Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots

Quantifying Nitrogen Uptake Rates of Maize Roots Using Stable Isotopes

Nitrogen is an essential element for plant growth and development; however, application of nitrogen (N)-based fertilizers comes with a high environmental cost. This includes the energy required for production, volatilization from fields, and runoff or leaching to waterways triggering algal blooms. As such, a key goal in plant breeding programs is to develop varieties that maintain yield while requiring less fertilization. Central to this goal is understanding how roots take up nitrogen and finding traits that represent improvements in the net uptake. Maize, one of the most widely produced crops in the world, has seminal, crown, and brace root types, each under independent developmental control. Recent evidence suggests that these independent developmental patterns may result in different nutrient uptake characteristics. As such, understanding the uptake dynamics of each root type under different environmental conditions is an essential aspect for the selection of new maize varieties. A key method for tracking nitrogen uptake is the use of the 15N stable isotope, which is naturally less abundant than the main 14N isotope. This method involves replacing the 14N in nutrient solutions with 15N, exogenously providing it to the plant tissues (roots in this case), and then measuring the 15N content of the tissues after a fixed amount of time. Here, we provide a brief overview of nitrogen uptake and remobilization in maize, and discuss current techniques for measuring nutrient uptake, with a focus on methods using stable isotopes of nitrogen.

Methods for Measuring Nutrient Uptake in Maize Using Nitrogen Stable Isotopes

Nitrogen is a key nutrient for plant growth and development, and understanding nutrient uptake is central to improving nitrogen use efficiency in crops, including maize. Reducing the need for fertilizer without reducing yield is extremely important, as nitrogen fertilizers come with a high environmental cost, in terms of both emissions from manufacturing and losses to waterways or volatilization off fields. Maize develops multiple different root types, including primary, seminal, crown, and brace roots. Part of improving efficiency in maize involves understanding the differences in nutrient uptake via each distinct root type, but these differences have been largely ignored to date. Here, we describe a protocol that uses stable isotopes for determining nitrogen uptake rates by maize root types. We describe the steps both for intact roots, for which we use rhizoboxes with openable front windows that allow access to the roots without disturbing the rest of the plant, and for field-grown plants, for which intact analysis is not feasible and requires excising the roots. The methods described here can also be modified to measure uptake kinetics and for monitoring nutrient translocation between roots and shoots. Advancing our understanding of root physiology and nutrient dynamics will improve breeding opportunities for efficient nutrient uptake varieties, reducing the need for fertilizer additions.

Soil Microbiota Modulates Root Transcriptome With Divergent Effect on Maize Growth Under Low and High Phosphorus Inputs

Plant growth can be promoted by beneficial microorganisms, or inhibited by detrimental ones. Although the interaction process between a single microbial species and its host has been extensively studied, the growth and transcriptional response of the host to soil microbiota is poorly understood. We planted maize in natural or sterile soil collected from a long-term experimental site with two different soil phosphate (P) regimes. We examined the composition of microbial communities inhabiting root-associated niches in natural soil. In parallel, we determined the biomass, ionomes, and root transcriptome profiling of maize grown in natural or sterile soil. Soil microbiota could promote or inhibit different P starvation-responsive (PSR) genes, as well as induce several defense-related metabolic processes independently of external P levels. Soil microbiota accompanied by long-term application of P fertilizer induced lower intensity of PSR and defense responses, inhibiting maize growth. Under a low P regime, the PSR and defense responses were induced to a higher extent, promoting P absorption and growth. Our findings suggest a soil P-dependent effect of microbiota on maize growth by integrating PSR and defense responses and provide a more refined understanding of the interaction between root growth and soil microbiota.

How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP.

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Recent advances in research on phosphate starvation signaling in plants

Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.

