre-symbiotic stages of the interaction remain largely unexplored in ORM. In this study, we investigated the pre-symbiotic responses of the ORM fungus Tulasnella sp. SV6 to plantlets of the orchid host Serapias vomeracea in a dual in vitro cultivation system. The fungal mycelium was harvested prior to physical contact with the orchid roots and the fungal transcriptome and metabolome were analyzed using RNA-seq and untargeted metabolomics approaches. The results revealed distinct transcriptomic and metabolomic remodelling of the ORM fungus in the presence of orchid plantlets, as compared to the free-living condition. The ORM fungus responds to the presence of the host plant with a significant up-regulation of genes associated with protein synthesis, amino acid and lipid biosynthesis, indicating increased metabolic activity. Metabolomic analysis supported the RNA-seq data, showing increased levels of amino acids and phospholipids, suggesting a remodelling of cell structure and signalling during the pre-symbiotic interaction. In addition, we identified an increase of transcripts of a small secreted protein that may play a role in early symbiotic signalling. Taken together, our results suggest that Tulasnella sp. SV6 may perceive information from orchid roots, leading to a readjustment of its transcriptomic and metabolomic profiles.

Discovery of Arbuscular Mycorrhizae in Mosses of the Pottiaceae Family from the Chaco Serrano (Tucumán, Argentina)

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi that associate with the vast majority of terrestrial plants. Among non-vascular plants, while AMF associations are well-documented in liverworts and hornworts, there is a broad consensus that symbiotic associations do not occur in mosses. Here, we report the presence of AMF in the living material of mosses found in Chaco Serrano (Tucumán, Argentina). We found all characteristic structures of AMF when establishing an intimate connection with two moss species of Pottiaceae (Bryophyta). While Gertrudiella uncinicoma exhibited AMF with both Arum- and Paris-type morphologies, Pleurochaete luteola only displayed an Arum-type morphology. Plant tissue samples were subjected to high-throughput sequencing for AMF identification. We determined that Rhizophagus irregularis was a clear dominant species in both moss species, with Glomus sp. also being present as a less abundant element. In addition, we also reported the presence of vesicles, arbuscules, and spores adhered to the hyphae and the presence of septate endophytes. This finding expands our understanding of the interactions between AMF and non-vascular plants and prompt us to further characterize this interaction by considering the diversity of mycorrhizal associations with concurrent implications for the ecology of mosses and the functionality of the ecosystems.

Functional genomic perspectives on plant terrestrialization

Plant evolutionary research has made leaps in exploring the deep evolutionary roots of embryophytes. A solid phylogenomic framework was established, allowing evolutionary inferences. Comparative genomic approaches revealed that many genes coding for transcription factors, morphogenetic regulators, specialized metabolic enzymes, phytohormone signaling, and more are not innovations of land plants but have a deep streptophyte algal ancestry. Are these just spurious homologs, or do they actualize traits we deem important in embryophytes? Building on streptophyte algae genome data, current endeavors delve into the functional significance of whole cohorts of homologs by leveraging the power of comparative high-throughput approaches. This ushered in the identification of recurrent themes in function, ultimately providing a functional genomic definition for the toolkit of plant terrestrialization.

Symbiotic synergy: How Arbuscular Mycorrhizal Fungi enhance nutrient uptake, stress tolerance, and soil health through molecular mechanisms and hormonal regulation

Arbuscular Mycorrhizal (AM) symbiosis is integral to sustainable agriculture and enhances plant resilience to abiotic and biotic stressors. Through their symbiotic association with plant roots, AM improves nutrient and water uptake, activates antioxidant defenses, and facilitates hormonal regulation, contributing to improved plant health and productivity. Plants release strigolactones, which trigger AM spore germination and hyphal branching, a process regulated by genes, such as D27, CCD7, CCD8, and MAX1. AM recognition by plants is mediated by receptor-like kinases (RLKs) and LysM domains, leading to the formation of arbuscules that optimize nutrient exchange. Hormonal regulation plays a pivotal role in this symbiosis; cytokinins enhance AM colonization, auxins support arbuscule formation, and brassinosteroids regulate root growth. Other hormones, such as salicylic acid, gibberellins, ethylene, jasmonic acid, and abscisic acid, also influence AM colonization and stress responses, further bolstering plant resilience. In addition to plant health, AM enhances soil health by improving microbial diversity, soil structure, nutrient cycling, and carbon sequestration. This symbiosis supports soil pH regulation and pathogen suppression, offering a sustainable alternative to chemical fertilizers and improving soil fertility. To maximize AM 's potential of AM in agriculture, future research should focus on refining inoculation strategies, enhancing compatibility with different crops, and assessing the long-term ecological and economic benefits. Optimizing AM applications is critical for improving agricultural resilience, food security, and sustainable farming practices.

A pair of LysM receptors mediates symbiosis and immunity discrimination in Marchantia

Most land plants form symbioses with microbes to acquire nutrients but also must restrict infection by pathogens. Here, we show that a single pair of lysin-motif-containing receptor-like kinases, MpaLYR and MpaCERK1, mediates both immunity and symbiosis in the liverwort Marchantia paleacea. MpaLYR has a higher affinity for long-chain (CO7) versus short-chain chitin oligomers (CO4). Although both CO7 and CO4 can activate symbiosis-related genes, CO7 triggers stronger immune responses than CO4 in a dosage-dependent manner. CO4 can inhibit CO7-induced strong immune responses, recapitulating the early response to inoculation with the symbiont arbuscular mycorrhizal fungi. We show that phosphate starvation of plants increases their production of strigolactone, which stimulates CO4/CO5 secretion from mycorrhizal fungi, thereby prioritizing symbiosis over immunity. Thus, a single pair of LysM receptors mediates dosage-dependent perception of different chitin oligomers to discern symbiotic and pathogenic microbes in M. paleacea, which may facilitate terrestrialization.

