Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize

Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

BACKGROUND

The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.

RESULTS

We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others.

CONCLUSIONS

This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.

Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis

Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.

Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis

Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.

Molecular Biology in the Improvement of Biological Nitrogen Fixation by Rhizobia and Extending the Scope to Cereals

The contribution of biological nitrogen fixation to the total N requirement of food and feed crops diminished in importance with the advent of synthetic N fertilizers, which fueled the “green revolution”. Despite being environmentally unfriendly, the synthetic versions gained prominence primarily due to their low cost, and the fact that most important staple crops never evolved symbiotic associations with bacteria. In the recent past, advances in our knowledge of symbiosis and nitrogen fixation and the development and application of recombinant DNA technology have created opportunities that could help increase the share of symbiotically-driven nitrogen in global consumption. With the availability of molecular biology tools, rapid improvements in symbiotic characteristics of rhizobial strains became possible. Further, the technology allowed probing the possibility of establishing a symbiotic dialogue between rhizobia and cereals. Because the evolutionary process did not forge a symbiotic relationship with the latter, the potential of molecular manipulations has been tested to incorporate a functional mechanism of nitrogen reduction independent of microbes. In this review, we discuss various strategies applied to improve rhizobial strains for higher nitrogen fixation efficiency, more competitiveness and enhanced fitness under unfavorable environments. The challenges and progress made towards nitrogen self-sufficiency of cereals are also reviewed. An approach to integrate the genetically modified elite rhizobia strains in crop production systems is highlighted.

Mechanism and application of Sesbania root-nodulating bacteria: an alternative for chemical fertilizers and sustainable development

Chemical fertilizers are used in large-scale throughout the globe to satisfy the food and feed requirement of the world. Demanding cropping with the enhanced application of chemical fertilizers, linked with a decline in the recycling of natural or other waste materials, has led to a decrease in the organic carbon levels in soils, impaired soil physical properties and shrinking soil microbial biodiversity. Sustenance and improvement of soil fertility are fundamental for comprehensive food security and ecological sustainability. To feed the large-scale growing population, the role of biofertilizers and their study tends to be an essential aspect globally. In this review, we have emphasized the nitrogen-fixing plants of Sesbania species. It is a plant that is able to accumulate nitrogen-rich biomass and used as a green manure, which help in soil amelioration. Problems of soil infertility due to salinity, alkalinity and waterlogging could be alleviated through the use of biologically fixed nitrogen by Sesbania plants leading to the conversion of futile land into a fertile one. A group of plant growth-promoting rhizobacteria termed as "rhizobia" are able to nodulate a variety of legumes including Sesbania. The host-specific rhizobial strains can be used as potential alternative for nitrogenous fertilizers as they help the host plant in growth and development and enhance their endurance under stressed conditions. The review gives the depth understanding of how the agriculturally important microorganisms can be used for the reduction of broad-scale application of chemical fertilizers with special attention to Sesbania-nodulating rhizobia.

Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection

Symbiosis between soybean (Glycine max) and rhizobia is essential for efficient nitrogen fixation. Rhizobial effectors secreted through the type-III secretion system are key for mediating the interactions between plants and rhizobia, but the molecular mechanism remains largely unknown. Here, our genome-wide association study for nodule number identified G. max Nodule Number Locus 1 (GmNNL1), which encodes a new R protein. GmNNL1 directly interacts with the nodulation outer protein P (NopP) effector from Bradyrhizobium USDA110 to trigger immunity and inhibit nodulation through root hair infection. The insertion of a 179 bp short interspersed nuclear element (SINE)-like transposon into GmNNL1 leads to the loss of function of GmNNL1, enabling bradyrhizobia to successfully nodulate soybeans through the root hair infection route and enhancing nitrogen fixation. Our findings provide important insights into the coevolution of soybean-bradyrhizobia compatibility and offer a way to design new legume-rhizobia interactions for efficient symbiotic nitrogen fixation.

Articulating the effect of food systems innovation on the Sustainable Development Goals

Food system innovations will be instrumental to achieving multiple Sustainable Development Goals (SDGs). However, major innovation breakthroughs can trigger profound and disruptive changes, leading to simultaneous and interlinked reconfigurations of multiple parts of the global food system. The emergence of new technologies or social solutions, therefore, have very different impact profiles, with favourable consequences for some SDGs and unintended adverse side-effects for others. Stand-alone innovations seldom achieve positive outcomes over multiple sustainability dimensions. Instead, they should be embedded as part of systemic changes that facilitate the implementation of the SDGs. Emerging trade-offs need to be intentionally addressed to achieve true sustainability, particularly those involving social aspects like inequality in its many forms, social justice, and strong institutions, which remain challenging. Trade-offs with undesirable consequences are manageable through the development of well planned transition pathways, careful monitoring of key indicators, and through the implementation of transparent science targets at the local level.

Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review

Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.

30 years of free-air carbon dioxide enrichment (FACE): What have we learned about future crop productivity and its potential for adaptation?

