Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

Chemical and physical characteristics of wheat root mucilage influenced by Serendipita indica symbiosis: a comparison among four cultivars

Although there is evidence to suggest that the endophytic fungus Serendipita indica plays a crucial role in enhancing plant tolerance against biotic/abiotic stressors, less is known about the impacts of this symbiosis association on root mucilage chemical composition and its physical functions. The mucilage of inoculated and non-inoculated seedlings of four wheat cultivars (i.e., Roshan, Ghods, Kavir and Pishtaz) were extracted using an aeroponic method. Total solute concentration (TCm), carbon content (Cmucilage), electrical conductivity (EC), pH, fatty acids, surface tension (σm), and viscosity (ηm) of mucilage were measured. Ghods and Kavir had the highest and lowest root colonization percents, respectively. Saturated fatty acids, including palmitic and stearic acids, were dominant over unsaturated fatty acids in wheat root mucilage. However, their compositions were significantly different among wheat cultivars. S. indica colonization, especially for Ghods, increased the TCm, Cmucilage, and palmitic acid. Moreover, root mucilage of S. indica-inoculated Ghods had lower σm and greater ηm. An increased amount of powerful surfactants like palmitic acid in the mucilage of S. indica inoculated treatments led to lower σm and greater ηm. Such studies provide further support for the idea that plant-released mucilage plays a major role in modifying the physical environment of the rhizosphere. This knowledge toward truly understanding the rhizosphere can be potentially used for improving the rhizosphere soil quality and increasing crop growth and yield.

Regulation of Bacterial Growth and Behavior by Host Plant

Plants are associated with diverse bacteria in nature. Some bacteria are pathogens that decrease plant fitness, and others are beneficial bacteria that promote plant growth and stress resistance. Emerging evidence also suggests that plant-associated commensal bacteria collectively contribute to plant health and are essential for plant survival in nature. Bacteria with different characteristics simultaneously colonize plant tissues. Thus, plants need to accommodate bacteria that provide service to the host plants, but they need to defend against pathogens at the same time. How do plants achieve this? In this review, we summarize how plants use physical barriers, control common goods such as water and nutrients, and produce antibacterial molecules to regulate bacterial growth and behavior. Furthermore, we highlight that plants use specialized metabolites that support or inhibit specific bacteria, thereby selectively recruiting plant-associated bacterial communities and regulating their function. We also raise important questions that need to be addressed to improve our understanding of plant-bacteria interactions.

Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases

Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.

The bryophyte rhizoid-sphere microbiome responds to water deficit

The roots of vascular plants are colonised by a multitude of microbes, which play an important role in plant health and stress resilience. Drought stress in particular is devastating for crop yield and causes major shifts in the rhizosphere microbial communities. However, the microbiome associated to the rhizoids (hereafter termed rhizoid-sphere) of the nonvascular bryophytes remains largely unexplored. Here, we use amplicon sequencing to explore the rhizoid-sphere microbiome of three bryophyte species under drought and well-watered conditions. Comparing rhizoid-sphere microbial communities associated with the two liverworts Marchantia polymorpha and Marchantia paleacea and the moss Physcomitrium patens showed characteristic differences in composition between host species and both conserved and unique changes under drought. At phylum level, these changes were similar to changes in the rhizosphere of angiosperms under drought. Furthermore, we observed strong differences in rhizoid-sphere colonisation between bryophyte species for taxa known for nitrogen fixation and plant growth promotion. Interestingly, M. polymorpha prioritised the growth of belowground organs under osmotic stress, as is the case for angiosperms under drought. Taken together, our results show interesting parallels between bryophytes and angiosperms in the relation with their rhizo(id-)sphere, suggesting evolutionary conservation among land plants in their response to drought stress.

The Biotechnological Potential of Plant Growth-Promoting Rhizobacteria Isolated from Maize (Zea mays L.) Cultivations in the San Martin Region, Peru

Maize (Zea mays L.) is an essential commodity for global food security and the agricultural economy, particularly in regions such as San Martin, Peru. This study investigated the plant growth-promoting characteristics of native rhizobacteria isolated from maize crops in the San Martin region of Peru with the aim of identifying microorganisms with biotechnological potential. Soil and root samples were collected from maize plants in four productive zones in the region: Lamas, El Dorado, Picota, and Bellavista. The potential of twelve bacterial isolates was evaluated through traits, such as biological nitrogen fixation, indole acetic acid (IAA) production, phosphate solubilization, and siderophore production, and a completely randomized design was used for these assays. A completely randomized block design was employed to assess the effects of bacterial strains and nitrogen doses on maize seedlings. The B3, B5, and NSM3 strains, as well as maize seeds of the yellow hard 'Advanta 9139' variety, were used in this experiment. Two of these isolates, B5 and NSM3, exhibited outstanding characteristics as plant growth promoters; these strains were capable of nitrogen fixation, IAA production (35.65 and 26.94 µg mL-1, respectively), phosphate solubilization (233.91 and 193.31 µg mL-1, respectively), and siderophore production (34.05 and 89.19%, respectively). Furthermore, molecular sequencing identified the NSM3 isolate as belonging to Sporosarcina sp. NSM3 OP861656, while the B5 isolate was identified as Peribacillus sp. B5 OP861655. These strains show promising potential for future use as biofertilizers, which could promote more sustainable agricultural practices in the region.