KAI2-dependent signaling controls vegetative reproduction in Marchantia polymorpha through activation of LOG-mediated cytokinin synthesis (14)

Marchantia polymorpha reproduces vegetatively (asexually) by producing propagules known as gemmae within gemma cups and sexually through spores. We previously reported that KARRIKIN INSENSITIVE2 (KAI2)-dependent signaling promotes gemma cup and gemma formation. KAI2A perceives unidentified endogenous ligand(s), tentatively referred to as KAI2 ligands (KL). Perception of KL by KAI2 triggers MORE AXILLARY GROWTH2 (MAX2)-dependent proteolysis of MpSUPPRESSOR of MORE AXILLALRY GROWTH2 1-LIKE (MpSMXL). In this study, we identify genes working downstream of KAI2-dependent signaling in M. polymorpha. We find that KAI2-dependent signaling positively controls the expression of MpLONELY GUY (MpLOG), encoding a cytokinin biosynthesis enzyme. Disruption of the MpLOG function decreases endogenous cytokinin levels and causes defects similar to KAI2-dependent signaling mutants. Moreover, supplying exogenous cytokinins rescues the defects of Mplog and KAI2-dependent signaling mutants, implying that cytokinins work downstream of KAI2-dependent signaling. Activation of MpLOG by KAI2-dependent signaling occurs in a highly cell-type-specific manner, leading to cell-specific induction of GEMMA CUP-ASSOCIATED MYB1 (GCAM1), the master regulator of vegetative reproduction of M. polymorpha. We propose a genetic cascade, starting from KAI2-dependent signaling, that promotes vegetative reproduction through the induction of MpLOG and GCAM1. The interaction between KAI2-dependent signaling and cytokinin in M. polymorpha provides insights into the function and evolution of KAI2-dependent signaling.

Strigolactone insensitivity affects differential shoot and root transcriptome in barley

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development.

The Small Key to the Treasure Chest: Endogenous Plant Peptides Involved in Symbiotic Interactions

Plant growth and development are inextricably connected with rhizosphere organisms. Plants have to balance between strong defenses against pathogens while modulating their immune responses to recruit beneficial organisms such as bacteria and fungi. In recent years, there has been increasing evidence that regulatory peptides are essential in establishing these symbiotic relationships, orchestrating processes that include nutrient acquisition, root architecture modification, and immune modulation. In this review, we provide a comprehensive summary of the peptide families that facilitate beneficial relationships between plants and rhizosphere organisms.

Effects of exogenous SLs on growth and physiological characteristics of flue-cured tobacco seedlings under different degrees of drought stress

Background

Drought stress severely affects global crop yields, reduces water availability, and hinders growth. Strigolactones can alleviate damage caused by various abiotic stresses in plants; however, limited research has been conducted on their ability to enhance drought tolerance in tobacco.

Methods

This study evaluated the drought tolerance of 'Qin Tobacco 96' (drought-tolerant) and 'Yun Tobacco 116' (moisture-sensitive) before and after the application of gibberellic acid lactone at a concentration of 0.2 mg·L⁻¹ under three drought conditions: mild, moderate, and severe. The primary drought tolerance traits were identified from 29 related indicators, including agronomic traits, photosynthetic efficiency, reactive oxygen metabolism, antioxidant enzyme activities, osmotic regulators, and hormone regulation, using affiliation function, principal component analysis, and cluster analysis to categorize the traits. The degree of drought tolerance enhancement in the two tobacco varieties was evaluated under various treatments.

Results

Spraying exogenous strigolactones reduced the adverse effects of drought stress, particularly in the moisture-sensitive Y116 variety. Under drought stress, chlorophyll content and photosynthetic parameters significantly decreased, whereas strigolactone treatment increased both chlorophyll content and photosynthetic efficiency. Strigolactones reduced the accumulation of reactive oxygen species and malondialdehyde content, enhancing the antioxidant capacity of both varieties. Additionally, strigolactones increased the levels of osmoregulatory substances and activated the production of antioxidant enzymes, thereby enhancing drought tolerance. Furthermore, drought stress disrupted the balance of endogenous hormones, decreasing levels of auxin, gibberellic acid, and ribosylzeatin, while increasing abscisic acid levels. Exogenous strigolactones restored this hormonal balance.

Conclusion

Sixteen traits associated with drought tolerance in tobacco were analyzed using principal component analysis, the traits were classified using cluster analysis, and the magnitude of the D-value was determined by calculating the values of the affiliation function and their respective weights. The results indicated that a concentration of 0.2 mg·L⁻¹ of strigolactones enhanced the drought tolerance of tobacco across different levels of drought stress and promoted the growth and development of flue-cured tobacco. However, the interactions between strigolactones and various hormones under drought stress require further investigation to elucidate the underlying molecular mechanisms. The application methods of strigolactones should be optimized.