Free-air CO₂ enrichment (FACE) allows open-air elevation of [CO₂ ] without altering the microclimate. Its scale uniquely supports simultaneous study from physiology and yield to soil processes and disease. In 2005 we summarized results of then 28 published observations by meta-analysis. Subsequent studies have combined FACE with temperature, drought, ozone, and nitrogen treatments. Here, we summarize the results of now almost 250 observations, spanning 14 sites and five continents. Across 186 independent studies of 18 C₃ crops, elevation of [CO₂ ] by ca. 200 ppm caused a ca. 18% increase in yield under non-stress conditions. Legumes and root crops showed a greater increase and cereals less. Nitrogen deficiency reduced the average increase to 10%, as did warming by ca. 2°C. Two conclusions of the 2005 analysis were that C₄ crops would not be more productive in elevated [CO₂ ], except under drought, and that yield responses of C₃ crops were diminished by nitrogen deficiency and wet conditions. Both stand the test of time. Further studies of maize and sorghum showed no yield increase, except in drought, while soybean productivity was negatively affected by early growing season wet conditions. Subsequent study showed reduced levels of nutrients, notably Zn and Fe in most crops, and lower nitrogen and protein in the seeds of non-leguminous crops. Testing across crop germplasm revealed sufficient variation to maintain nutrient content under rising [CO₂ ]. A strong correlation of yield response under elevated [CO₂ ] to genetic yield potential in both rice and soybean was observed. Rice cultivars with the highest yield potential showed a 35% yield increase in elevated [CO₂ ] compared to an average of 14%. Future FACE experiments have the potential to develop cultivars and management strategies for co-promoting sustainability and productivity under future elevated [CO₂ ].

Microbial Inoculants: Silver Bullet or Microbial Jurassic Park?

The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology. In our desire to harness the power of plant-microbial symbioses, are we ignoring the possibility of precipitating microbial invasions, potentially setting ourselves up for a microbial Jurassic Park? Here, we outline potential negative consequences of microbial invasions and describe a set of practices (Testing, Regulation, Engineering, and Eradication, TREE) based on the four stages of invasion to prevent microbial inoculants from becoming invasive. We aim to stimulate discussion about best practices to proactively prevent microbial invasions.

Plant Biosystems Design Research Roadmap 1.0

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.

Exploring bacterial community structure and function associated with polychlorinated biphenyl biodegradation in two hydrogen-amended soils

Hydrogen (H₂) is a universal energy source supplying survival energy for numerous microbial functions. Diffusive fluxes of H₂ released by rhizobacterial symbiont nodules in which H₂ is an obligate by-product of dinitrogen fixation may act as an additional energy input shaping microbial community structure and function in soils. However, the effects of H₂ at the soil-nodule interface on soil contaminant degradation processes are poorly understood. Here, we mimicked the hydrogen conditions present at the soil-nodule interface (10,000 ppmv) to test the impact of elevated H₂ concentrations on soil microbial removal of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) and examined the associated bacterial communities and their functions by conducting a microcosm experiment using two different soil types at three PCB contamination levels (0.5, 1.0 and 5.0 mg kg^-1). After incubation for 84 days the PCB77 removal rates in the elevated H₂ treatments in the Paddy soil were significantly promoted (by 4.88 to 6.41%) compared with the control (0.5 ppmv H₂) but no significant effect was observed in a Fluvo-aquic soil. This is consistent with changes in the abundance of functional genes for PCB-degraders as shown by quantitative real-time PCR (Q-PCR) and phylogenetic investigation of bacterial communities by reconstruction of unobserved states (PICRUSt). 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genera to potential PCB degradation. The abundance of a total of four potentially PCB-degrading bacterial genera (Bacillus, Streptomyces, Ramlibacter and Paenibacillus) increased with increasing H₂ level. In addition, the abundance of hydrogenase in the elevated H₂ treatments was higher than in the control across different contamination levels in both soil types. Thus, elevated H₂ stimulated soil PCB degradation with direct effects (aerobic PCB-degrading bacteria directly utilized H₂ as an energy source for growth and thus enhanced PCB degradation efficiency) and indirect effects (aerobic PCB-degrading bacteria acted synergistically with other hydrogenotrophs to enhance PCB degradation efficiency by exchange of substances and energy). These results help to further understand the role of elevated hydrogen amendment in the PCB biodegradation process and provide evidence that H₂ supports metabolic and energetic flexibility in microorganisms supplying a range of ecosystem services.

Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the “Farmer-2” rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the “Candidatus” category were found to be robustly enriched the rhizosphere of “Moitree”. Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of “Moitree” had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. “Moitree” with a profuse root system exhibited better N fixation and translocation ability due to a good “foraging strategy” for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, “Farmer-2” revealed a better “mining strategy” for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar–microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.

