Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity

Harnessing root-soil-microbiota interactions for drought-resilient cereals

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm

The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.

Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC)

This chapter presents a holistic and quantitative approach to the carbon cycle in plant systems biology. It includes (rapid) phenotyping and monitoring of physiological key interactions of plants with its respective soil and atmospheric environment (soil plant atmospheric continuum-SPAC). The approach aims at qualifying and quantifying key components of this microhabitat as influenced by a single plant or a local group of plants in order to contribute to a flux-based modelling approach. The toolset consists of plant biometry, gas exchange, metabolomics, ionomics, root exudate characterization as well as soil biological and physical-chemical characterization. The results are presented as a basic interaction and input-output model aka conceptual system model employing H. T. Odum-style plots based on empirical data.

Quantifying the impact of dynamic plant-environment interactions on metabolic regulation

A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.

Progressive drought alters the root exudate metabolome and differentially activates metabolic pathways in cotton (Gossypium hirsutum)

Root exudates comprise various primary and secondary metabolites that are responsive to plant stressors, including drought. As increasing drought episodes are predicted with climate change, identifying shifts in the metabolome profile of drought-induced root exudation is necessary to understand the molecular interactions that govern the relationships between plants, microbiomes, and the environment, which will ultimately aid in developing strategies for sustainable agriculture management. This study utilized an aeroponic system to simulate progressive drought and recovery while non-destructively collecting cotton (Gossypium hirsutum) root exudates. The molecular composition of the collected root exudates was characterized by untargeted metabolomics using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) and mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Over 700 unique drought-induced metabolites were identified throughout the water-deficit phase. Potential KEGG pathways and KEGG modules associated with the biosynthesis of flavonoid compounds, plant hormones (abscisic acid and jasmonic acid), and other secondary metabolites were highly induced under severe drought, but not at the wilting point. Additionally, the associated precursors of these metabolites, such as amino acids (phenylalanine and tyrosine), phenylpropanoids, and carotenoids, were also mapped. The potential biochemical transformations were further calculated using the data generated by FT-ICR MS. Under severe drought stress, the highest number of potential biochemical transformations, including methylation, ethyl addition, and oxidation/hydroxylation, were identified, many of which are known reactions in some of the mapped pathways. With the application of FT-ICR MS, we revealed the dynamics of drought-induced secondary metabolites in root exudates in response to drought, providing valuable information for drought-tolerance strategies in cotton.

Genetic variation among elite inbred lines suggests potential to breed for BNI-capacity in maize

Biological nitrification inhibition (BNI) is a plant function where root systems release antibiotic compounds (BNIs) specifically aimed at suppressing nitrifiers to limit soil-nitrate formation in the root zone. Little is known about BNI-activity in maize (Zea mays L.), the most important food, feed, and energy crop. Two categories of BNIs are released from maize roots; hydrophobic and hydrophilic BNIs, that determine BNI-capacity in root systems. Zeanone is a recently discovered hydrophobic compound with BNI-activity, released from maize roots. The objectives of this study were to understand/quantify the relationship between zeanone activity and hydrophobic BNI-capacity. We assessed genetic variability among 250 CIMMYT maize lines (CMLs) characterized for hydrophobic BNI-capacity and zeanone activity, towards developing genetic markers linked to this trait in maize. CMLs with high BNI-capacity and ability to release zeanone from roots were identified. GWAS was performed using 27,085 SNPs (with unique positions on the B73v.4 reference genome, and false discovery rate = 10), and phenotypic information for BNI-capacity and zeanone production from root systems. Eighteen significant markers were identified; three associated with specific BNI-activity (SBNI), four with BNI-activity per plant (BNIPP), another ten were common between SBNI and BNIPP, and one with zeanone release. Further, 30 annotated genes were associated with the significant SNPs; most of these genes are involved in pathways of "biological process", and one (AMT5) in ammonium regulation in maize roots. Although the inbred lines in this study were not developed for BNI-traits, the identification of markers associated with BNI-capacity suggests the possibility of using these genomic tools in marker-assisted selection to improve hydrophobic BNI-capacity in maize.

Benefits of biological nitrification inhibition of Leymus chinensis under alkaline stress: the regulatory function of ammonium-N exceeds its nutritional function

Introduction

The production of root exudates with biological nitrification inhibition (BNI) effects is a strategy adopted by ammonium-N (NH4+-N) tolerant plant species that occur in N-limited environments. Most knowledge on BNI comes from plant species that occur in acidic soils.

Methods

Here, combining field sampling and laboratory culture, we assessed the BNI-capacity of Leymus chinensis, a dominant grass species in alkaline grasslands in eastern Asia, and explored why L. chinensis has BNI ability.