Evolution of interorganismal strigolactone biosynthesis in seed plants

Strigolactones (SLs) are methylbutenolide molecules derived from β-carotene through an intermediate carlactonoic acid (CLA). Canonical SLs act as signals to microbes and plants, whereas noncanonical SLs are primarily plant hormones. The cytochrome P450 CYP722C catalyzes a critical step, converting CLA to canonical SLs in most angiosperms. Using synthetic biology, we investigated the function of CYP722A, an evolutionary predecessor of CYP722C. CYP722A converts CLA into 16-hydroxy-CLA (16-OH-CLA), a noncanonical SL detected exclusively in the shoots of various flowering plants. 16-OH-CLA application restores control of shoot branching to SL-deficient mutants in Arabidopsis thaliana and is perceived by the SL signaling pathway. We hypothesize that biosynthesis of 16-OH-CLA by CYP722A was a metabolic stepping stone in the evolution of canonical SLs that mediate rhizospheric signaling in many flowering plants.

Conservation of symbiotic signaling since the most recent common ancestor of land plants

Plants have colonized lands 450 million years ago. This terrestrialization was facilitated by developmental and functional innovations. Recent evo-devo approaches have demonstrated that one of these innovations was the mutualistic arbuscular mycorrhizal symbiosis (AMS). The genetic pathways that have been involved in the establishment and functioning of AMS since its evolution remain poorly described. Here, we found that intracellular colonization by AM fungi induces a transcriptional reporter of the common symbiosis pathway, well-described in angiosperms, in the liverwort Marchantia paleacea. Mutants of either of the three main genes of this pathway, SYMRK, CCaMK, and CYCLOPS, disrupt the ability of M. paleacea to associate with AM fungi. Finally, overexpressing gain-of-function CCaMK or CYCLOPS leads to convergent transcriptomic signatures that partially overlap with AMS. Altogether, our data indicate that plants have maintained three genes of the common symbiotic pathway to support symbiotic interactions since their most recent common ancestor.

Effect of exogenous treatment with zaxinone and its mimics on rice root microbiota across different growth stages

Enhancing crops productivity to ensure food security is one of the major challenges encountering agriculture today. A promising solution is the use of biostimulants, which encompass molecules that enhance plant fitness, growth, and productivity. The regulatory metabolite zaxinone and its mimics (MiZax3 and MiZax5) showed promising results in improving the growth and yield of several crops. Here, the impact of their exogenous application on soil and rice root microbiota was investigated. Plants grown in native paddy soil were treated with zaxinone, MiZax3, and MiZax5 and the composition of bacterial and fungal communities in soil, rhizosphere, and endosphere at the tillering and the milky stage was assessed. Furthermore, shoot metabolome profile and nutrient content of the seeds were evaluated. Results show that treatment with zaxinone and its mimics predominantly influenced the root endosphere prokaryotic community, causing a partial depletion of plant-beneficial microbes at the tillering stage, followed by a recovery of the prokaryotic community structure during the milky stage. Our study provides new insights into the role of zaxinone and MiZax in the interplay between rice and its root-associated microbiota and paves the way for their practical application in the field as ecologically friendly biostimulants to enhance crop productivity.

Different roles of the phytohormone gibberellin in the wide-spread arbuscular mycorrhiza and in orchid mycorrhiza

Gibberellin (GA) is a classical plant hormone that regulates many physiological processes, such as plant growth, development, and environmental responses. GA inhibits arbuscular mycorrhizal (AM) symbiosis, the most ancient and widespread type of mycorrhizal symbiosis. Knowledge about mycorrhizal symbioses at the molecular level has been obtained mainly in model plants such as legumes and rice. In contrast, molecular mechanisms in non-model plants are still unclear. Recent studies have revealed the novel roles of GA in mycorrhizal symbioses: its positive effect in Paris-type AM symbiosis in Eustoma grandiflorum and its negative effect on both seed germination and mycorrhizal symbiosis in orchids. This review focuses on the recent data on GA function in AM and orchid mycorrhizal symbioses.

Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest

Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.

Current and future perspectives for enhancing our understanding of the evolution of plant metabolism

The special issue 'The evolution of plant metabolism' has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future. This article is part of the theme issue 'The evolution of plant metabolism'.

Evolution of small molecule-mediated regulation of arbuscular mycorrhiza symbiosis

The arbuscular mycorrhizal (AM) symbiosis formed by most extant land plants with symbiotic fungi evolved 450 Ma. AM promotes plant growth by improving mineral nutrient and water uptake, while the symbiotic fungi obtain carbon in return. A number of plant genes regulating the steps leading to an efficient symbiosis have been identified; however, our understanding of the metabolic processes involved in the symbiosis and how they were wired to symbiosis regulation during plant evolution remains limited. Among them, the exchange of chemical signals, the activation of dedicated biosynthesis pathways and the production of secondary metabolites regulating late stages of the AM symbiosis begin to be well described across several land plant clades. Here, we review our current understanding of these processes and propose future directions to fully grasp the phylogenetic distribution and role played by small molecules during this ancient plant symbiosis. This article is part of the theme issue 'The evolution of plant metabolism'.

Conserved carotenoid pigmentation in reproductive organs of Charophyceae

Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red-probably protectant-pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'.

Cytochromes P450 evolution in the plant terrestrialization context

Plants started to colonize land around 500 million years ago. It meant dealing with new challenges like absence of buoyancy, water and nutrients shortage, increased light radiation, reproduction on land, and interaction with new microorganisms. This obviously required the acquisition of novel functions and metabolic capacities. Cytochrome P450 (CYP) monooxygenases form the largest superfamily of enzymes and are present to catalyse critical and rate-limiting steps in most plant-specific pathways. The different families of CYP enzymes are typically associated with specific functions. CYP family emergence and evolution in the green lineage thus offer the opportunity to obtain a glimpse into the timing of the evolution of the critical functions that were required (or became dispensable) for the plant transition to land. Based on the analysis of currently available genomic data, this review provides an evolutionary history of plant CYPs in the context of plant terrestrialization and describes the associated functions in the different lineages. Without surprise it highlights the relevance of the biosynthesis of antioxidants and UV screens, biopolymers, and critical signalling pathways. It also points to important unsolved questions that would deserve to be answered to improve our understanding of plant adaptation to challenging environments and the management of agricultural traits. This article is part of the theme issue 'The evolution of plant metabolism'.