Beneficial features of plant growth-promoting rhizobacteria for improving plant growth and health in challenging conditions: A methodical review

New eco-friendly approaches are required to improve plant biomass production. Beneficial plant growth-promoting (PGP) bacteria may be exploited as excellent and efficient biotechnological tools to improve plant growth in various - including stressful - environments. We present an overview of bacterial mechanisms which contribute to plant health, growth, and development. Plant growth promoting rhizobacteria (PGPR) can interact with plants directly by increasing the availability of essential nutrients (e.g. nitrogen, phosphorus, iron), production and regulation of compounds involved in plant growth (e.g. phytohormones), and stress hormonal status (e.g. ethylene levels by ACC-deaminase). They can also indirectly affect plants by protecting them against diseases via competition with pathogens for highly limited nutrients, biocontrol of pathogens through production of aseptic-activity compounds, synthesis of fungal cell wall lysing enzymes, and induction of systemic responses in host plants. The potential of PGPR to facilitate plant growth is of fundamental importance, especially in case of abiotic stress, where bacteria can support plant fitness, stress tolerance, and/or even assist in remediation of pollutants. Providing additional evidence and better understanding of bacterial traits underlying plant growth-promotion can inspire and stir up the development of innovative solutions exploiting PGPR in times of highly variable environmental and climatological conditions.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

MtCOPT2 is a Cu+ transporter specifically expressed in Medicago truncatula mycorrhizal roots

Arbuscular mycorrhizal fungi are critical participants in plant nutrition in natural ecosystems and in sustainable agriculture. A large proportion of the phosphorus, nitrogen, sulfur, and transition metal elements that the host plant requires are obtained from the soil by the fungal mycelium and released at the arbuscules in exchange for photosynthates. While many of the plant transporters responsible for obtaining macronutrients at the periarbuscular space have been characterized, the identities of those mediating transition metal uptake remain unknown. In this work, MtCOPT2 has been identified as the only member of the copper transporter family COPT in the model legume Medicago truncatula to be specifically expressed in mycorrhizal roots. Fusing a C-terminal GFP tag to MtCOPT2 expressed under its own promoter showed a distribution pattern that corresponds with arbuscule distribution in the roots. When expressed in tobacco leaves, MtCOPT2-GFP co-localizes with a plasma membrane marker. MtCOPT2 is intimately related to the rhizobial nodule-specific MtCOPT1, which is suggestive of a shared evolutionary lineage that links transition metal nutrition in the two main root endosymbioses in legumes.

La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria

La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.

The ex planta signal activity of a Medicago ribosomal uL2 protein suggests a moonlighting role in controlling secondary rhizobial infection

We recently described a regulatory loop, which we termed autoregulation of infection (AOI), by which Sinorhizobium meliloti, a Medicago endosymbiont, downregulates the root susceptibility to secondary infection events via ethylene. AOI is initially triggered by so-far unidentified Medicago nodule signals named signal 1 and signal 1' whose transduction in bacteroids requires the S. meliloti outer-membrane-associated NsrA receptor protein and the cognate inner-membrane-associated adenylate cyclases, CyaK and CyaD1/D2, respectively. Here, we report on advances in signal 1 identification. Signal 1 activity is widespread as we robustly detected it in Medicago nodule extracts as well as in yeast and bacteria cell extracts. Biochemical analyses indicated a peptidic nature for signal 1 and, together with proteomic analyses, a universally conserved Medicago ribosomal protein of the uL2 family was identified as a candidate signal 1. Specifically, MtRPuL2A (MtrunA17Chr7g0247311) displays a strong signal activity that requires S. meliloti NsrA and CyaK, as endogenous signal 1. We have shown that MtRPuL2A is active in signaling only in a non-ribosomal form. A Medicago truncatula mutant in the major symbiotic transcriptional regulator MtNF-YA1 lacked most signal 1 activity, suggesting that signal 1 is under developmental control. Altogether, our results point to the MtRPuL2A ribosomal protein as the candidate for signal 1. Based on the Mtnf-ya1 mutant, we suggest a link between root infectiveness and nodule development. We discuss our findings in the context of ribosomal protein moonlighting.

Medicago truncatula Ferroportin2 mediates iron import into nodule symbiosomes

Iron is an essential cofactor for symbiotic nitrogen fixation, required by many of the enzymes involved, including signal transduction proteins, O₂ homeostasis systems, and nitrogenase itself. Consequently, host plants have developed a transport network to deliver essential iron to nitrogen-fixing nodule cells. Ferroportin family members in model legume Medicago truncatula were identified and their expression was determined. Yeast complementation assays, immunolocalization, characterization of a tnt1 insertional mutant line, and synchrotron-based X-ray fluorescence assays were carried out in the nodule-specific M. truncatula ferroportin Medicago truncatula nodule-specific gene Ferroportin2 (MtFPN2) is an iron-efflux protein. MtFPN2 is located in intracellular membranes in the nodule vasculature and in inner nodule tissues, as well as in the symbiosome membranes in the interzone and early-fixation zone of the nodules. Loss-of-function of MtFPN2 alters iron distribution and speciation in nodules, reducing nitrogenase activity and biomass production. Using promoters with different tissular activity to drive MtFPN2 expression in MtFPN2 mutants, we determined that expression in the inner nodule tissues is sufficient to restore the phenotype, while confining MtFPN2 expression to the vasculature did not improve the mutant phenotype. These data indicate that MtFPN2 plays a primary role in iron delivery to nitrogen-fixing bacteroids in M. truncatula nodules.