Scripting a new dialogue between diazotrophs and crops

Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N2) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.

Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Precipitation affects soil nitrogen fixation by regulating active diazotrophs and nitrate nitrogen in an alpine grassland of Qinghai-Tibetan Plateau

Soil asymbiotic nitrogen (N) fixation provides a critical N source to support plant growth in alpine grasslands, and precipitation change is expected to lead to shifts in soil asymbiotic N fixation. However, large gaps remain in understanding the response of soil asymbiotic N fixation to precipitation gradients. Here we simulated five precipitation gradients (10 % (0.1P), 50 % (0.5P), 70 % (0.7P), 100 % (1.0P) and 150 % (1.5P) of the natural precipitation) in an alpine grassland of Qinghai-Tibetan Plateau and examined the soil nitrogenase activity and N fixation rate for each gradient. Quantitative PCR and high-throughput sequencing were used to measure the abundance and community composition of the soil nifH DNA (total diazotrophs) and nifH RNA reverse transcription (active diazotrophs) gene. Our results showed that the soil diazotrophic abundance, diversity and nifH gene expression rate peaked under the 0.5P. Soil nitrogenase activity and N fixation rate varied in the range 0.032-0.073 nmol·C2H4·g-1·h-1 and 0.008-0.022 nmol·N2·g-1·h-1 respectively, being highest under the 0.5P. The 50 % precipitation reduction enhanced the gene expression rates of Azospirillum and Halorhodospira which were likely responsible for the high N fixation potential. The 0.5P treatment also possessed a larger and more complex active diazotrophic network than the other treatments, which facilitated the resistance of diazotrophic community to environmental stress and thus maintained a high N fixation potential. The active diazotrophic abundance had the largest positive effect on soil N fixation, while nitrate nitrogen had the largest negative effect. Together, our study suggested that appropriate precipitation reduction can enhance soil N fixation through promoting the abundance of the soil active diazotrophs and decreasing soil nitrate nitrogen, and soil active diazotrophs and nitrate nitrogen should be considered in predicting soil N inputs in the alpine grassland of Qinghai-Tibetan Plateau under precipitation change.

Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'

BACKGROUND

The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.

RESULTS

Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.

CONCLUSIONS

In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

Identification of genetic and environmental factors influencing aerial root traits that support biological nitrogen fixation in sorghum

Plant breeding and genetics play a major role in the adaptation of plants to meet human needs. The current requirement to make agriculture more sustainable can be partly met by a greater reliance on biological nitrogen fixation by symbiotic diazotrophic microorganisms that provide crop plants with ammonium. Select accessions of the cereal crop sorghum (Sorghum bicolor (L.) Moench) form mucilage-producing aerial roots that harbor nitrogen-fixing bacteria. Breeding programs aimed at developing sorghum varieties that support diazotrophs will benefit from a detailed understanding of the genetic and environmental factors contributing to aerial root formation. A genome-wide association study of the sorghum minicore, a collection of 242 landraces, and 30 accessions from the sorghum association panel was conducted in Florida and Wisconsin and under 2 fertilizer treatments to identify loci associated with the number of nodes with aerial roots and aerial root diameter. Sequence variation in genes encoding transcription factors that control phytohormone signaling and root system architecture showed significant associations with these traits. In addition, the location had a significant effect on the phenotypes. Concurrently, we developed F2 populations from crosses between bioenergy sorghums and a landrace that produced extensive aerial roots to evaluate the mode of inheritance of the loci identified by the genome-wide association study. Furthermore, the mucilage collected from aerial roots contained polysaccharides rich in galactose, arabinose, and fucose, whose composition displayed minimal variation among 10 genotypes and 2 fertilizer treatments. These combined results support the development of sorghums with the ability to acquire nitrogen via biological nitrogen fixation.

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (-18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes

The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. This work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.

Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera

IMPORTANCE

Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

Promoting plant resilience against stress by engineering root microenvironment with Streptomyces inoculants