Characterization of a β-carotene isomerase from the cyanobacterium Cyanobacteria aponinum

Carotenoids are essential components of the photosynthetic apparatus and precursors of plant hormones, such as strigolactones (SLs). SLs are involved in various aspects of plant development and stress-response processes, including the establishment of root and shoot architecture. SL biosynthesis begins with the reversible isomerization of all-trans-carotene into 9-cis-β-carotene, catalysed by DWARF27 β-carotene isomerase (D27). Sequence comparisons have revealed the presence of D27-related proteins in photosynthetic eukaryotes and cyanobacteria lacking SLs. To gain insight into the evolution of SL biosynthesis, we characterized the activity of a cyanobacterial D27 protein (CaD27) from Cyanobacterim aponinum, using carotenoid-accumulating Escherichia coli cells and in vitro enzymatic assays. Our results demonstrate that CaD27 is an all-trans/cis and cis/cis-β-carotene isomerase, with a cis/cis conversion preference. CaD27 catalysed 13-cis/15-cis-, all-trans/9-cis-β-carotene, and neurosporene isomerization. Compared with plant enzymes, it exhibited a lower 9-cis-/all-trans-β-carotene conversion ratio. A comprehensive genome survey revealed the presence of D27 as a single-copy gene in the genomes of 20 out of 200 cyanobacteria species analysed. Phylogenetic and enzymatic analysis of CaD27 indicated that cyanobacterial D27 genes form a single orthologous group, which is considered an ancestral type of those found in photosynthetic eukaryotes. This article is part of the theme issue 'The evolution of plant meta‌bolism'.

Evolution of plant metabolism: the state-of-the-art

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.

Modulation of fungal phosphate homeostasis by the plant hormone strigolactone

Inter-kingdom communication through small molecules is essential to the coexistence of organisms in an ecosystem. In soil communities, the plant root is a nexus of interactions for a remarkable number of fungi and is a source of small-molecule plant hormones that shape fungal compositions. Although hormone signaling pathways are established in plants, how fungi perceive and respond to molecules is unclear because many plant-associated fungi are recalcitrant to experimentation. Here, we develop an approach using the model fungus, Saccharomyces cerevisiae, to elucidate mechanisms of fungal response to plant hormones. Two plant hormones, strigolactone and methyl jasmonate, produce unique transcript profiles in yeast, affecting phosphate and sugar metabolism, respectively. Genetic analysis in combination with structural studies suggests that SLs require the high-affinity transporter Pho84 to modulate phosphate homeostasis. The ability to study small-molecule plant hormones in a tractable genetic system should have utility in understanding fungal-plant interactions.

Strigolactones: A promising tool for nutrient acquisition through arbuscular mycorrhizal fungi symbiosis and abiotic stress tolerance

Strigolactones (SLs) constitute essential phytohormones that control pathogen defense, resilience to phosphate deficiency and abiotic stresses. Furthermore, SLs are released into the soil by roots, especially in conditions in which there is inadequate phosphate or nitrogen available. SLs have the aptitude to stimulate the root parasite plants and symbiotic cooperation with arbuscular mycorrhizal (AM) fungi in rhizosphere. The use of mineral resources, especially phosphorus (P), by host plants is accelerated by AMF, which also improves plant growth and resilience to a series of biotic and abiotic stresses. Thus, these SL treatments that promote rhizobial symbiosis are substitutes for artificial fertilizers and other chemicals, supporting ecologically friendly farming practices. Moreover, SLs have become a fascinating target for abiotic stress adaptation in plants, with an array of uses in sustainable agriculture. In this review, the biological activity has been summarized that SLs as a signaling hormone for AMF symbiosis, nutrient acquisition, and abiotic stress tolerance through interaction with other hormones. Furthermore, the processes behind the alterations in the microbial population caused by SL are clarified, emphasizing the interplay with other signaling mechanisms. This review covers the latest developments in SL studies as well as the properties of SLs on microbial populations, plant hormone transductions, interactions and abiotic stress tolerance.

OsCYP706C2 diverts rice strigolactone biosynthesis to a noncanonical pathway branch

Strigolactones exhibit dual functionality as regulators of plant architecture and signaling molecules in the rhizosphere. The important model crop rice exudes a blend of different strigolactones from its roots. Here, we identify the inaugural noncanonical strigolactone, 4-oxo-methyl carlactonoate (4-oxo-MeCLA), in rice root exudate. Comprehensive, cross-species coexpression analysis allowed us to identify a cytochrome P450, OsCYP706C2, and two methyl transferases as candidate enzymes for this noncanonical rice strigolactone biosynthetic pathway. Heterologous expression in yeast and Nicotiana benthamiana indeed demonstrated the role of these enzymes in the biosynthesis of 4-oxo-MeCLA, which, expectedly, is derived from carlactone as substrate. The oscyp706c2 mutants do not exhibit a tillering phenotype but do have delayed mycorrhizal colonization and altered root phenotype. This work sheds light onto the intricate complexity of strigolactone biosynthesis in rice and delineates its role in symbiosis and development.