Brassinosteroids play multiple roles in nodulation of pea via interactions with ethylene and auxin

MAIN CONCLUSION

A comprehensive analysis of the role of brassinosteroids in nodulation, including their interactions with auxin and ethylene revealed that brassinosteroids inhibit infection, promote nodule initiation but do not influence nodule organogenesis or function. Nodulation, the symbiosis between legumes and rhizobial bacteria, is regulated by a suite of hormones including brassinosteroids. Previous studies have found that brassinosteroids promote nodule number by inhibiting ethylene biosynthesis. In this study, we examined the influence of brassinosteroids on the various stages of infection and nodule development. We utilise pea mutants, including brassinosteroid mutants lk, lka and lkb, the ethylene insensitive ein2 mutant and the lk ein2 double mutant, along with transgenic lines expressing the DR5::GUS auxin activity marker to investigate how brassinosteroids interact with ethylene and auxin during nodulation. We show that brassinosteroids inhibit the early stages of nodulation, including auxin accumulation, root hair deformation and infection thread formation, and demonstrate that infection thread formation is regulated by brassinosteroids in an ethylene independent manner. In contrast, brassinosteroids appear to act as promoters of nodule initiation through both an ethylene dependent and independent pathway. Although brassinosteroids positively influence the ultimate number of nodules formed, we found that brassinosteroid-deficiency did not influence nodule structure including the vascular pattern of auxin activity or nitrogen-fixation capacity. These findings suggest that brassinosteroids are negative regulators of infection but positive regulators of nodule initiation. Furthermore, brassinosteroids do not appear to be essential for nodule organogenesis or function. Given the influence of brassinosteroids on discreet stages of nodulation but not nodule function, manipulation of brassinosteroids may be an interesting avenue for future research on the optimisation of nodulation.

Does Canavalia ensiformis inoculation with Bradyrhizobium sp. enhance phytoremediation of sulfentrazone-contaminated soil?

Symbiosis among herbicide-metabolising microorganisms and phytoremediation plants may be an efficient alternative to remediate sulfentrazone-contaminated soils. This work evaluated the bioremediation of sulfentrazone-contaminated soils by symbiosis between bacteria (Bradyrhizobium sp.) and jack bean (Canavalia ensiformis L.). The experiment was carried out in a greenhouse between March and May of 2018, in the Universidade Federal do Espírito Santo (UFES). Four doses of sulfentrazone (0, 400, 800, and 1200 g ha^-1 a. i.) were tested with and without inoculation with Bradyrhizobium sp. BR 2003 (SEMIA 6156) After 80 days of cultivation, plants were cut and soil was collected for determination of the herbicide residual levels and millet bioassay. The sulfentrazone concentration was significantly reduced by plant inoculation with Bradyrhizobium sp.: on average, concentrations were 18.97%, 23.82%, and 22.10% lower than in the absence of inoculation at doses of 400, 800, and 1200 g ha^-1, respectively. Symbiosis promoted a reduction of up to 65% in residual soil herbicides. Under the 1200 g ha^-1 dose, inoculation promoted greater plant height than in the uninoculated plant. Regardless of the dose of sulfentrazone, the dry root mass was higher in the inoculated plants. The microbiological indicators showed satisfactory results mainly for the dose of 400 g ha^-1. The results of this study highlight the potential of positive interactions between symbiotic microorganisms and leguminous species, aiming toward the phytoremediation of sulfentrazone herbicide.

Exploiting Biological Nitrogen Fixation: A Route Towards a Sustainable Agriculture

For all living organisms, nitrogen is an essential element, while being the most limiting in ecosystems and for crop production. Despite the significant contribution of synthetic fertilizers, nitrogen requirements for food production increase from year to year, while the overuse of agrochemicals compromise soil health and agricultural sustainability. One alternative to overcome this problem is biological nitrogen fixation (BNF). Indeed, more than 60% of the fixed N on Earth results from BNF. Therefore, optimizing BNF in agriculture is more and more urgent to help meet the demand of the food production needs for the growing world population. This optimization will require a good knowledge of the diversity of nitrogen-fixing microorganisms, the mechanisms of fixation, and the selection and formulation of efficient N-fixing microorganisms as biofertilizers. Good understanding of BNF process may allow the transfer of this ability to other non-fixing microorganisms or to non-leguminous plants with high added value. This minireview covers a brief history on BNF, cycle and mechanisms of nitrogen fixation, biofertilizers market value, and use of biofertilizers in agriculture. The minireview focuses particularly on some of the most effective microbial products marketed to date, their efficiency, and success-limiting in agriculture. It also highlights opportunities and difficulties of transferring nitrogen fixation capacity in cereals.