Plant growth is directly influenced by biotic and abiotic stress factors resulting from environmental changes. Plant growth-promoting rhizobacteria (PGPR) have become a crucial area of research aimed at addressing these challenges. However, a knowledge gap exists regarding how PGPR impacts the microenvironments surrounding plant roots. The purpose of this study is to elucidate the effects of two distinct PGPR strains, Streptomyces griseorubiginosus BTU6 (known for its resistance to smut disease) and S. chartreusis WZS021, on sugarcane roots. Additionally, we compare the resultant modifications in the physicochemical characteristics of the rhizospheric soil and root architecture. The results reveal that following the inoculation of S. chartreusis WZS021, there was a significant increase in the active chemicals associated with nitrogen metabolism in sugarcane roots. This enhancement led to a substantial enrichment of nitrogen-cycling microbes like Pseudomonas and Gemmatimona. This finding supports earlier research indicating that S. chartreusis WZS021 enhances sugarcane's capacity to utilize nitrogen effectively. Furthermore, after treatment with S. chartreusis, Aspergillus became the predominant strain among endophytic fungi, resulting in alterations to their community structure that conferred drought resistance. In contrast, the relative abundance of Xanthomonas in the root environment decreased following inoculation with S. griseorubiginosus. Instead, Gemmatimona became more prevalent, creating a favorable environment for plants to bolster their resistance against disease. Notably, inoculations with S. chartreusis WZS021 and S. griseorubiginosus BTU6 led to substantial changes in the chemical composition, enzymatic activity, and microbial community composition in the soil surrounding sugarcane roots. However, there were distinct differences in the specific alterations induced by each strain. These findings enhance plant resilience to stress by shedding light on PGPR-mediated modifications in root microenvironments.

Harnessing biological nitrogen fixation in plant leaves

The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.

Potential of root acid phosphatase activity to reduce phosphorus fertilization in maize cultivated in Brazil

It is urgent to mitigate the environmental impacts resulting from agriculture, especially in highly biodiverse and threatened areas, as the Brazilian Cerrado. We aim to investigate whether root acid phosphatase activity is alternative plant strategies for nutrient acquisition in maize genotypes cultivated under fertilized and unfertilized conditions in Brazil, potentially contributing to reducing the use of phosphate fertilizers needed for production. Three experiments were performed: the first was conducted in a glasshouse, with 17 experimental maize inbred lines and two phosphorus (P) treatments; the second in the field, with three maize inbred lines and two treatments, one without fertilization and another with NPK fertilization; and the third was also carried out in the field, with 13 commercial hybrids, grown either under NK or under NPK treatment. Plant variables were measured and tested for the response to fertilization, differences amongst genotypes and response to root acid phosphatase activity. The activity of root acid phosphatase was modulated by the availability of P and nitrogen (N) in the soil and promoted grain filling of commercial hybrids in soils with low P availability. These results demonstrate that it is possible to select genotypes that are more adapted to low soil P availability aiming at organic production, or to use genotypes that have high phosphatase activity under P fertilization to reduce the amount of added P needed for maize production in Brazil.

Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria

Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.

Running the numbers on plant synthetic biology solutions to global problems

Synthetic biology and metabolic engineering promise to deliver sustainable solutions to global problems such as phasing out fossil fuels and replacing industrial nitrogen fixation. While this promise is real, scale matters, and so do knock-on effects of implementing solutions. Both scale and knock-on effects can be estimated by 'Fermi calculations' (aka 'back-of-envelope calculations') that use uncontroversial input data plus simple arithmetic to reach rough but reliable conclusions. Here, we illustrate how this is done and how informative it can be using two cases: oilcane (sugarcane engineered to accumulate triglycerides instead of sugar) as a source of bio-jet fuel, and nitrogen fixation by bacteria in mucilage secreted by maize aerial roots. We estimate that oilcane could meet no more than about 1% of today's U.S. jet fuel demand if grown on all current U.S. sugarcane land and that, if cane land were expanded to meet two-thirds of this demand, the fertilizer and refinery requirements would create a large carbon footprint. Conversely, we estimate that nitrogen fixation in aerial-root mucilage could replace up to 10% of the fertilizer nitrogen applied to U.S. maize, that 2% of plant carbon income used for growth would suffice to fuel the fixation, and that this extra carbon consumption would likely reduce grain yield only slightly.

Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction

Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

Transcriptional Profiling and Transposon Mutagenesis Study of the Endophyte Pantoea eucalypti FBS135 Adapting to Nitrogen Starvation

The research on plant endophytes has been drawing a lot of attention in recent years. Pantoea belongs to a group of endophytes with plant growth-promoting activity and has been widely used in agricultural fields. In our earlier studies, Pantoea eucalypti FBS135 was isolated from healthy-growing Pinus massoniana and was able to promote pine growth. P. eucalypti FBS135 can grow under extremely low nitrogen conditions. To understand the mechanism of the low-nitrogen tolerance of this bacterium, the transcriptome of FBS135 in the absence of nitrogen was examined in this study. We found that FBS135 actively regulates its gene expression in response to nitrogen deficiency. Nearly half of the number (4475) of genes in FBS135 were differentially expressed under this condition, mostly downregulated, while it significantly upregulated many transportation-associated genes and some nitrogen metabolism-related genes. In the downregulated genes, the ribosome pathway-related ones were significantly enriched. Meanwhile, we constructed a Tn5 transposon library of FBS135, from which four genes involved in low-nitrogen tolerance were screened out, including the gene for the host-specific protein J, RNA polymerase σ factor RpoS, phosphoribosamine-glycine ligase, and serine acetyltransferase. Functional analysis of the genes revealed their potential roles in the adaptation to nitrogen limitation. The results obtained in this work shed light on the mechanism of endophytes represented by P. eucalypti FBS135, at the overall transcriptional level, to an environmentally limited nitrogen supply and provided a basis for further investigation on this topic.