Distinguishing the functions of canonical strigolactones as rhizospheric signals

Strigolactones (SLs) act as regulators of plant architecture as well as signals in rhizospheric communications. Reduced availability of minerals, particularly phosphorus, leads to an increase in the formation and release of SLs that enable adaptation of root and shoot architecture to nutrient limitation and, simultaneously, attract arbuscular mycorrhizal fungi (AMF) for establishing beneficial symbiosis. Based on their chemical structure, SLs are designated as either canonical or non-canonical; however, the question of whether the two classes are also distinguished in their biological functions remained largely elusive until recently. In this review we summarize the latest advances in SL biosynthesis and highlight new findings pointing to rhizospheric signaling as the major function of canonical SLs.

The receptor-like kinase ARK controls symbiotic balance across land plants

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.

Δ4-dn-iso-OPDA, a bioactive plant hormone of Marchantia polymorpha

Significant progress has been recently made in our understanding of the evolution of jasmonates biosynthesis and signaling. The bioactive jasmonate activating COI1-JAZ co-receptor differs in bryophytes and vascular plants. Dinor-iso-12-oxo-phytodienoic acid (dn-iso-OPDA) is the bioactive hormone in bryophytes and lycophytes. However, further studies showed that the full activation of hormone signaling in Marchantia polymorpha requires additional unidentified hormones. Δ4-dn-OPDAs were previously identified as novel bioactive jasmonates in M. polymorpha. In this paper, we describe the major bioactive isomer of Δ4-dn-OPDAs as Δ4-dn-iso-OPDA through chemical synthesis, receptor binding assay, and biological activity in M. polymorpha. In addition, we disclosed that Δ4-dn-cis-OPDA is a biosynthetic precursor of Δ4-dn-iso-OPDA. We demonstrated that in planta cis-to-iso conversion of Δ4-dn-cis-OPDA occurs in the biosynthesis of Δ4-dn-iso-OPDA, defining a key biosynthetic step in the chemical evolution of hormone structure. We predict that these findings will facilitate further understanding of the molecular evolution of plant hormone signaling.

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.

MyC Factor Analogue CO5 Promotes the Growth of Lotus japonicus and Enhances Stress Resistance by Activating the Expression of Relevant Genes

The symbiotic relationship between arbuscular mycorrhizal fungi (AMF) and plants is well known for its benefits in enhancing plant growth and stress resistance. Research on whether key components of the AMF colonization process, such as MyC factors, can be directly utilized to activate plant symbiotic pathways and key functional gene expression is still lacking. In this paper, we found that, using a hydroponics system with Lotus japonicus, MyC factor analogue chitin oligomer 5 (CO5) had a more pronounced growth-promoting effect compared to symbiosis with AMF at the optimal concentration. Additionally, CO5 significantly enhanced the resistance of Lotus japonicus to various environmental stresses. The addition of CO5 activated symbiosis, nutrient absorption, and stress-related signaling pathways, like AMF symbiosis, and CO5 also activated a higher and more extensive gene expression profile compared to AMF colonization. Overall, the study demonstrated that the addition of MyC factor analogue CO5, by activating relevant pathways, had a superior effect on promoting plant growth and enhancing stress resistance compared to colonization by AMF. These findings suggest that utilizing MyC factor analogues like CO5 could be a promising alternative to traditional AMF colonization methods in enhancing plant growth and stress tolerance in agriculture.

DWARF27 and CAROTENOID CLEAVAGE DIOXYGENASE 7 genes regulate release, germination and growth of gemma in Marchantia polymorpha

Strigolactones (SLs), a class of carotenoid-derived hormones, play a crucial role in flowering plants by regulating underground communication with symbiotic arbuscular mycorrhizal fungi (AM) and controlling shoot and root architecture. While the functions of core SL genes have been characterized in many plants, their roles in non-tracheophyte plants like liverworts require further investigation. In this study, we employed the model liverwort species Marchantia polymorpha, which lacks detectable SL production and orthologs of key SL biosynthetic genes, including CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8) and MORE AXILLARY GROWTH 1 (MAX1). However, it retains some SL pathway components, including DWARF27 (D27) and CCD7. To help elucidate the function of these remaining components in M. polymorpha, knockout mutants were generated for MpD27-1, MpD27-2 and MpCCD7. Phenotypic comparisons of these mutants with the wild-type control revealed a novel role for these genes in regulating the release of gemmae from the gemma cup and the germination and growth of gemmae in the dark. Mpd27-1, Mpd27-2, and Mpccd7 mutants showed lower transcript abundance of genes involved in photosynthesis, such as EARLY LIGHT INDUCED (ELI), and stress responses such as LATE EMBRYOGENESIS ABUNDANT (LEA) but exhibited higher transcript levels of ETHYLENE RESPONSE FACTORS (ERFs) and SL and carotenoid related genes, such as TERPENE SYNTHASE (TS), CCD7 and LECITHIN-RETINAL ACYL TRANSFERASE (LRAT). Furthermore, the mutants of M. polymorpha in the SL pathway exhibited increased contents of carotenoid. This unveils a previously unrecognized role for MpD27-1, MpD27-2 and MpCCD7 in controlling release, germination, and growth of gemmae in response to varying light conditions. These discoveries enhance our comprehension of the regulatory functions of SL biosynthesis genes in non-flowering plants.