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.

Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean

Rhizobia-legume symbiosis is an important type of plant-microbe mutualism; however, the establishment of this association is complicated and can be affected by many factors. The soybean rhizosphere has a specific microbial community, yet whether these organisms affect rhizobial nodulation has not been well investigated. Here, we analyzed the compositions and relationships of soybean rhizocompartment microbiota in three types of soil. First, we found that the rhizosphere community composition of soybean varied significantly in different soils, and the association network between rhizobia and other rhizosphere bacteria was examined. Second, we found that some rhizosphere microbes were correlated with the composition of bradyrhizobia and sinorhizobia in nodules. We cultivated 278 candidate Bacillus isolates from alkaline soil. Finally, interaction and nodulation assays showed that the Bacillus cereus group specifically promotes and suppresses the growth of sinorhizobia and bradyrhizobia, respectively, and alleviates the effects of saline-alkali conditions on the nodulation of sinorhizobia as well as affecting its colonization in nodules. Our findings demonstrate a crucial role of the bacterial microbiota in shaping rhizobia-host interactions in soybean, and provide a framework for improving the symbiotic efficiency of this system of mutualism through the use of synthetic bacterial communities.

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges

The long atmospheric residence time of CO2 creates an urgent need to add atmospheric carbon drawdown to CO2 regulatory strategies. Synthetic and systems biology (SSB), which enables manipulation of cellular phenotypes, offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric carbon. The participants (in attendance: Christina Agapakis, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Charles DeLisi, Dan Drell, Sheldon Glashow, Steve Hamburg, Henry Jacoby, Henry Kelly, Mark Kon, Todd Kuiken, Mary Lidstrom, Mike MacCracken, June Medford, Jerry Melillo, Ron Milo, Pilar Ossorio, Ari Patrinos, Keith Paustian, Kristala Jones Prather, Kent Redford, David Resnik, John Reilly, Richard J. Roberts, Daniel Segre, Susan Solomon, Elizabeth Strychalski, Chris Voigt, Dominic Woolf, Stan Wullschleger, and Xiaohan Yang) identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and adaptation. These include, among other possibilities, engineering plants to convert CO2 produced by respiration into a stable carbonate, designing plants with an increased root-to-shoot ratio, and creating plants with the ability to self-fertilize. A number of serious ecological and societal challenges must, however, be confronted and resolved before any such application can be fully assessed, realized, and deployed.

Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph

Plants depend upon beneficial interactions between roots and root-associated microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecological role that has been long underappreciated in modern agriculture for efficient crop production systems. Long-term ecological studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fixing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-associated diazotroph can restore ammonium production in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-associated proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field experiments, remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in commercial applications to supply fixed nitrogen to cereal crops.

Beneficial soil-borne bacteria and fungi: a promising way to improve plant nitrogen acquisition

Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative impacts on the environment. Exploiting the potential of beneficial microbes and identifying crop genotypes that can capitalize on symbiotic associations may be possible ways to significantly reduce the use of N fertilizers. The best-known example of symbiotic association that can reduce the use of N fertilizers is the N2-fixing rhizobial bacteria and legumes. Bacterial taxa other than rhizobial species can develop associative symbiotic interactions with plants and also fix N. These include bacteria of the genera Azospirillum, Azotobacter, and Bacillus, some of which are commercialized as bio-inoculants. Arbuscular mycorrhizal fungi are other microorganisms that can develop symbiotic associations with most terrestrial plants, favoring access to nutrients in a larger soil volume through their extraradical mycelium. Using combinations of different beneficial microbial species is a promising strategy to boost plant N acquisition and foster a synergistic beneficial effect between symbiotic microorganisms. Complex biological mechanisms including molecular, metabolic, and physiological processes dictate the establishment and efficiency of such multipartite symbiotic associations. In this review, we present an overview of the current knowledge and future prospects regarding plant N nutrition improvement through the use of beneficial bacteria and fungi associated with plants, individually or in combination.

Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments

A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.

Synthesis of the tetrasaccharide repeating unit of the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71T using linear and one-pot iterative glycosylations

A straightforward synthetic strategy was developed for the synthesis of the tetrasaccharide repeating unit corresponding to the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71^T in a very good yield adopting sequential glycosylation followed by removal of the p-methoxybenzyl (PMB) group in the same pot. Further, the synthetic strategy was modified by carrying out three stereoselective iterative glycosylations followed by in situ removal of the PMB group in one pot. The stereochemical outcome of the newly formed glycosidic linkages was excellent using thioglycoside derivatives as glycosyl donors and a combination of N-iodosuccinimide (NIS) and perchloric acid supported on silica (HClO₄-SiO₂) as the glycosyl activator.