Engineering the Crop Microbiota Through Host Genetics

The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.

How could actinobacteria augment the growth and redox homeostasis in barley plants grown in TiO2NPs-contaminated soils? A growth and biochemical study

The increases in titanium dioxide nanoparticles (TiO2-NPs) released into the environment have raised concerns about their toxicity. However, their phytotoxic impact on plants is not well studied. Therefore, this study aimed at a deeper understanding of the TiO2-NPs phytotoxic impact on barley (Hordeum vulgare) growth and stress defense. We also hypothesized that soil inoculation with bioactive Rhodospirillum sp. JY3 strain can be applied as a biological fertilizer to alleviate TiO2-NPs phytotoxicity. At TiO2-NPs phytotoxicity level, photosynthesis was significantly retarded (∼50% reduction) in TiO2-NPs treated-barley plants which accordingly affect the biomass of barley plants. This retardation was accompanied by a remarkable induction of oxidative damage (H2O2, lipid peroxidation) with a concomitant reduction in the antioxidant defense metabolism. At a glance, Rhodospirillum sp. JY3 ameliorated the reduction in growth by enhancing the photosynthetic efficiency in contaminated barley plants. Moreover, Rhodospirillum sp. JY3 inoculation reduced the oxidative damage induced by TiO2-NPs via quenching H2O2 production and lipid peroxidation. Regarding the antioxidant defense arsenal, Rhodospirillum sp. JY3 enhanced both enzymatic (e.g. peroxidase (POX), catalase (CAT), superoxide dismutase (SOD), …. etc.) and non-enzymatic (glutathione (GSH), ascorbate (ASC), polyphenols, flavonoids, tocopherols) antioxidants in shoots and to a greater extent roots of barley plants. Moreover, the inoculation significantly enhanced the heavy metal-detoxifying metabolites (eg. phytochelatins, glutaredoxin, thioredoxin, peroxiredoxin) as well as metal-detoxifying enzymes in barley shoots and more apparently in roots of TiO2-NPs stressed plants. Furthermore, there was an organ-specific response to TiO2-NPs and Rhodospirillum sp. JY3. To this end, this study shed light, for the first time, on the molecular bases underlie TiO2-NPs stress mitigating impact of Rhodospirillum sp. JY3 and it introduced Rhodospirillum sp. JY3 as a promising eco-friendly tool in managing environmental risks to maintain agricultural sustainability.

Differences in mucilage properties and stomatal sensitivity of locally adapted Zea mays in relation with precipitation seasonality and vapour pressure deficit regime of their native environment

With ongoing climate change and the increase in extreme weather events, especially droughts, the challenge of maintaining food security is becoming ever greater. Locally adapted landraces of crops represent a valuable source of adaptation to stressful environments. In the light of future droughts-both by altered soil water supply and increasing atmospheric water demand (vapor pressure deficit [VPD])-plants need to improve their water efficiency. To do so, plants can enhance their access to soil water by improving rhizosphere hydraulic conductivity via the exudation of mucilage. Furthermore, plants can reduce transpirational water loss via stomatal regulation. Although the role of mucilage and stomata regulation on plant water management have been extensively studied, little is known about a possible coordination between root mucilage properties and stomatal sensitivity as well as abiotic drivers shaping the development of drought resistant trait suits within landraces. Mucilage properties and stomatal sensitivity of eight Mexican landraces of Zea mays in contrast with one inbred line were first quantified under controlled conditions and second related to water demand and supply at their respective site of origin. Mucilage physical properties-namely, viscosity, contact angle, and surface tension-differed between the investigated maize varieties. We found strong influences of precipitation seasonality, thus plant water availability, on mucilage production (R 2 = .88, p < .01) and mucilage viscosity (R 2 = .93, p < .01). Further, stomatal sensitivity to increased atmospheric water demand was related to mucilage viscosity and contact angle, both of which are crucial in determining mucilage's water repellent, thus maladaptive, behavior upon soil drying. The identification of landraces with pre-adapted suitable trait sets with regard to drought resistance is of utmost importance, for example, trait combinations such as exhibited in one of the here investigated landraces. Our results suggest a strong environmental selective force of seasonality in plant water availability on mucilage properties as well as regulatory stomatal effects to avoid mucilage's maladaptive potential upon drying and likely delay critical levels of hydraulic dysfunction. By this, landraces from highly seasonal climates may exhibit beneficial mucilage and stomatal traits to prolong plant functioning under edaphic drought. These findings may help breeders to efficiently screen for local landraces with pre-adaptations to drought to ultimately increase crop yield resistance under future climatic variability.

Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria

Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.

Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan

The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).