Integrated transcriptomics and metabolomics reveal specific phenolic and flavonoid accumulation in licorice (Glycyrrhiza uralensis Fisch.) induced by arbuscular mycorrhiza symbiosis under drought stress

Arbuscular mycorrhizal (AM) symbiosis can strengthen plant defense against abiotic stress, such as drought, through multiple mechanisms; however, the specialized chemical defenses induced by AM symbiosis are largely unknown. In a pot experiment, licorice (Glycyrrhiza uralensis Fisch.) inoculated with and without arbuscular mycorrhizal fungus Rhizophagus irregularis Schenck & Smith were grown under well-watered or water deficit conditions. Transcriptomic and metabolomic analyses were combined to investigate licorice root specialized metabolism induced by AM symbiosis under drought stress. Results showed that mycorrhizal plants had few dead leaves, less biomass reduction, and less differentially expressed genes and metabolite features in response to drought compared with nonmycorrhizal plants. Transcriptomic and metabolomic data revealed that mycorrhizal roots generally accumulated lignin regardless of the water regime; however, the expression of genes involved in lignin biosynthesis was significantly downregulated by drought stress in mycorrhizal plants. By contrast, AM inoculation significantly decreased specialized metabolites accumulation, including phenolics and flavonoids under well-watered conditions, whereas these decreases turned to be nonsignificant under drought stress. Moreover, these specific phenolics and flavonoids showed significant drought-induced accumulation pattern in mycorrhizal roots. These results highlight that accumulation of specific root phenolics and flavonoids may support the drought tolerance of mycorrhizal plants.

The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status

Phosphate (P_i ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of P_i . The mechanisms to cope with P_i limitation as well as direct uptake of P_i from the substrate via the root epidermis are regulated by a conserved P_i starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain P_i indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for P_i . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant P_i uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Aboveground herbivory does not affect mycorrhiza-dependent nitrogen acquisition from soil but inhibits mycorrhizal network-mediated nitrogen interplant transfer in maize

Arbuscular mycorrhizal fungi (AMF) are considered biofertilizers for sustainable agriculture due to their ability to facilitate plant uptake of important mineral elements, such as nitrogen (N). However, plant mycorrhiza-dependent N uptake and interplant transfer may be highly context-dependent, and whether it is affected by aboveground herbivory remains largely unknown. Here, we used ¹⁵N labeling and tracking to examine the effect of aboveground insect herbivory by Spodoptera frugiperda on mycorrhiza-dependent N uptake in maize (Zea mays L.). To minimize consumption differences and ¹⁵N loss due to insect chewing, insect herbivory was simulated by mechanical wounding and oral secretion of S. frugiperda larvae. Inoculation with Rhizophagus irregularis (Rir) significantly improved maize growth, and N/P uptake. The ¹⁵N labeling experiment showed that maize plants absorbed N from soils via the extraradical mycelium of mycorrhizal fungi and from neighboring plants transferred by common mycorrhizal networks (CMNs). Simulated aboveground leaf herbivory did not affect mycorrhiza-mediated N acquisition from soil. However, CMN-mediated N transfer from neighboring plants was blocked by leaf simulated herbivory. Our findings suggest that aboveground herbivory inhibits CMN-mediated N transfer between plants but does not affect N acquisition from soil solutions via extraradical mycorrhizal mycelium.

Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites

Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles.

Plant Age and Soil Texture Rather Than the Presence of Root Hairs Cause Differences in Maize Resource Allocation and Root Gene Expression in the Field

Understanding the biological roles of root hairs is key to projecting their contributions to plant growth and to assess their relevance for plant breeding. The objective of this study was to assess the importance of root hairs for maize nutrition, carbon allocation and root gene expression in a field experiment. Applying wild type and root hairless rth3 maize grown on loam and sand, we examined the period of growth including 4-leaf, 9-leaf and tassel emergence stages, accompanied with a low precipitation rate. rth3 maize had lower shoot growth and lower total amounts of mineral nutrients than wild type, but the concentrations of mineral elements, root gene expression, or carbon allocation were largely unchanged. For these parameters, growth stage accounted for the main differences, followed by substrate. Substrate-related changes were pronounced during tassel emergence, where the concentrations of several elements in leaves as well as cell wall formation-related root gene expression and C allocation decreased. In conclusion, the presence of root hairs stimulated maize shoot growth and total nutrient uptake, but other parameters were more impacted by growth stage and soil texture. Further research should relate root hair functioning to the observed losses in maize productivity and growth efficiency.

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland

Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.