The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops

Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.

Connecting signals and benefits through partner choice in plant-microbe interactions

Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.

Transfer of Nitrogen Fixation (nif) Genes to Non-diazotrophic Hosts

Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture. Biological nitrogen fixation, the conversion of atmospheric N2 to NH3 , is an important source of nitrogen input in agriculture and represents a promising substitute for chemical nitrogen fertilizers. However, nitrogen fixation is only sporadically distributed within bacteria and archaea (diazotrophs). Thus, many biologists hope to reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host, with the final aim of developing N2 -fixing cereal crops. With the advent of synthetic biology and a deep understanding of the fundamental genetic determinants necessary to sustain nitrogen fixation in bacteria, much progress has been made toward this goal. Transfer of native and refactored nif (nitrogen fixation) genes to non-diazotrophs has been attempted in model bacteria, yeast, and plants. Specifically, nif genes from Klebsiella oxytoca, Azotobacter vinelandii, and Paenibacillus polymyxa have been successfully transferred and expressed in Escherichia coli, Saccharomyces cerevisiae, and even in the tobacco plant. These advances have laid the groundwork to enable cereal crops to "fix" nitrogen themselves to sustain their growth and yield.

Assessing the Systematic Effects of the Concentration of Nitrogen Supplied to Dual-Root Systems of Soybean Plants on Nodulation and Nitrogen Fixation

The specific mechanisms by which nitrogen affects the nodulation and nitrogen fixation of soybean plants are unclear. Investigating the relationship between nitrogen, nodulation and nitrogen fixation can provide new insights for the rational and proper use of nitrogen fertilizer in soybean plants. In this study, we grafted soybean roots to construct a dual-root system with a single nodulated side. Experiment I was performed at the third trifoliate leaf to initial seed filling (V3-R3) growth stages (for 30 days) for long-term nitrogen supply, and Experiment II was performed at the third trifoliate leaf to fourth trifoliate leaf (V3-V4) growth stages (for 5 days) for short-term nitrogen supply. For the two experiments, a nutrient solution providing 15NH415NO3 or NH4NO3 as the nitrogen source was added to the non-nodulated side, while a nitrogen-free nutrient solution was added to the nodulated side. The concentrations of nitrogen supplied were 0 mg/L, 25 mg/L, 50 mg/L, 75 mg/L, and 100 mg/L. The results showed the following: (1) Short-term nitrogen supply systematically regulated the specific nitrogenase activity (SNA), thereby inhibiting the acetylene reduction activity (ARA). Under long-term nitrogen supply, the recovery of SNA was generally consistent across treatments, and the concentration of nitrogen supplied systematically regulated the growth of root nodules, thereby inhibiting the ARA. (2) Using the 15N tracer method, the concentration of fertilizer nitrogen was positively correlated with the amount of nitrogen redistributed to other organs. Although the percentage of nitrogen derived from the atmosphere (Ndfa%) decreased significantly with increasing concentrations of nitrogen supplied, the effect on the accumulation of nitrogen fixed by nodules (Naccumulation of nodules) was not significant. By establishing the relationships between the ARA (measured by the acetylene reduction method), Ndfa% (based on 15N calculations), and Naccumulation nodules (based on 15N calculations), it was found that the ARA reliably reflected the Ndfa% but not the Naccumulation of nodules.

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium

The mutualistic association between leguminous plants and endosymbiotic rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, we report the reconstruction and modelling of a genome-scale metabolic network of Medicago truncatula (plant) nodulated by Sinorhizobium meliloti (bacterium). The reconstructed nodule tissue contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggests that the metabolic costs associated with symbiotic nitrogen fixation are primarily related to supporting nitrogenase activity, and increasing N2-fixation efficiency is associated with diminishing returns in terms of plant growth. Our analyses support that differentiating bacteroids have access to sugars as major carbon sources, ammonium is the main nitrogen export product of N2-fixing bacteria, and N2 fixation depends on proton transfer from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. We expect that our model, called 'Virtual Nodule Environment' (ViNE), will contribute to a better understanding of the functioning of legume nodules, and may guide experimental studies and engineering of symbiotic nitrogen fixation.

Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N2 -Fixing Bacterium Bradyrhizobium diazoefficiens