Chemistry of Strigolactones, Key Players in Plant Communication

Today, the use of artificial pesticides is questionable and the adaptation to global warming is a necessity. The promotion of favorable natural interactions in the rhizosphere offers interesting perspectives for changing the type of agriculture. Strigolactones (SLs), the latest class of phytohormones to be discovered, are also chemical mediators in the rhizosphere. We present in this review the diversity of natural SLs, their analogs, mimics, and probes essential for the biological studies of this class of compounds. Their biosynthesis and access by organic synthesis are highlighted especially concerning noncanonical SLs, the more recently discovered natural SLs. Organic synthesis of analogs, stable isotope-labeled standards, mimics, and probes are also reviewed here. In the last part, the knowledge about the SL perception is described as well as the different inhibitors of SL receptors that have been developed.

Evolution of endosymbiosis-mediated nuclear calcium signaling in land plants

The ability of fungi to establish mycorrhizal associations with plants and enhance the acquisition of mineral nutrients stands out as a key feature of terrestrial life. Evidence indicates that arbuscular mycorrhizal (AM) association is a trait present in the common ancestor of land plants,1,2,3,4 suggesting that AM symbiosis was an important adaptation for plants in terrestrial environments.5 The activation of nuclear calcium signaling in roots is essential for AM within flowering plants.6 Given that the earliest land plants lacked roots, whether nuclear calcium signals are required for AM in non-flowering plants is unknown. To address this question, we explored the functional conservation of symbiont-induced nuclear calcium signals between the liverwort Marchantia paleacea and the legume Medicago truncatula. In M. paleacea, AM fungi penetrate the rhizoids and form arbuscules in the thalli.7 Here, we demonstrate that AM germinating spore exudate (GSE) activates nuclear calcium signals in the rhizoids of M. paleacea and that this activation is dependent on the nuclear-localized ion channel DOES NOT MAKE INFECTIONS 1 (MpaDMI1). However, unlike flowering plants, MpaDMI1-mediated calcium signaling is only required for the thalli colonization but not for the AM penetration within rhizoids. We further demonstrate that the mechanism of regulation of DMI1 has diverged between M. paleacea and M. truncatula, including a key amino acid residue essential to sustain DMI1 in an inactive state. Our study reveals functional evolution of nuclear calcium signaling between liverworts and flowering plants and opens new avenues of research into the mechanism of endosymbiosis signaling.

Efficiently recording and processing data from arbuscular mycorrhizal colonization assays using AMScorer and AMReader

Arbuscular mycorrhizal (AM) fungi engage with land plants in a widespread, mutualistic endosymbiosis which provides their hosts with increased access to nutrients and enhanced biotic and abiotic stress resistance. The potential for reducing fertiliser use and improving crop resilience has resulted in rapidly increasing scientific interest. Microscopic quantification of the level of AM colonization is of fundamental importance to this research, however the methods for recording and processing these data are time-consuming and tedious. In order to streamline these processes, we have developed AMScorer, an easy-to-use Excel spreadsheet, which enables the user to record data rapidly during from microscopy-based assays, and instantly performs the subsequent data processing steps. In our hands, AMScorer has more than halved the time required for data collection compared to paper-based methods. Subsequently, we developed AMReader, a user-friendly R package, which enables easy visualization and statistical analyses of data from AMScorer. These tools require only limited skills in Excel and R, and can accelerate research into AM symbioses, help researchers with variable resources to conduct research, and facilitate the storage and sharing of data from AM colonization assays. They are available for download at https://github.com/EJarrattBarnham/AMReader, along with an extensive user manual.

SUPPRESSOR OF MAX2 1-LIKE (SMXL) homologs are MAX2-dependent repressors of Physcomitrium patens growth

SUPPRESSOR OF MAX2 (SMAX)1-LIKE (SMXL) proteins are a plant-specific clade of type I HSP100/Clp-ATPases. SMXL genes are present in virtually all land plant genomes. However, they have mainly been studied in angiosperms. In Arabidopsis (Arabidopsis thaliana), 3 functional SMXL subclades have been identified: SMAX1/SMXL2, SMXL345, and SMXL678. Of these, 2 subclades ensure endogenous phytohormone signal transduction. SMAX1/SMXL2 proteins are involved in KAI2 ligand (KL) signaling, while SMXL678 proteins are involved in strigolactone (SL) signaling. Many questions remain regarding the mode of action of these proteins, as well as their ancestral roles. We addressed these questions by investigating the functions of the 4 SMXL genes in the moss Physcomitrium patens. We demonstrate that PpSMXL proteins are involved in the conserved ancestral MAX2-dependent KL signaling pathway and negatively regulate growth. However, PpSMXL proteins expressed in Arabidopsis cannot replace SMAX1 or SMXL2 function in KL signaling, whereas they can functionally replace SMXL4 and SMXL5 and restore root growth. Therefore, the molecular functions of SMXL proteins are conserved, but their interaction networks are not. Moreover, the PpSMXLC/D clade positively regulates SL signal transduction in P. patens. Overall, our data reveal that SMXL proteins in moss mediate crosstalk between the SL and KL signaling pathways.