Mucilage secretion by aerial roots in sorghum (Sorghum bicolor): sugar profile, genetic diversity, GWAS and transcriptomic analysis

Aerial root mucilage can enhance nitrogen fixation by providing sugar and low oxygen environment to the rhizosphere microbiome in Sierra Mixe maize. Aerial root mucilage has long been documented in sorghum (Sorghum bicolor), but little is known about the biological significance, genotypic variation, and genetic regulation of this biological process. In the present study, we found that a large variation of mucilage secretion capacity existed in a sorghum panel consisting of 146 accessions. Mucilage secretion occurred primarily in young aerial roots under adequately humid conditions but decreased or stopped in mature long aerial roots or under dry conditions. The main components of the mucilage-soluble were glucose and fructose, as revealed by sugar profiling of cultivated and wild sorghum. The mucilage secretion capacity of landrace grain sorghum was significantly higher than that of wild sorghum. Transcriptome analysis revealed that 1844 genes were upregulated and 2617 genes were downregulated in mucilage secreting roots. Amongst these 4461 differentially expressed genes, 82 genes belonged to glycosyltransferases and glucuronidation pathways. Sobic.010G120200, encoding a UDP-glycosyltransferase, was identified by both GWAS and transcriptome analysis as a candidate gene, which may be involved in the regulation of mucilage secretion in sorghum through a negative regulatory mechanism.

Diversity and regulation of symbiotic nitrogen fixation in plants

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

Promotion of the growth and yield of Zea mays by synthetic microbial communities from Jala maize

Plant growth-promoting bacteria (PGPB) are a source of nutrient supply, stimulate plant growth, and even act in the biocontrol of phytopathogens. However, these phenotypic traits have rarely been explored in culturable bacteria from native maize landraces. In this study, synthetic microbial communities (SynCom) were assembled with a set of PGPB isolated from the Jala maize landrace, some of them with additional abilities for the biocontrol of phytopathogenic fungi and the stimulation of plant-induced systemic resistance (ISR). Three SynCom were designed considering the phenotypic traits of bacterial strains, including Achromobacter xylosoxidans Z2K8, Burkholderia sp. Z1AL11, Klebsiella variicola R3J3HD7, Kosakonia pseudosacchari Z2WD1, Pantoea ananatis E2HD8, Pantoea sp. E2AD2, Phytobacter diazotrophicus Z2WL1, Pseudomonas protegens E1BL2, and P. protegens E2HL9. Plant growth promotion in gnotobiotic and greenhouse seedlings assays was performed with Conejo landrace; meanwhile, open field tests were carried out on hybrid CPL9105W maize. In all experimental models, a significant promotion of plant growth was observed. In gnotobiotic assays, the roots and shoot length of the maize seedlings increased 4.2 and 3.0 times, respectively, compared to the untreated control. Similarly, the sizes and weights of the roots and shoots of the plants increased significantly in the greenhouse assays. In the open field assay performed with hybrid CPL9105W maize, the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated with SynCom 3. In addition, the incidence of rust fungal infections decreased significantly from 12.5% in the control to 8% in the treatment with SynCom 3. All SynCom designs promoted the growth of maize in all assays. However, SynCom 3 formulated with A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola R3J3HD7, P. ananatis E2HD8, P. diazotrophicus Z2WL1, and P. protegens E1BL2 displayed the best results for promoting plant growth, their yield, and the inhibition of fungal rust. This study demonstrated the biotechnological eco-friendly plant growth-promoting potential of SynCom assemblies with culturable bacteria from native maize landraces for more sustainable and economic agriculture.

Plant-Environment Response Pathway Regulation Uncovered by Investigating Non-Typical Legume Symbiosis and Nodulation

Nitrogen is an essential element needed for plants to survive, and legumes are well known to recruit rhizobia to fix atmospheric nitrogen. In this widely studied symbiosis, legumes develop specific structures on the roots to host specific symbionts. This review explores alternate nodule structures and their functions outside of the more widely studied legume-rhizobial symbiosis, as well as discussing other unusual aspects of nodulation. This includes actinorhizal-Frankia, cycad-cyanobacteria, and the non-legume Parasponia andersonii-rhizobia symbioses. Nodules are also not restricted to the roots, either, with examples found within stems and leaves. Recent research has shown that legume-rhizobia nodulation brings a great many other benefits, some direct and some indirect. Rhizobial symbiosis can lead to modifications in other pathways, including the priming of defence responses, and to modulated or enhanced resistance to biotic and abiotic stress. With so many avenues to explore, this review discusses recent discoveries and highlights future directions in the study of nodulation.

Effects of Rhizosphere Microorganisms on the Uptake and Translocation of Organic Compounds in Maize Seedlings

The plant root is a key pathway to absorb insecticides from soil and is colonized by beneficial and pathogenic microbial communities. Our study demonstrated that colonizing roots by nitrogen-fixing bacterium Pseudomonas stutzeri and pathogenic Fusarium graminearum and Pythium ultimum increased the uptake of insecticides into maize roots from soil. An alteration in the permeability of root cells contributed to this increased uptake. For the subsequent root-to-shoot translocation, the relationship between translocation and log P of the compound satisfied a Gaussian distribution. Relatively beneficial P. stutzeri can promote maize seedling growth and increase translocation, whereas Fusarium and Pythium pathogens can retard the seedling growth and reduce the translocation. Furthermore, the relationship between the concentration difference (difference of an insecticide from inoculation treatment to control) and log P also showed a Gaussian distribution. The maximum concentration difference from the Gaussian equation can be applied to assess the capacity of rhizosphere microorganisms to influence translocation.