The pathogenicity and antimicrobial properties of engineered nanomaterials (ENMs) are relatively well studied. However, less is known regarding the interactions of ENMs and agriculturally beneficial microorganisms that affect food security. Nanoceria (CeO2 nanoparticles (NPs)), multiwall carbon nanotubes (MWCNTs), graphene nanoplatelets (GNPs), and carbon black (CB) have been previously shown to inhibit symbiotic N2 fixation in soybeans, but direct rhizobial susceptibility is uncertain. Here, Bradyrhizobium diazoefficiens associated with symbiotic N2 fixation in soybeans is assessed, evaluating the role of soybean root exudates (RE) on ENM-bacterial interactions and the effects of CeO2 NPs, MWCNTs, GNPs, and CB on bacterial growth and gene expression. Although bacterial growth is inhibited by 50 mg L-1 CeO2 NPs, MWCNTs, and CB, all ENMs at 0.1 and 10 mg L-1 cause a global transcriptomic response that is mitigated by RE. ENMs may interfere with plant-bacterial signaling, as evidenced by suppressed upregulation of genes induced by RE, and downregulation of genes encoding transport RNA, which facilitates nodulation signaling. MWCNTs and CeO2 NPs inhibit the expression of genes conferring B. diazoefficiens nodulation competitiveness. Surprisingly, the transcriptomic effects on B. diazoefficiens are similar for these two ENMs, indicating that physical, not chemical, ENM properties explain the observed effects.

Receptor-Like Kinases Sustain Symbiotic Scrutiny

Plant receptor-like kinases (RLKs) control the initiation, development, and maintenance of symbioses with beneficial mycorrhizal fungi and nitrogen-fixing bacteria. Carbohydrate perception activates symbiosis signaling via Lysin-motif RLKs and subsequently the common symbiosis signaling pathway. As the receptors activated are often also immune receptors in multiple species, exactly how carbohydrate identities avoid immune activation and drive symbiotic outcome is still not fully understood. This may involve the coincident detection of additional signaling molecules that provide specificity. Because of the metabolic costs of supporting symbionts, the level of symbiosis development is fine-tuned by a range of local and mobile signals that are activated by various RLKs. Beyond early, precontact symbiotic signaling, signal exchanges ensue throughout infection, nutrient exchange, and turnover of symbiosis. Here, we review the latest understanding of plant symbiosis signaling from the perspective of RLK-mediated pathways.

Electricity-powered artificial root nodule

Root nodules are agricultural-important symbiotic plant-microbe composites in which microorganisms receive energy from plants and reduce dinitrogen (N2) into fertilizers. Mimicking root nodules using artificial devices can enable renewable energy-driven fertilizer production. This task is challenging due to the necessity of a microscopic dioxygen (O2) concentration gradient, which reconciles anaerobic N2 fixation with O2-rich atmosphere. Here we report our designed electricity-powered biological|inorganic hybrid system that possesses the function of root nodules. We construct silicon-based microwire array electrodes and replicate the O2 gradient of root nodules in the array. The wire array compatibly accommodates N2-fixing symbiotic bacteria, which receive energy and reducing equivalents from inorganic catalysts on microwires, and fix N2 in the air into biomass and free ammonia. A N2 reduction rate up to 6.5 mg N2 per gram dry biomass per hour is observed in the device, about two orders of magnitude higher than the natural counterparts.

Microbial Protein out of Thin Air: Fixation of Nitrogen Gas by an Autotrophic Hydrogen-Oxidizing Bacterial Enrichment

For the production of edible microbial protein (MP), ammonia generated by the Haber-Bosch process or reclaimed ammonia from waste streams is typically considered as the nitrogen source. These processes for ammonia production are highly energy intensive. In this study, the potential for using nitrogen gas (N₂) as a direct nitrogen source for MP production by hydrogen-oxidizing bacteria (HOB) was evaluated. The use of N₂ versus ammonium as nitrogen source during the enrichment process resulted in differentiation of the bacterial community composition of the enrichments. A few previously unknown potential N₂-fixing HOB taxa (i.e., representatives of the genus Azonexus and the family Comamonadaceae) dominated the enrichments. The biomass yield of a N₂-fixing HOB enrichment was 30-50% lower than that of the ammonium-based HOB enrichment from the same inoculum source. The dried biomass of N₂-fixing HOB had a high protein content (62.0 ± 6.3%) and an essential amino acid profile comparable to MP from ammonium-based HOB. MP from N₂-fixing HOB could potentially be produced in situ without entailing the emissions caused by ammonia production and transportation by conventional means. It could be a promising substitute for N₂-fixing protein-rich soybean because it has 70% higher protein content and double energy conversion efficiency from solar energy to biomass.

The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis

Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.

A Model for Nitrogen Fixation in Cereal Crops

Nitrogen-fixing microbial associations with cereals have been of intense interest for more than a century (Roesch et al., Plant Soil 2008;302:91-104; Triplett, Plant Soil 1996;186:29-38; Mus et al., Appl. Environ. Microbiol. 2016;82:3698-3710; Beatty and Good, Science 2011;333:416-417). A recent report demonstrated that an indigenous Sierra Mixe maize landrace, characterized by an extensive development of aerial roots that secrete large amounts of mucilage, can acquire 28-82% of its nitrogen from atmospheric dinitrogen (Van Deynze et al., PLoS Biol. 2018;16:e2006352). Although the Sierra Mixe maize landrace is unique in the large quantity of mucilage produced, other cereal crops secrete mucilage from underground and aerial roots and we hypothesize that this may represent a general mechanism for cereals to support associations with microbial diazotrophs. We propose a model for the association of nitrogen-fixing microbes with maize mucilage and identify the four main functionalities for such a productive diazotrophic association.