Functionally-explicit sampling can answer key questions about the specificity of plant-microbe interactions

The rhizosphere is a nexus for plant-microbe interactions and, as a host-structured environment, a location of high activity for distinct microbes and plant species. Although our insights into this habitat have exploded in recent years, we are still limited in our ability to answer key questions about the specificity of these root-microbial relationships. In particular, it can be difficult to confirm or reject microbiome heritability in many plant systems and to pinpoint which microbial taxa are key to plant functioning. Like other host-structured environments, the rhizosphere is structurally, chemically, and biologically complex, driven largely by differences in root anatomy, location, and function. In this Correspondence, we describe a review of 377 "rhizosphere microbiome" research papers and demonstrate how matching a sampling method to the biological question can advance our understanding of host-microbe interactions in a functionally heterogeneous environment. We found that the vast majority of studies (92%) pool all roots from a root system during sampling, ignoring variation in microbial composition between roots of different function and limiting insight into key root-microbial relationships. Furthermore, approaches for removing root-associated microbes are highly variable and non-standard, complicating multi-study analyses. Our understanding of the strength and nature of host-microbe relationships in heterogenous host-microbiome environments can be clarified by targeting sampling to locations of high interaction. While the high complexity of the rhizosphere creates logistical challenges, we suggest that unambiguous language and refined approaches will improve our ability to match methods to research questions and advance our understanding of the specificity of plant-microbial interactions.

Host Plant Selection Imprints Structure and Assembly of Fungal Community along the Soil-Root Continuum

The soil fungal community plays pivotal roles in soil nutrient cycling and plant health and productivity in agricultural ecosystems. However, the differential adaptability of soil fungi to different microenvironments (niches) is a bottleneck limiting their application in agriculture. Hence, the understanding of ecological processes that drive fungal microbiome assembly along the soil-root continuum is fundamental to harnessing the plant-associated microbiome for sustainable agriculture. Here, we investigated the factors that shape fungal community structure and assembly in three compartment niches (the bulk soil, rhizosphere, and rhizoplane) associated with tobacco (Nicotiana tabacum L.), with four soil types tested under controlled greenhouse conditions. Our results demonstrate that fungal community assembly along the soil-root continuum is governed by host plant rather than soil type and that soil chemical properties exert a negligible effect on the fungal community assembly in the rhizoplane. Fungal diversity and network complexity decreased in the order bulk soil > rhizosphere > rhizoplane, with a dramatic decrease in Ascomycota species number and abundance along the soil-root continuum. However, facilitations (positive interactions) were enhanced among fungal taxa in the rhizoplane niche. The rhizoplane supported species specialization with enrichment of some rare species, contributing to assimilative community assembly in the rhizoplane in all soil types. Mortierella and Pyrenochaetopsis were identified as important indicator genera of the soil-root microbiome continuum and good predictors of plant agronomic traits. The findings provide empirical evidence for host plant selection and enrichment/depletion processes of fungal microbiome assembly along the soil-root continuum.

IMPORTANCE Fungal community assembly along the soil-root continuum is shaped largely by the host plant rather than the soil type. This finding facilitates the implementations of fungi-associated biocontrol and growth-promoting for specific plants in agriculture practice, regardless of the impacts from variations in geographical environments. Furthermore, the depletion of complex ecological associations in the fungal community along the soil-root continuum and the enhancement of facilitations among rhizoplane-associated fungal taxa provide empirical evidence for the potential of community simplification as an approach to target the plant rhizoplane for specific applications. The identified indicators Mortierella and Pyrenochaetopsis along the soil-root microbiome continuum are good predictors of tobacco plant agronomic traits, which should be given attention when manipulating the root-associated microbiome.

Plant Foraging Strategies Driven by Distinct Genetic Modules: Cross-Ecosystem Transcriptomics Approach

Plants have evolved diverse strategies for foraging, e.g., mycorrhizae, modification of root system architecture, and secretion of phosphatase. Despite extensive molecular/physiological studies on individual strategies under laboratory/greenhouse conditions, there is little information about how plants orchestrate these strategies in the field. We hypothesized that individual strategies are independently driven by corresponding genetic modules in response to deficiency/unbalance in nutrients. Roots colonized by mycorrhizal fungi, leaves, and root-zone soils were collected from 251 maize plants grown across the United States Corn Belt and Japan, which provided a large gradient of soil characteristics/agricultural practice and thus gene expression for foraging. RNA was extracted from the roots, sequenced, and subjected to gene coexpression network analysis. Nineteen genetic modules were defined and functionally characterized, from which three genetic modules, mycorrhiza formation, phosphate starvation response (PSR), and root development, were selected as those directly involved in foraging. The mycorrhizal module consists of genes responsible for mycorrhiza formation and was upregulated by both phosphorus and nitrogen deficiencies. The PSR module that consists of genes encoding phosphate transporter, secreted acid phosphatase, and enzymes involved in internal-phosphate recycling was regulated independent of the mycorrhizal module and strongly upregulated by phosphorus deficiency relative to nitrogen. The root development module that consists of regulatory genes for root development and cellulose biogenesis was upregulated by phosphorus and nitrogen enrichment. The expression of this module was negatively correlated with that of the mycorrhizal module, suggesting that root development is intrinsically an opposite strategy of mycorrhizae. Our approach provides new insights into understanding plant foraging strategies in complex environments at the molecular level.

Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes

In many soils, the bioavailability of Phosphorus (P), an essential macronutrient is a limiting factor for crop production. Among the mechanisms developed to facilitate the absorption of phosphorus, the plant, as a holobiont, can rely on its rhizospheric microbial partners. Therefore, microbial P-solubilizing inoculants are proposed to improve soil P fertility in agriculture. However, a better understanding of the interactions of the soil-plant-microorganism continuum with the phosphorus cycle is needed to propose efficient inoculants. Before proposing further methods of research, we carried out a critical review of the literature in two parts. First, we focused on the diversity of P-chemical forms. After a review of P forms in soils, we describe multiple factors that shape these forms in soil and their turnover. Second, we provide an analysis of P as a driver of microbial community diversity in soil. Even if no rule enabling to explain the changes in the composition of microbial communities according to phosphorus has been shown, this element has been perfectly targeted as linked to the presence/absence and/or abundance of particular bacterial taxa. In conclusion, we point out the need to link soil phosphorus chemistry with soil microbiology in order to understand the variations in the composition of microbial communities as a function of P bioavailability. This knowledge will make it possible to propose advanced microbial-based inoculant engineering for the improvement of bioavailable P for plants in sustainable agriculture.

Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms

Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.

Maize Field Study Reveals Covaried Microbiota and Metabolic Changes in Roots over Plant Growth

Plant roots are colonized by microorganisms from the surrounding soil that belong to different kingdoms and form a multikingdom microbial community called the root microbiota. Despite their importance for plant growth, the relationship between soil management, the root microbiota, and plant performance remains unknown. Here, we characterize the maize root-associated bacterial, fungal, and oomycetal communities during the vegetative and reproductive growth stages of four maize inbred lines and the pht1;6 phosphate transporter mutant. These plants were grown in two long-term experimental fields under four contrasting soil managements, including phosphate-deficient and -sufficient conditions. We showed that the maize root-associated microbiota is influenced by soil management and changes during host growth stages. We identified stable bacterial and fungal root-associated taxa that persist throughout the host life cycle. These taxa were accompanied by dynamic members that covary with changes in root metabolites. We observed an inverse stable-to-dynamic ratio between root-associated bacterial and fungal communities. We also found a host footprint on the soil biota, characterized by a convergence between soil, rhizosphere, and root bacterial communities during reproductive maize growth. Our study reveals the spatiotemporal dynamics of the maize root-associated microbiota and suggests that the fungal assemblage is less responsive to changes in root metabolites than the bacterial community.

Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale)

Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

Prioritizing host phenotype to understand microbiome heritability in plants

Breeders and evolutionary geneticists have grappled with the complexity of the 'genotype-to-phenotype map' for decades. Now, recent studies highlight the relevance of this concept for understanding heritability of plant microbiomes. Because host phenotype is a more proximate cause of microbiome variation than host genotype, microbiome heritability varies across plant anatomy and development. Fine-scale variation of plant traits within organs suggests that the well-established concept of 'microbiome compartment' should be refined. Additionally, recent work shows that the balance of deterministic processes (including host genetic effects) vs stochastic processes also varies over time and space. Together, these findings suggest that re-centering plant phenotype - both as a predictor and a readout of microbiome function - will accelerate new insights into microbiome heritability.