Results and discussion

The results showed that L. chinensis has strong BNI-capacity. At a concentration of 1 mg mL^-1, L. chinensis' root exudates inhibited nitrification in soils influenced by Puccinellia tenuiflora by 72.44%, while DCD only inhibited it by 68.29%. The nitrification potential of the soil of L. chinensis community was only 53% of the P. tenuiflora or 41% of the Suaeda salsa community. We also showed that the supply of NH4+-N driven by L. chinensis' BNI can meet its requirements . In addition, NH4+-N can enhance plant adaptation to alkaline stress by regulating pH, and in turn, the uptake of nitrate-N (NO3--N). We further demonstrated that the regulatory function of NH4+-N is greater than its nutritional function in alkaline environment. The results offer novel insights into how L. chinensis adapts to high pH and nutrient deficiency stress by secreting BNIs, and reveal, for the first time, differences in the functional roles of NH4+-N and NO3--N in growth and adaptation under alkaline conditions in a grass species.

An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition activity

Several plant species have been reported to inhibit nitrification via their root exudates, the so-called biological nitrification inhibition (BNI). Given the potential of BNI-producing plants to sustainably mitigate N losses in agrosystems, identification of BNI activity in existing germplasms is of paramount importance. A hydroponic system was combined with an optimized Nitrosomonas europaea-based bioassay to determine the BNI activity of root exudates. The pipeline allows collecting and processing hundreds of root exudates simultaneously. An additional assay was established to assess the potential bactericide effect of the root exudates. The pipeline was used to unravel the impact of developmental stage, temperature and osmotic stress on the BNI trait in selected wheat genotypes. Biological nitrification inhibition activity appeared consistently higher in wheat at the pretillering stage as compared to the tillering stage. While low-temperatures did not alter BNI activities in root exudates, osmotic stress appeared to change the BNI activity in a genotype-dependent manner. Further analysis of Nitrosomonas culture after pre-exposure to root exudates suggested that BNI activity has no or limited bactericide effects. The present pipeline will be instrumental to further investigating the dynamics of BNI activity and to uncover the diversity of the BNI trait in plant species.

Integrated Microbiome and Metabolomic Analysis Reveal Responses of Rhizosphere Bacterial Communities and Root exudate Composition to Drought and Genotype in Rice (Oryza sativa L.)

BACKGROUND

As climate change events become more frequent, drought is an increasing threat to agricultural production and food security. Crop rhizosphere microbiome and root exudates are critical regulators for drought adaptation, yet our understanding on the rhizosphere bacterial communities and root exudate composition as affected by drought stress is far from complete. In this study, we performed 16S rRNA gene amplicon sequencing and widely targeted metabolomic analysis of rhizosphere soil and root exudates from two contrasting rice genotypes (Nipponbare and Luodao 998) exposed to drought stress.

RESULTS

A reduction in plant phenotypes was observed under drought, and the inhibition was greater for roots than for shoots. Additionally, drought exerted a negligible effect on the alpha diversity of rhizosphere bacterial communities, but obviously altered their composition. In particular, drought led to a significant enrichment of Actinobacteria but a decrease in Firmicutes. We also found that abscisic acid in root exudates was clearly higher under drought, whereas lower jasmonic acid and L-cystine concentrations. As for plant genotypes, variations in plant traits of the drought-tolerant genotype Luodao 998 after drought were smaller than those of Nipponbare. Interestingly, drought triggered an increase in Bacillus, as well as an upregulation of most organic acids and a downregulation of all amino acids in Luodao 998. Notably, both Procrustes analysis and Mantel test demonstrated that rhizosphere microbiome and root exudate metabolomic profiles were highly correlated. A number of differentially abundant genera responded to drought and genotype, including Streptomyces, Bacillus and some members of Actinobacteria, were significantly associated with organic acid and amino acid contents in root exudates. Further soil incubation experiments showed that Streptomyces was regulated by abscisic acid and jasmonic acid under drought.

CONCLUSIONS

Our results reveal that both drought and genotype drive changes in the compositions of rice rhizosphere bacterial communities and root exudates under the greenhouse condition, and that organic acid exudation and suppression of amino acid exudation to select specific rhizosphere bacterial communities may be an important strategy for rice to cope with drought. These findings have important implications for improving the adaptability of rice to drought from the perspective of plant-microbe interactions.

Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems

Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.