The effect of plant compartments on the Broussonetia papyrifera-associated fungal and bacterial communities

Plants associate with numerous microbes, but little is known about how microbiome components, especially fungi, adapt to specific plant compartments. The adaptability of microbial function to the plant compartment is also not clear especially for woody species. Here, we characterized the bacterial and fungal communities in root endosphere, stems, and rhizospheres of 33 Broussonetia papyrifera seedlings, based on amplification of 16S and ITS rRNA. Results showed that the α-diversity indexes of the bacterial community were significantly different in different plant compartments and they significantly increased from stem to root endosphere to the rhizosphere, whereas those of the fungal community were similar (p > 0.05). However, the result of constrained PCoA (CPCoA) and analysis of similarity (ANOSIM) showed that both bacterial and fungal compositions were significantly affected by plant compartments (p < 0.01). In detail, the operational taxonomic units (OTUs) distribution of the bacterial community was significantly different, but 249 of 252 fungal OTUs were shared in different plant compartments. Both the bacterial and fungal compositions were significantly influenced by plant compartments, based on the result on phyla, core OTUs, and indicator OTUs level. Further, 40 of 42 enriched KEGG pathways involving the bacteria also differed significantly among plant compartments (p < 0.01). This study provides an understanding of the influence of plant compartments on the microbiome and confirms that the disperse limitation of fungal OTUs across different plant compartments is smaller. This study sheds light on how the microbial community adapts to and thrives in different plant compartments.

Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection

In many legumes, the colonization of roots by rhizobia is via "root hair entry" and its molecular mechanisms have been extensively studied. However, the nodulation of peanuts (Arachis hypogaea L.) by Bradyrhizobium strains requires an intercellular colonization process called "crack entry," which is understudied. To understand the intercellular crack entry process, it is critical to develop the tools and resources related to the rhizobium in addition to focus on investigating the mechanisms of the plant host. In this study, we isolated a Bradyrhizobium sp. strain, Lb8 from peanut root nodules and sequenced it using PacBio long reads. The complete genome sequence was a circular chromosome of 8,718,147 base-pair (bp) with an average GC content of 63.14%. No plasmid sequence was detected in the sequenced DNA sample. A total of 8,433 potential protein-encoding genes, one rRNA cluster, and 51 tRNA genes were annotated. Fifty-eight percent of the predicted genes showed similarity to genes of known functions and were classified into 27 subsystems representing various biological processes. The genome shared 92% of the gene families with B. diazoefficens USDA 110^T. A presumptive symbiosis island of 778 Kb was detected, which included two clusters of nif and nod genes. A total of 711 putative protein-encoding genes were in this region, among which 455 genes have potential functions related to symbiotic nitrogen fixation and DNA transmission. Of 21 genes annotated as transposase, 16 were located in the symbiosis island. Lb8 possessed both Type III and Type IV protein secretion systems, and our work elucidated the association of flagellar Type III secretion systems in bradyrhizobia. These observations suggested that complex rearrangement, such as horizontal transfer and insertion of different DNA elements, might be responsible for the plasticity of the Bradyrhizobium genome.

Anabolic/anticatabolic and adaptogenic effects of 24-epibrassinolide on Lupinus angustifolius: Causes and consequences

Lupinus angustifolius L. is a legume culture known as a source of valuable feed protein and the N₂-fixator for improving soil fertility. However, its low ecological resistance does not allow for a stable yield of the crop. Earlier, we have shown that steroid phytohormone 24-epibrassinolide (EBR) increases the tolerance of lupine to chlorine ions by activating the protective proteins in ripening seeds (such as proteinase inhibitors that prevent protein breakdown) and lectins. Here we investigated the effect of EBR on the functional status of the N₂-fixing system in root nodules, protein synthesis in ripening seeds and the resistance of lupine plants to various pathogens. It was found that EBR enhanced the nodulation process, N₂-fixing activity of nitrogenase and the accumulation of poly-β-hydroxybutirate in the bacteroides, increased the leghemoglobin content in the nodules as well as the metabolic activity of bacteroides. According to data on the inclusion of ¹⁴C-leucine in maturing seed proteins, EBR increased the accumulation of protein in them against the background of a short-term decrease in protein synthesis and its subsequent regeneration to the control level. Gradual inhibition of protein synthesis, characteristic of other legumes, was observed in control variants of lupine. EBR increased lupine resistance to phytopathogenic fungi of Colletotrichum genus and insects of Noctuidae and Scarabaeidae families. We concluded that a more complete implementation of the potential productivity and sustainability of lupine under the action of EBR was achieved due to the anabolic/anti-catabolic effect on the N₂ fixation system in root nodules, as well as on protein synthesis in ripening seeds.

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix⁺) or a fix^- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix^- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix^- strain, perhaps reflecting a plant defense response.