Responses of Root Endophytes to Phosphorus Availability in Peach Rootstocks With Contrasting Phosphorus-Use Efficiencies

Phosphorus (P) is an important macronutrient for all lives, but it is also a finite resource. Therefore, it is important to understand how to increase the P availability and plant uptake. The endophytes can help host plants to improve P uptake and will be apparently affected by plant genotypes. To investigate the mechanism of root endophytes in promoting P uptake of peach rootstocks, we analyzed the variations of the root endophytic fungal and bacterial communities of peach rootstocks with different P efficiencies under high or low level of P addition. Results showed that Proteobacteria was the dominant bacterial phylum in the roots of all rootstocks under the two levels of P addition. At low P level, the abundance of Actinoplanes in phosphorus-inefficiency root system was apparently higher than that at high P level. Actinoplanes produced important secondary metabolites, improving the stress resistance of plants. Under high P condition, the abundance of Ferrovibrio was higher in Qing Zhou Mi Tao than in Du Shi. Fe oxides considerably reduced the availability of applied P, which partially explained why the P utilization in Qing Zhou Mi Tao is inefficient. Further, Ascomycota was the dominant fungal phylum in the roots of all rootstocks under different levels of P addition. The fungi community of roots varied in different rootstocks at each P level, but was similar for the same rootstock at different P levels, which indicated that genotype had a greater effect than P addition on the fungal community of peach rootstocks.

The microbiomes on the roots of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) exhibit significant differences in structure between root types and along root axes

There is increasing interest in understanding how the microbial communities on roots can be manipulated to improve plant productivity. Root systems are not homogeneous organs but are comprised of different root types of various ages and anatomies that perform different functions. Relatively little is known about how this variation influences the distribution and abundance of microorganisms on roots and in the rhizosphere. Such information is important for understanding how root-microbe interactions might affect root function and prevent diseases. This study tested specific hypotheses related to the spatial variation of bacterial and fungal communities on wheat (Triticum aestivum L.) and rice (Oryza sativa L.) roots grown in contrasting soils. We demonstrate that microbial communities differed significantly between soil type, between host species, between root types, and with position along the root axes. The magnitude of variation between different root types and along individual roots was comparable with the variation detected between different plant species. We discuss the general patterns that emerged in this variation and identify bacterial and fungal taxa that were consistently more abundant on specific regions of the root system. We argue that these patterns should be measured more routinely so that localised root-microbe interactions can be better linked with root system design, plant health and performance.

Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation

Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. Nevertheless, the molecular mechanisms controlling the feedback between root architecture and microbial community structure remain elusive in maize. Here, we demonstrate that transcriptomic gradients along the longitudinal root axis associate with specific shifts in rhizosphere microbial diversity. Moreover, we have established that root-derived flavones predominantly promote the enrichment of bacteria of the taxa Oxalobacteraceae in the rhizosphere, which in turn promote maize growth and nitrogen acquisition. Genetic experiments demonstrate that LRT1-mediated lateral root development coordinates the interactions of the root system with flavone-dependent Oxalobacteraceae under nitrogen deprivation. In summary, these experiments reveal the genetic basis of the reciprocal interactions between root architecture and the composition and diversity of specific microbial taxa in the rhizosphere resulting in improved plant performance. These findings may open new avenues towards the breeding of high-yielding and nutrient-efficient crops by exploiting their interaction with beneficial soil microorganisms.

Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota

Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.

Impacts of Urbanization Undermine Nestedness of the Plant-Arbuscular Mycorrhizal Fungal Network

Cities are prone to ecological problems, yet the impacts of rapid global urbanization on the feedback between above- and belowground subsystems remain largely unknown. We sampled the roots of 8 common herbaceous plants within the Fifth Ring (urban areas) and in Jiufeng National Forest Park (rural areas) in Beijing (China) to assess the impacts of urbanization on the network of plant-arbuscular mycorrhizal (AM) fungal associations. Using Illumina MiSeq sequencing, 81 AM fungal OTUs were identified in 78 herb root samples. The Shannon, Simpson, and Pielou indices of root AM fungi in urban areas were significantly higher than those in rural areas. In this study, a significantly nested mycorrhizal association network was observed in rural areas (NODF = 64.68), whereas a non-nested pattern was observed in urban areas (NODF = 55.50). The competition index C-score (0.0769) of AM fungi in urban areas was slightly lower than that in rural areas (0.1431), and the species specialization (d’) of 8 host plants and fungal dissimilarity among 8 host plants in urban areas were significantly lower than those in rural areas. Convergent associations among hosts may be an important factor influencing this non-nested pattern of the plant-AM fungi network in urban areas. Generalists, rather than specialists, were enhanced during the establishment of mycorrhizal associations in urban areas. Our results suggest that reduced selectivity of host plants, and generalist promotion and specialist reduction of AM fungi during urbanization may contribute to the non-nested network of plant-AM fungal associations.