A pan-grass transcriptome reveals patterns of cellular divergence in crops

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage

BACKGROUND

Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis.

RESULTS

Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat. Metabolite and microbiota profiling showed that the aerial root mucilage is enriched in carbohydrates and diazotrophic bacteria. Nitrogen isotope-labeling experiments, ¹⁵N natural abundance, and gene expression analysis indicated that the aerial root-mucilage microbiota could fix atmospheric nitrogen to support plant growth. While the aerial root mucilage is a hotspot of nutrients, we did not observe high abundance of other environmental and pathogenic microbes inside. We further identified a fungus isolate in mucilage that has shown broad-spectrum antimicrobial activities, but solely allows the growth of diazotrophic bacteria. This "friendly" fungus may be the key driver to maintain nitrogen fixation function in the mucilage microhabitat. Video Abstract CONCLUSION: The discovery of new biological function and mucilage-habitat friendly fungi provides insights into microbial homeostasis maintenance of microenvironmental function and rhizosphere ecology.

Biological nitrogen fixation in cereal crops: Progress, strategies, and perspectives

Nitrogen is abundant in the atmosphere but is generally the most limiting nutrient for plants. The inability of many crop plants, such as cereals, to directly utilize freely available atmospheric nitrogen gas means that their growth and production often rely heavily on the application of chemical fertilizers, which leads to greenhouse gas emissions and the eutrophication of water. By contrast, legumes gain access to nitrogen through symbiotic association with rhizobia. These bacteria convert nitrogen gas into biologically available ammonia in nodules through a process termed symbiotic biological nitrogen fixation, which plays a decisive role in ecosystem functioning. Engineering cereal crops that can fix nitrogen like legumes or associate with nitrogen-fixing microbiomes could help to avoid the problems caused by the overuse of synthetic nitrogen fertilizer. With the development of synthetic biology, various efforts have been undertaken with the aim of creating so-called "N-self-fertilizing" crops capable of performing autonomous nitrogen fixation to avoid the need for chemical fertilizers. In this review, we briefly summarize the history and current status of engineering N-self-fertilizing crops. We also propose several potential biotechnological approaches for incorporating biological nitrogen fixation capacity into non-legume plants.

Agronomic performance and quality of baby corn in response to the inoculation of seeds with Azospirillum brasilense and nitrogen fertilization in the summer harvest

The association with Azospirillum brasilense promotes better growth and development in corn plants due to biological N fixation, the capacity to help in the synthesis of phytohormones and to improve the use of nutrients by crop plants. However, there aren't specific recommendations for the use of inoculation in baby corn crop. Thus, this study aimed to evaluate the effects of seed inoculation with A. brasilense, associated with nitrogen fertilization management, on the agronomic performance and chemical quality of baby corn grown in three summer growing seasons (2014/2015; 2015/2016 and 2016/2017). The evaluated treatments consisted of combination of five levels of seed inoculation (0.0, 50, 100, 150 and 200 mL 60,000 seeds^-1) based on Azospirillum brasilense, two levels of nitrogen fertilization at sowing time (0.0 and 30.0 kg of N ha^-1) and two levels of nitrogen in topdressing (0.0 and 110.0 kg of N ha^-1), applied at the V4 stage of the popcorn hybrid IAC 125. The characteristics evaluated were: leaf area index (LAI), leaf nitrogen content (LNC), total husked spikelets yield (HSY) and commercial spikelets yield (CSY), and the chemical characteristics of the commercial spikelets: crude protein content (CPC), starch content (STC) and total sugar content (TSC). The inoculation, when combined with nitrogen fertilization, provided positive responses for LAI and provided an average increment of 6 kg ha^-1 to CSY for every 10 mL 60,000 seeds^-1 of inoculant added to the seeds. The LNC, CPC, STC and TSC weren't affected by seed inoculation. Nitrogen fertilization provided increments for all characteristics evaluated, except for TSC, which was negatively affected by nitrogen topdressing. The baby corn crop responded positively to seed inoculation with Azospirillum brasilense, combined with Nitrogen fertilization.

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Environmental implication of MoS2 nanosheets: Effects on maize plant growth and soil microorganisms

Molybdenum disulfide (MoS₂) nanosheets have been used extensively in a variety of fields including medical and industrial. However, little is known about their toxicity effects, especially to edible plants. In this greenhouse study, maize (Zea mays) seedlings were exposed for 4 weeks, through the soil route, to 10 and 100 mg/kg of 2H MoS₂ nanosheets. Plant growth, physiological parameters (chlorophyll, antioxidants, and MDA), along with Mo and nutrient element contents were determined in plant tissues. Results showed that at both doses, the nanosheets decreased plant growth. Inductively coupled plasma-mass spectrometry data also showed that both 2H MoS₂ concentrations allowed Mo absorption and translocation by maize plants. Additionally, at 100 mg/kg the nanosheets significantly reduced Ca, Mg, Mn, and Zn in leaves, and Na in roots. Gene sequencing data of 16S rRNA showed, that MoS₂ nanosheets changed the soil microbial community structure, compared with the untreated control. In addition, nitrogen-fixing microorganisms such as Burkholderiales, Rhizobiales and Xanthobacteraceae were enriched. Overall, the data suggest that, even at low dose (10 mg/kg), the 2H MoS₂ nanosheets perturbed both the nutrient uptake by maize plants and the soil microbial communities.

Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution

Globally, agriculture depends on industrial nitrogen fertilizer to improve crop growth. Fertilizer production consumes fossil fuels and contributes to environmental nitrogen pollution. A potential solution would be to harness nitrogenases-enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions. It is therefore a major goal of synthetic biology to engineer functional nitrogenases into crop plants, or bacteria that form symbiotic relationships with crops, to support growth and reduce dependence on industrially produced fertilizer. This review paper highlights recent work toward understanding the functional requirements for nitrogenase expression and manipulating nitrogenase gene expression in heterologous hosts to improve activity and oxygen tolerance and potentially to engineer synthetic symbiotic relationships with plants.

Maize Breeding for Low Nitrogen Inputs in Agriculture: Mechanisms Underlying the Tolerance to the Abiotic Stress

Nitrogen (N) is essential for sustaining life on Earth and plays a vital role in plant growth and thus agricultural production. The excessive use of N fertilizers not only harms the economy, but also the environment. In the context of the environmental impacts caused by agriculture, global maize improvement programs aim to develop cultivars with high N-use efficiency (NUE) to reduce the use of N fertilizers. Since N is highly mobile in plants, NUE is related to numerous little-known morphophysiological and molecular mechanisms. In this review paper we present an overview of the morpho-physiological adaptations of shoot and root, molecular mechanisms involved in plant response to low nitrogen environment, and the genetic effects involved in the control of key traits for NUE. Some studies show that the efficiency of cultivars growing under low N is related to deep root architecture, more lateral roots (LR), and sparser branching of LR, resulting in lower metabolic costs. The NUE cultivars also exhibit more efficient photosynthesis, which affects plant growth under suboptimal nitrogen conditions. In this sense, obtaining superior genotypes for NUE can be achieved with the exploitation of heterosis, as non-additive effects are more important in the expression of traits associated with NUE.

Climate change challenges, plant science solutions

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

Maize plants and the brace roots that support them

Brace roots are a unique but poorly understood set of organs found in some large cereal crops such as maize. These roots develop from aerial stem nodes and can remain aerial or grow into the ground. Despite their name, the function of these roots to brace the plant was only recently shown. In this article, I discuss the current understanding of brace root function and development, as well as the multitude of open questions that remain about these fascinating organs.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Rhodospirillum sp. JY3: An innovative tool to mitigate the phytotoxic impact of galaxolide on wheat (Triticum aestivum) and faba bean (Vicia faba) plants

To date, several studies have considered the phytotoxic impact of cosmetics and personal care products on crop plants. Nonetheless, data are scarce about the toxic impact of galaxolide [hexahydro-hexamethyl cyclopentabenzopyran (HHCB)] on the growth, physiology, and biochemistry of plants from different functional groups. To this end, the impact of HHCB on biomass, photosynthetic efficiency, antioxidant production, and detoxification metabolism of grass (wheat) and legume (faba bean) plants has been investigated. On the other hand, plant growth-promoting bacteria (PGPB) can be effectively applied to reduce HHCB phytotoxicity. HHCB significantly reduced the biomass accumulation and the photosynthetic machinery of both crops, but to more extent for wheat. This growth reduction was concomitant with induced oxidative damage and decreased antioxidant defense system. To mitigate HHCB toxicity, a bioactive strain of diazotrophic plant growth-promoting Rhodospirillum sp. JY3 was isolated from heavy metal-contaminated soil in Jazan, Kingdom of Saudi Arabia, and applied to both crops. Overall, Rhodospirillum mitigated HHCB-induced stress by differently modulating the oxidative burst [malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and protein oxidation] in both wheat and faba beans. This alleviation was coincident with improvement in plant biomass and photosynthetic efficiency, particularly in wheat crops. Considering the antioxidant defense system, JY3 augmented the antioxidants in both wheat and faba beans and the detoxification metabolism under HHCB stress conditions. More interestingly, inoculation with JY3 further enhanced the tolerance level of both wheat and faba beans against contamination with HHCB via quenching the lignin metabolism. Overall, this study advanced our understanding of the physiological and biochemical mechanisms underlying HHCB stress and mitigating its impact using Rhodospirillum sp. JY3, which may strikingly reduce the environmental risks on agriculture sustainability.

Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap's integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.

Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.