Confronting Secondary Metabolites with Water Uptake and Transport in Plants under Abiotic Stress

Phenolic compounds and glucosinolates are secondary plant metabolites that play fundamental roles in plant resistance to abiotic stress. These compounds have been found to increase in stress situations related to plant adaptive capacity. This review assesses the functions of phenolic compounds and glucosinolates in plant interactions involving abiotic stresses such as drought, salinity, high temperature, metals toxicity, and mineral deficiency or excess. Furthermore, their relation with water uptake and transport mediated through aquaporins is reviewed. In this way, the increases of phenolic compounds and glucosinolate synthesis have been related to primary responses to abiotic stress and induction of resistance. Thus, their metabolic pathways, root exudation, and external application are related to internal cell and tissue movement, with a lack of information in this latter aspect.

PANOMICS at the interface of root-soil microbiome and BNI

Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N₂O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.

The root signals in rhizospheric inter-organismal communications

Root exudates play a key role in mediating plant-plant and plant-rhizomicrobiome interactions, including regulating biochemical/physiological aspects of plant-associated microorganisms, to enhance host plant growth and resilience. Root exudates can act as signals to reduce the competition from neighboring plants and recruiting/choreographing a wide range of diverse rhizomicrobiome members to make the host plant a good fit with its immediate environment. Root exudate production is a dynamic and key process, but there is a limited understanding of the metabolites or metabolic pathways involved in the inter-organismal communications facilitated by them. Given the well-known symbiotic relationships between plants and associated rhizomicrobiome members, adding root exudates to microbial isolation media may allow some of the large segments of rhizomicrobiome members that are not currently culturable to be grown in vitro. This will provide new insights into how root signals orchestrate associated microbes, will benefit agricultural production in the face of challenges posed by climate change, and will help to sustainably provide food for a growing global human population.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

(±)-Catechin—A Mass-Spectrometry-Based Exploration Coordination Complex Formation with FeII and FeIII

Catechin is an extensively investigated plant flavan-3-ol with a beneficial impact on human health that is often associated with antioxidant activities and iron coordination complex formation. The aim of this study was to explore these properties with FeII and FeIII using a combination of nanoelectrospray-mass spectrometry, differential pulse voltammetry, site-specific deoxyribose degradation assay, FeII autoxidation assay, and brine shrimp mortality assay. Catechin primarily favored coordination complex formation with Fe ions of the stoichiometry catechin:Fe in the ratio of 1:1 or 2:1. In the detected Fe–catechin coordination complexes, FeII prevailed. Differential pulse voltammetry, the site-specific deoxyribose degradation, and FeII autoxidation assays proved that coordination complex formation affected catechin’s antioxidant effects. In situ formed Fe–catechin coordination complexes showed no toxic activities in the brine shrimp mortality assay. In summary, catechin has properties for the possible treatment of pathological processes associated with ageing and degeneration, such as Alzheimer’s and Parkinson’s diseases.

Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture

Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.

An ex ante life cycle assessment of wheat with high biological nitrification inhibition capacity

It is essential to increase food production to meet the projected population increase while reducing environmental loads. Biological nitrification inhibition (BNI)-enabled wheat genetic stocks are under development through chromosome engineering by transferring chromosomal regions carrying the BNI trait from a wild relative (Leymus racemosus (Lam.) Tzvelev) into elite wheat varieties; field evaluation of these newly developed BNI-wheat varieties has started. Ten years from now, BNI-enabled elite wheat varieties are expected to be deployed in wheat production systems. This study aims to evaluate the impacts of introducing these novel genetic solutions on life cycle greenhouse gas (LC-GHG) emissions, nitrogen (N) fertilizer application rates and N-use efficiency (NUE). Scenarios were developed based on evidence of nitrification inhibition and nitrous oxide (N₂O) emission reduction by BNI crops and by synthetic nitrification inhibitors (SNIs), as both BNI-wheat and SNIs slow the nitrification process. Scenarios including BNI-wheat will inhibit nitrification by 30% by 2030 and 40% by 2050. It was assumed that N fertilizer application rates can potentially be reduced, as N losses through N₂O emissions, leaching and runoff are expected to be lower. The results show that the impacts from BNI-wheat with 40% nitrification inhibition by 2050 are assessed to be positive: a 15.0% reduction in N fertilization, a 15.9% reduction in LC-GHG emissions, and a 16.7% improvement in NUE at the farm level. An increase in ammonia volatilization had little influence on the reduction in LC-GHG emissions. The GHG emissions associated with N fertilizer production and soil N₂O emissions can be reduced between 7.3 and 9.5% across the wheat-harvested area worldwide by BNI-wheat with 30% and 40% nitrification inhibition, respectively. However, the present study recommends further technological developments (e.g. further developments in BNI-wheat and the development of more powerful SNIs) to reduce environmental impacts while improving wheat production to meet the increasing worldwide demand.

Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination

The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.