Response of bacterial and fungal communities to high petroleum pollution in different soils

Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

Host selection shapes crop microbiome assembly and network complexity

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.

Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop

Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant-mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil-plant continuums (rhizosphere, phyllosphere and endosphere) in the maize-wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.

Cooperation between Broussonetia papyrifera and Its Symbiotic Fungal Community To Improve Local Adaptation of the Host

The genetic basis of plant local adaptation has been extensively studied, yet the interplay between local adaptation, plant genetic divergence, and the microbial community remains unclear. Our study used the restriction-site associated DNA sequencing (RAD-seq) approach to explore genetic divergence in Broussonetia papyrifera and used internal transcribed spacers (ITS) to characterize fungal community. RAD-seq results show that B. papyrifera individuals could be divided into three genotypes; this genotyping result was consistent with the classification of climate type at the sample site. Most of the 101 highly differentiated genes were related to stress resistance and the microbiome. Moreover, β-diversity results indicated that genetic divergence had a significant effect on fungal community across all compartments (P < 0.01). At genus and operational taxonomic unit (OTU) level, Mortierella, Hannaella oryzae, OTU81578 (Mortierella), and OTU1665209 (H. oryzae) were found to be the major OTUs that contribute to differences in fungal community. The properties of cooccurrence networks vary greatly among three genotypes. The results of redundancy analysis (RDA) indicated that B. papyrifera-associated fungal community was significantly related to its local adaptability. Our findings suggest that genetic divergence of B. papyrifera is closely related to local adaptation, with significant effects on the associated fungal community, which in turn would enhance host local adaptability. This improves present understanding about the coevolution of microbial communities and the host plant.IMPORTANCE The coevolution of plants with the associated fungal community and its effect on plant adaptability are not clear, especially for native trees. This study focuses on the genetic basis of local adaptation in plants and the effect of genetic divergence of Broussonetia papyrifera on the associated fungal community. We identified genes related to the microbiome that are important for local adaptation of the host. Our results show that genetic divergence in B. papyrifera significantly affects the fungal community, which has a close connection with local adaptation. This helps us to understand the relationship between local adaptation, genetic divergence, and associated fungal communities. This study highlights the effect of plant genetic divergence on associated fungal community for native trees and establishes a close connection between this effect and local adaptability in the host. In addition, these observations lay a foundation for the research of coevolution of plants and their symbiotic microbiome through genome-wide association study (GWAS).

Neighboring plants divergently modulate effects of loss-of-function in maize mycorrhizal phosphate uptake on host physiology and root fungal microbiota

Maize, a main crop worldwide, establishes a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi providing nutrients to the roots from soil volumes which are normally not in reach of the non-colonized root. The mycorrhizal phosphate uptake pathway (MPU) spans from extraradical hyphae to root cortex cells housing fungal arbuscules and promotes the supply of phosphate to the mycorrhizal host in exchange for photosynthetic carbon. This symbiotic association with the mycobiont has been shown to affect plant host nutritional status and growth performance. However, whether and how the MPU affects the root microbial community associated with mycorrhizal hosts in association with neighboring plants, remains to be demonstrated. Here the maize germinal Mu transposon insertion mutant pht1;6, defective in mycorrhiza-specific Pi transporter PHT1;6 gene, and wild type B73 (wt) plants were grown in mono- and mixed culture and examined under greenhouse and field conditions. Disruption of the MPU in pht1;6 resulted in strongly diminished growth performance, in reduced P allocation to photosynthetic source leaves, and in imbalances in leaf elemental composition beyond P. At the microbial community level a loss of MPU activity had a minor effect on the root-associated fungal microbiome which was almost fully restricted to AM fungi of the Glomeromycotina. Moreover, while wt grew better in presence of pht1;6, pht1;6 accumulated little biomass irrespective of whether it was grown in mono- or mixed culture and despite of an enhanced fungal colonization of its roots in co-culture with wt. This suggested that a functional MPU is prerequisite to maintain maize growth and that neighboring plants competed for AM fungal Pi in low P soil. Thus future strategies towards improving yield in maize populations on soils with low inputs of P fertilizer could be realized by enhancing MPU at the individual plant level while leaving the root-associated fungal community largely unaffected.

MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.