Genome-wide association study reveals the genetic basis of brace root angle and diameter in maize

Brace roots are the main organ to support the above-ground part of maize plant. It involves in plant growth and development by water absorption and lodging resistance. The bracing root angle (BRA) and diameter (BRD) are important components of brace root traits. Illuminating the genetic basis of BRA and BRD will contribute the improvement for mechanized harvest and increasing production. A GWAS of BRA and BRD was conducted using an associated panel composed of 508 inbred lines of maize. The broad-sense heritability of BRA and BRD was estimated to be respectively 71% ± 0.19 and 52% ± 0.14. The phenotypic variation of BRA and BRD in the non-stiff stalk subgroup (NSS) and the stiff stalk subgroup (SS) subgroups are significantly higher than that in the tropical/subtropical subgroup (TST) subgroups. In addition, BRA and BRD are significantly positive with plant height (PH), ear length (EL), and kernel number per row (KNPR). GWAS revealed 27 candidate genes within the threshold of p < 1.84 × 10⁻⁶ by both MLM and BLINK models. Among them, three genes, GRMZM2G174736, GRMZM2G445169 and GRMZM2G479243 were involved in cell wall function, and GRMZM2G038073 encoded the NAC transcription factor family proteins. These results provide theoretical support for clarifying the genetic basis of brace roots traits.

Functional expression of the nitrogenase Fe protein in transgenic rice

Engineering cereals to express functional nitrogenase is a long-term goal of plant biotechnology and would permit partial or total replacement of synthetic N fertilizers by metabolization of atmospheric N2. Developing this technology is hindered by the genetic and biochemical complexity of nitrogenase biosynthesis. Nitrogenase and many of the accessory proteins involved in its assembly and function are O2 sensitive and only sparingly soluble in non-native hosts. We generated transgenic rice plants expressing the nitrogenase structural component, Fe protein (NifH), which carries a [4Fe-4S] cluster in its active form. NifH from Hydrogenobacter thermophilus was targeted to mitochondria together with the putative peptidyl prolyl cis-trans isomerase NifM from Azotobacter vinelandii to assist in NifH polypeptide folding. The isolated NifH was partially active in electron transfer to the MoFe protein nitrogenase component (NifDK) and in the biosynthesis of the nitrogenase iron-molybdenum cofactor (FeMo-co), two fundamental roles for NifH in N2 fixation. NifH functionality was, however, limited by poor [4Fe-4S] cluster occupancy, highlighting the importance of in vivo [Fe-S] cluster insertion and stability to achieve biological N2 fixation in planta. Nevertheless, the expression and activity of a nitrogenase component in rice plants represents the first major step to engineer functional nitrogenase in cereal crops.

The Role of Endophytes in Combating Fungal- and Bacterial-Induced Stress in Plants

Plants are subjected to multifaceted stresses that significantly jeopardize crop production. Pathogenic microbes influence biotic stress in plants, which ultimately causes annual crop loss worldwide. Although the use of pesticides and fungicides can curb the proliferation of pathogens in plants and enhance crop production, they pollute the environment and cause several health issues in humans and animals. Hence, there is a need for alternative biocontrol agents that offer an eco-friendly mode of controlling plant diseases. This review discusses fungal- and bacterial-induced stress in plants, which causes various plant diseases, and the role of biocontrol defense mechanisms, for example, the production of hydrolytic enzymes, secondary metabolites, and siderophores by stress-tolerant fungi and bacteria to combat plant pathogens. It is observed that beneficial endophytes could sustain crop production and resolve the issues regarding crop yield caused by bacterial and fungal pathogens. The collated literature review indicates that future research is necessary to identify potential biocontrol agents that can minimize the utility of synthetic pesticides and increase the tenable agricultural production.

Plant-endophyte mediated improvement in physiological and bio-protective abilities of marigold (Tagetes patula)

Endophytic bacteria improve the growth, physiology, and metabolite profile of plants. They are known as potential biocontrol agents of soil-borne diseases. This study evaluated the effects of endophytic bacterial strains on growth, vase life, biochemical attributes, and antioxidant and nematicidal activities of French marigold (Tagetes patula). French marigold seeds were sole and consortium inoculated with three promising endophytic bacterial strains, Burkholderia phytofirmans (PsJN), Enterobacter sp. (MN17), and Bacillus sp. (MN54). The vase life of French marigold was promoted by 66.6% in the individual application of PsJN and 100% in plants treated with consortium compared to the uninoculated control. The shoot and root fresh weights were also increased by 65.9 and 68.7%, with the combined application of all three strains. The total phenolics, flavonoid, and protein contents were higher in consortium treatment with an increase of up to 38.0, 55.9, and 65.9%, respectively, compared to the uninoculated control. Furthermore, combined application of endophytic bacterial strains promoted DPPH radical scavenging, mortality of plant-parasitic nematodes, and ferric reducing antioxidant power activities with increase of up to 278.0, 103.8, and 178.0%, respectively, compared to uninoculated control. An increase in antioxidant activities of ascorbate peroxidase (APX), catalase (CAT), glutathione peroxidase (GPX), and superoxide dismutase (SOD) were observed up to 77.3, 86.0, 91.6, and 102.9%, respectively by combined application of endophytic bacterial strains. So, given the economic importance of floriculture crops, endophytic bacterial isolates studied here have shown a great potential for improving the productivity of cultivated ornamental French marigold.