Two diversities meet in the rhizosphere: root specialized metabolites and microbiome

Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

SMXL5 attenuates strigolactone signaling in Arabidopsis thaliana by inhibiting SMXL7 degradation

Hormone-activated proteolysis is a recurring theme of plant hormone signaling mechanisms. In strigolactone signaling, the enzyme receptor DWARF14 (D14) and an F-box protein, MORE AXILLARY GROWTH2 (MAX2), mark SUPPRESSOR OF MAX2 1-LIKE (SMXL) family proteins SMXL6, SMXL7, and SMXL8 for rapid degradation. Removal of these transcriptional corepressors initiates downstream growth responses. The homologous proteins SMXL3, SMXL4, and SMXL5, however, are resistant to MAX2-mediated degradation. We discovered that the smxl4 smxl5 mutant has enhanced responses to strigolactone. SMXL5 attenuates strigolactone signaling by interfering with AtD14-SMXL7 interactions. SMXL5 interacts with AtD14 and SMXL7, providing two possible ways to inhibit SMXL7 degradation. SMXL5 function is partially dependent on an ethylene-responsive-element binding-factor-associated amphiphilic repression (EAR) motif, which typically mediates interactions with the TOPLESS family of transcriptional corepressors. However, we found that loss of the EAR motif reduces SMXL5-SMXL7 interactions and the attenuation of strigolactone signaling by SMXL5. We hypothesize that integration of SMXL5 into heteromeric SMXL complexes reduces the susceptibility of SMXL6/7/8 proteins to strigolactone-activated degradation and that the EAR motif promotes the formation or stability of these complexes. This mechanism may provide a way to spatially or temporally fine-tune strigolactone signaling through the regulation of SMXL5 expression or translation.

Unveiling the complexity of strigolactones: exploring structural diversity, biosynthesis pathways, and signaling mechanisms

Strigolactone is the collective name for compounds containing a butenolide as a part of their structure, first discovered as compounds that induce seed germination of root parasitic plants. They were later found to be rhizosphere signaling molecules that induce hyphal branching of arbuscular mycorrhizal fungi, and, finally, they emerged as a class of plant hormones. Strigolactones are found in root exudates, where they display a great variability in their chemical structure. Their structure varies among plant species, and multiple strigolactones can exist in one species. Over 30 strigolactones have been identified, yet the chemical structure of the strigolactone that functions as an endogenous hormone and is found in the above-ground parts of plants remains unknown. We discuss our current knowledge of the synthetic pathways of diverse strigolactones and their regulation, as well as recent progress in identifying strigolactones as plant hormones. Strigolactone is perceived by the DWARF14 (D14), receptor, an α/β hydrolase which originated by gene duplication of KARRIKIN INSENSITIVE 2 (KAI2). D14 and KAI2 signaling pathways are partially overlapping paralogous pathways. Progress in understanding the signaling mechanisms mediated by two α/β hydrolase receptors as well as remaining challenges in the field of strigolactone research are reviewed.

Cracking the enigma: understanding strigolactone signalling in the rhizosphere

The rhizosphere is a complex physical and chemical interface between plants and their underground environment, both biotic and abiotic. Plants exude a large number of chemicals into the rhizosphere in order to manipulate these biotic and abiotic components. Among such chemicals are strigolactones, ancient signalling molecules that in flowering plants act as both internal hormones and external rhizosphere signals. Plants exude strigolactones to communicate with their preferred symbiotic partners and neighbouring plants, but at least some classes of parasitic organisms are able to 'crack' these private messages and eavesdrop on the signals. In this review, we examine the intentional consequences of strigolactone exudation, and also the unintentional consequences caused by eavesdroppers. We examine the molecular mechanisms by which strigolactones act within the rhizosphere, and attempt to understand the enigma of the strigolactone molecular diversity synthesized and exuded into the rhizosphere by plants. We conclude by looking at the prospects of using improved understanding of strigolactones in agricultural contexts.

Perception of butenolides by Bacillus subtilis via the α/β hydrolase RsbQ

The regulation of behavioral and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi.1,2,3 DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous enzyme-receptors that perceive strigolactones and karrikins, respectively, and that require hydrolase activity to effect signal transduction.4,5,6,7 RsbQ, a homolog of D14 and KAI2 from the gram-positive bacterium Bacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB (σB).8,9 However, the molecular function of RsbQ is unknown. Here, we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilized by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signaling function of RsbQ in vivo, with dGR24 being 10-fold more potent. Application of dGR24 to B. subtilis phenocopied loss-of-function rsbQ mutations and led to a significant downregulation of σB-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signaling compounds between plants and bacteria to help shape rhizosphere communities.

At the root of plant symbioses: Untangling the genetic mechanisms behind mutualistic associations

Mutualistic interactions between plants and microorganisms shape the continuous evolution and adaptation of plants such as to the terrestrial environment that was a founding event of subsequent life on land. Such interactions also play a central role in the natural and agricultural ecosystems and are of primary importance for a sustainable future. To boost plant's productivity and resistance to biotic and abiotic stresses, new approaches involving associated symbiotic organisms have recently been explored. New discoveries on mutualistic symbioses evolution and the interaction between partners will be key steps to enhance plant potential.

Whispers in the dark: Signals regulating underground plant-plant interactions

Plants are able to actively detect and respond to the presence in neighboring plants, in order to optimize their physiology to promote survival and reproduction despite the presence of competing organisms. A key but still poorly understood mechanism for neighbor detection is through the perception of root exudates. In this review, we explore recent findings on the role of root exudates in plant-plant interactions, focusing both on general interactions and also the highly specialized example of root parasite-host plant interactions.

Evolution of immunity networks across embryophytes

Land plants (embryophytes), including vascular (tracheophytes) and non-vascular plants (bryophytes), co-evolved with microorganisms since descendants of an algal ancestor colonized terrestrial habitats around 500 million years ago. To cope with microbial pathogen infections, embryophytes evolved a complex immune system for pathogen perception and activation of defenses. With the growing number of sequenced genomes and transcriptome datasets from algae, bryophytes, tracheophytes, and available plant models, comparative analyses are increasing our understanding of the evolution of molecular mechanisms underpinning immune responses in different plant lineages. In this review, recent progress on plant immunity networks is highlighted with emphasis on the identification of key components that shaped immunity against pathogens in bryophytes compared to angiosperms during plant evolution.