Interactions between plants and soil shaping the root microbiome under abiotic stress

Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes - collectively termed the root microbiome - are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

Mechanisms and Impact of Symbiotic Phosphate Acquisition

Phosphorous is important for life but often limiting for plants. The symbiotic pathway of phosphate uptake via arbuscular mycorrhizal fungi (AMF) is evolutionarily ancient and today occurs in natural and agricultural ecosystems alike. Plants capable of this symbiosis can obtain up to all of the phosphate from symbiotic fungi, and this offers potential means to develop crops less dependent on unsustainable P fertilizers. Here, we review the mechanisms and insights gleaned from the fine-tuned signal exchanges that orchestrate the intimate mutualistic symbiosis between plants and AMF. As the currency of trade, nutrients have signaling functions beyond being the nutritional goal of mutualism. We propose that such signaling roles and metabolic reprogramming may represent commitments for a mutualistic symbiosis that act across the stages of symbiosis development.

Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.)

Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H₂PO₄)₂ (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.

Plasticity of Lateral Root Branching in Maize

Extensively branched root systems can efficiently capture soil resources by increasing their absorbing surface in soil. Lateral roots are the roots formed from pericycle cells of other roots that can be of any type. As a consequence, lateral roots provide a higher surface to volume ratio and are important for water and nutrients acquisition. Discoveries from recent studies have started to shed light on how plant root systems respond to environmental changes in order to improve capture of soil resources. In this Mini Review, we will mainly focus on the spatial distribution of lateral roots of maize and their developmental plasticity in response to the availability of water and nutrients.

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China

Few studies have investigated the effect of environment on the root-associated microbiome, especially for woody plants in their native environment. The roots and rhizosphere soils of a native woody species (Broussonetia papyrifera) sampled across four different climate types in China were used to elucidate the influence of environment on the root-associated microbiome. Our results showed that the B. papyrifera root-associated microbiome contained abundant Proteobacteria and Basidiomycota, especially Pseudomonas and Rhizobium. The root-associated microbiomes were found to be significantly different under different climate types except for the bacterial community in the rhizosphere, and the proportion of bacterial operational taxonomic units (OTUs) shared among different climate types was lower than that of fungi. More than 50% of the total variance between microbiomes could be explained by 15 environmental factors, six of which, especially soil concentration phosphate and nitrate, had a significant effect. This study provided a comprehensive understanding of the root-associated microbiome of B. papyrifera and further confirmed the effect of environment on the root-associated microbiome of B. papyrifera under different climate types, with some exceptions in the rhizobacterial community and fungal OTUs. Our findings advanced knowledge of the effect of environment through an exploration of environmental factors and found that the nitrogen and phosphorus content represented the key factors.

Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana

Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS2, we examined the changes in root-associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison with their P-deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.

Metabolic regulation of the maize rhizobiome by benzoxazinoids

The rhizobiome is an important regulator of plant growth and health. Plants shape their rhizobiome communities through production and release of primary and secondary root metabolites. Benzoxazinoids (BXs) are common tryptophan-derived secondary metabolites in grasses that regulate belowground and aboveground biotic interactions. In addition to their biocidal activity, BXs can regulate plant–biotic interactions as semiochemicals or within-plant defence signals. However, the full extent and mechanisms by which BXs shape the root-associated microbiome has remained largely unexplored. Here, we have taken a global approach to examine the regulatory activity of BXs on the maize root metabolome and associated bacterial and fungal communities. Using untargeted mass spectrometry analysis in combination with prokaryotic and fungal amplicon sequencing, we compared the impacts of three genetic mutations in different steps in the BX pathway. We show that BXs regulate global root metabolism and concurrently influence the rhizobiome in a root type-dependent manner. Correlation analysis between BX-controlled root metabolites and bacterial taxa suggested a dominant role for BX-dependent metabolites, particularly flavonoids, in constraining a range of soil microbial taxa, while stimulating methylophilic bacteria. Our study supports a multilateral model by which BXs control root–microbe interactions via a global regulatory function in root secondary metabolism.

Cell Type-Specific Transcriptomics of Lateral Root Formation and Plasticity

Lateral roots are a major determinant of root architecture and are instrumental for the efficient uptake of water and nutrients. Lateral roots consist of multiple cell types each expressing a unique transcriptome at a given developmental stage. Therefore, transcriptome analyses of complete lateral roots provide only average gene expression levels integrated over all cell types. Such analyses have the risk to mask genes, pathways and networks specifically expressed in a particular cell type during lateral root formation. Cell type-specific transcriptomics paves the way for a holistic understanding of the programming and re-programming of cells such as pericycle cells, involved in lateral root initiation. Recent discoveries have advanced the molecular understanding of the intrinsic genetic control of lateral root initiation and elongation. Moreover, the impact of nitrate availability on the transcriptional regulation of lateral root formation in Arabidopsis and cereals has been studied. In this review, we will focus on the systemic dissection of lateral root formation and its interaction with environmental nitrate through cell type-specific transcriptome analyses. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in plants.

Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis

Contents Summary 1031 I. Introduction 1031 II. Interkingdom communication enabling symbiosis 1032 III. Nutritional and regulatory roles for key metabolites in the AM symbiosis 1035 IV. The plant-fungus genotype combination determines the outcome of the symbiosis 1039 V. Perspectives 1039 Acknowledgements 1041 References 1041 SUMMARY: The evolutionary and ecological success of the arbuscular mycorrhizal (AM) symbiosis relies on an efficient and multifactorial communication system for partner recognition, and on a fine-tuned and reciprocal metabolic regulation of each symbiont to reach an optimal functional integration. Besides strigolactones, N-acetylglucosamine-derivatives released by the plant were recently suggested to trigger fungal reprogramming at the pre-contact stage. Remarkably, N-acetylglucosamine-based diffusible molecules also are symbiotic signals produced by AM fungi (AMF) and clues on the mechanisms of their perception by the plant are emerging. AMF genomes and transcriptomes contain a battery of putative effector genes that may have conserved and AMF- or host plant-specific functions. Nutrient exchange is the key feature of AM symbiosis. A mechanism of phosphate transport inside fungal hyphae has been suggested, and first insights into the regulatory mechanisms of root colonization in accordance with nutrient transfer and status were obtained. The recent discovery of the dependency of AMF on fatty acid transfer from the host has offered a convincing explanation for their obligate biotrophism. Novel studies highlighted the importance of plant and fungal genotypes for the outcome of the symbiosis. These findings open new perspectives for fundamental research and application of AMF in agriculture.

Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host-symbiont molecular mechanisms

Brassicaceae plants have lost symbiotic interactions with mutualistic mycorrhizal fungi, but, nonmycorrhizal Brassicaceae associate with diverse taxonomic groups of mutualistic root-endophytic fungi. Distantly related fungal endophytes of Brassicaceae plants transfer phosphorus to the hosts and promote plant growth, thereby suggesting that the beneficial function was independently acquired via convergent evolution. These beneficial interactions appear tightly regulated by the tryptophan-derived secondary metabolite pathway, which specifically developed in Brassicaceae. Importantly, phosphate availability and types of colonizing microbes appear to influence the metabolite pathway. Thus, endophytes of Brassicaceae may have evolved to adapt to the Brassicaceae-specific traits. Future comparative functional analyses among well-defined endophytic fungi and their relatives with distinct life strategies and host plants will help understand the mechanisms that establish and maintain beneficial interactions.

Iron Retention in Root Hemicelluloses Causes Genotypic Variability in the Tolerance to Iron Deficiency-Induced Chlorosis in Maize

Antagonistic interactions of phosphorus (P) hamper iron (Fe) acquisition by plants and can cause Fe deficiency-induced chlorosis. To determine the physiological processes underlying adverse Fe-P interactions, the maize lines B73 and Mo17, which differ in chlorosis susceptibility, were grown hydroponically at different Fe:P ratios. In the presence of P, Mo17 became more chlorotic than B73. The higher sensitivity of Mo17 to Fe deficiency was not related to Fe-P interactions in leaves but to lower Fe translocation to shoots, which coincided with a larger pool of Fe being fixed in the root apoplast of P-supplied Mo17 plants. Fractionating cell wall components from roots showed that most of the cell wall-contained P accumulated in pectin, whereas most of the Fe was bound to root hemicelluloses, revealing that co-precipitation of Fe and P in the apoplast was not responsible for Fe inactivation in roots. A negative correlation between chlorophyll index and hemicellulose-bound Fe in 85 inbred lines of the intermated maize B73 × Mo17 (IBM) population indicated that apoplastic Fe retention contributes to genotypic differences in chlorosis susceptibility of maize grown under low Fe supplies. Our study indicates that Fe retention in the hemicellulose fraction of roots is an important determinant in the tolerance to Fe deficiency-induced chlorosis of graminaceous plant species with low phytosiderophore release, like maize.