Immunobiodiversity: Conserved and specific immunity across land plants and beyond

Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.

Genome evolution in plants and the origins of innovation

Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.

Monoterpene glucosides in Eustoma grandiflorum roots promote hyphal branching in arbuscular mycorrhizal fungi

Host plant-derived strigolactones trigger hyphal branching in arbuscular mycorrhizal (AM) fungi, initiating a symbiotic interaction between land plants and AM fungi. However, our previous studies revealed that gibberellin-treated lisianthus (Eustoma grandiflorum, Gentianaceae) activates rhizospheric hyphal branching in AM fungi using unidentified molecules other than strigolactones. In this study, we analyzed independent transcriptomic data of E. grandiflorum and found that the biosynthesis of gentiopicroside (GPS) and swertiamarin (SWM), characteristic monoterpene glucosides in Gentianaceae, was upregulated in gibberellin-treated E. grandiflorum roots. Moreover, these metabolites considerably promoted hyphal branching in the Glomeraceae AM fungi Rhizophagus irregularis and Rhizophagus clarus. GPS treatment also enhanced R. irregularis colonization of the monocotyledonous crop chive (Allium schoenoprasum). Interestingly, these metabolites did not provoke the germination of the root parasitic plant common broomrape (Orobanche minor). Altogether, our study unveiled the role of GPS and SWM in activating the symbiotic relationship between AM fungi and E. grandiflorum.

CRISPR gene editing to improve crop resistance to parasitic plants

Parasitic plants pose a significant threat to global agriculture, causing substantial crop losses and hampering food security. In recent years, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology has emerged as a promising tool for developing resistance against various plant pathogens. Its application in combating parasitic plants, however, remains largely unexplored. This review aims to summarise current knowledge and research gaps in utilising CRISPR to develop resistance against parasitic plants. First, we outline recent improvements in CRISPR gene editing tools, and what has been used to combat various plant pathogens. To realise the immense potential of CRISPR, a greater understanding of the genetic basis underlying parasitic plant-host interactions is critical to identify suitable target genes for modification. Therefore, we discuss the intricate interactions between parasitic plants and their hosts, highlighting essential genes and molecular mechanisms involved in defence response and multilayer resistance. These include host resistance responses directly repressing parasitic plant germination or growth and indirectly influencing parasitic plant development via manipulating environmental factors. Finally, we evaluate CRISPR-mediated effectiveness and long-term implications for host resistance and crop improvement, including inducible resistance response and tissue-specific activity. In conclusion, this review highlights the challenges and opportunities CRISPR technology provides to combat parasitic plants and provides insights for future research directions to safeguard global agricultural productivity.

Novel Strigolactone Mimics That Modulate Photosynthesis and Biomass Accumulation in Chlorella sorokiniana

In terrestrial plants, strigolactones act as multifunctional endo- and exo-signals. On microalgae, the strigolactones determine akin effects: induce symbiosis formation with fungi and bacteria and enhance photosynthesis efficiency and accumulation of biomass. This work aims to synthesize and identify strigolactone mimics that promote photosynthesis and biomass accumulation in microalgae with biotechnological potential. Novel strigolactone mimics easily accessible in significant amounts were prepared and fully characterized. The first two novel compounds contain 3,5-disubstituted aryloxy moieties connected to the bioactive furan-2-one ring. In the second group of compounds, a benzothiazole ring is connected directly through the cyclic nitrogen atom to the bioactive furan-2-one ring. The novel strigolactone mimics were tested on Chlorella sorokiniana NIVA-CHL 176. All tested strigolactones increased the accumulation of chlorophyll b in microalgae biomass. The SL-F3 mimic, 3-(4-methyl-5-oxo-2,5-dihydrofuran-2-yl)-3H-benzothiazol-2-one (7), proved the most efficient. This compound, applied at a concentration of 10-7 M, determined a significant biomass accumulation, higher by more than 15% compared to untreated control, and improved the quantum yield efficiency of photosystem II. SL-F2 mimic, 5-(3,5-dibromophenoxy)-3-methyl-5H-furan-2-one (4), applied at a concentration of 10-9 M, improved protein production and slightly stimulated biomass accumulation. Potential utilization of the new strigolactone mimics as microalgae biostimulants is discussed.

KAI2 Can Do: Karrikin Receptor Function in Plant Development and Response to Abiotic and Biotic Factors

The α/β hydrolase KARRIKIN INSENSITIVE 2 (KAI2) functions as a receptor for a yet undiscovered phytohormone, provisionally termed KAI2 ligand (KL). In addition, it perceives karrikin, a butenolide compound found in the smoke of burnt plant material. KAI2-mediated signaling is involved in regulating seed germination and in shaping seedling and adult plant morphology, both above and below ground. It also governs responses to various abiotic stimuli and stresses and shapes biotic interactions. KAI2-mediated signaling is being linked to an elaborate cross-talk with other phytohormone pathways such as auxin, gibberellin, abscisic acid, ethylene and salicylic acid signaling, in addition to light and nutrient starvation signaling. Further connections will likely be revealed in the future. This article summarizes recent advances in unraveling the function of KAI2-mediated signaling and its interaction with other signaling pathways.