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Social Impact Statement: Terrestrial life depends on a thin layer of top‐soil measuring no more than a few cm to around a meter. This nutrient rich zone supports the growth of plants by providing minerals and water they need for growth and photosynthesis. It is in the dark underworld of soil that plant roots interact with perhaps the most complex microcosm of organisms, from bacteria, archaea and fungi to single‐celled animals as well as multicellular animals such as nematodes and earth worms. This soil microbiome profoundly alters plant growth and in turn depends on root secretion and is shaped by plant immunity. Summary: This article is about life underground. More specifically it is about the rhizosphere, the zone where plant roots meet the soil. The whole of terrestrial life depends on a few inches of soil. Soil is complicated. The nature of the soil is shaped by the presence of roots. In turn, the microbes in the soil immediately surrounding roots have a profound influence on plant growth and development. The soil microbiome is the community of soil microorganisms. Sampling and analyzing the soil microbiome and the way in which microbes and roots recognize and associate with each other are technically challenging. Here, we discuss new ways to reveal what is happening hidden beneath the soil surface. [ABSTRACT FROM AUTHOR]

The attachment of bacteria to roots constitutes the first physical step in many plant–microbe interactions. These interactions exert both positive and negative influences on agricultural systems depending on whether a growth-promoting, symbiotic or pathogenic relationship transpires. A common biphasic mechanism of root attachment exists across agriculturally important microbial species, including Rhizobium, Agrobacterium, Pseudomonas, Azospirillum and Salmonella. Attachment studies have revealed how plant–microbe interactions develop, and how to manipulate these relationships for agricultural benefit. Here, we review our current understanding of the molecular mechanisms governing plant–microbe root attachment and draw together a common biphasic model. [ABSTRACT FROM AUTHOR]

The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth. [ABSTRACT FROM AUTHOR]

The article focuses on the relationship between bacteria and roots which are critical to the terrestrial ecosystem. Topics discusses include regions of rhizosphere, offers information on microbiome which consists of commensals, symbionts and pathogens and imaging of roots with X-ray computed tomography scanning.

Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems. [ABSTRACT FROM AUTHOR]

Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems. [ABSTRACT FROM AUTHOR]

Bacteria have evolved a wide variety of metabolic strategies to cope with varied environments. Some are specialists and only able to survive in restricted environments; others are generalists and able to cope with diverse environmental conditions. Rhizobia (e.g. Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium and Azorhizobium species) can survive and compete for nutrients in soil and the plant rhizosphere but can also form a beneficial symbiosis with legumes in a highly specialized plant cell environment. Inside the legume-root nodule, the bacteria (bacteroids) reduce dinitrogen to ammonium, which is secreted to the plant in exchange for a carbon and energy source. A new and challenging aspect of nodule physiology is that nitrogen fixation requires the cycling of amino acids between the bacteroid and plant. This review aims to summarize the metabolic plasticity of rhizobia and the importance of amino acid cycling. [Copyright &y& Elsevier]

Discusses the occurrence of nitrogen fixation within legume nodules due to metabolic exchange between bacteria of the family Rhizobiaciae and the plant host. Supply of carbon to differentiated bacterial cells bacteroids; Transfer of fixed nitrogen to the plant; Regulation of the exchange of metabolites through bacteroids and plant-derived peribacteroid membrane.

Focuses on a study conducted to initiate how the dctA, dctB and dctD promoters are regulated by inducers with emphasis on the bacterium Phizobium leguminosarum. Identification of the materials used to conduct the study; Information on the study methodology; What the results showed; Discussion on the findings.

Demonstrates that the Tnc5 mutant (RU301) of Rhizobium leguminosarum is a lipopolysaccharide (LPS) rough mutant. Isolation of dct and LPS mutants of R. leguminosarum; Effect of calcium and magnesium levels on growth and LPS; Plant properties; Complementation and mapping of strain RU301; Localization of the dct and lps genes of R. leguminosarum.

Investigates the regulation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae. Isolation of mutants; Catabolite repression of the pathway for myo-inositol catabolism; Role of the dct system in the catabolite repression of myo-inositol-degrading enzymes; Properties on plants of mutant strains unable to utilize myo-inositol.

For nanowire-based sources of non-classical light, the rate at which photons are generated and the ability to efficiently collect them are determined by the nanowire geometry. Using selective-area vapour-liquid-solid epitaxy, we show how it is possible to control the nanowire geometry and tailor it to optimise device performance. High efficiency single photon generation with negligible multi-photon emission is demonstrated using a quantum dot embedded in a nanowire having a geometry tailored to optimise both collection efficiency and emission rate. [ABSTRACT FROM AUTHOR]

Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For this bacterium, gene expression data are available, but functional gene annotation is less well developed than for other model organisms. More annotations could lead to a better understanding of the pathways for growth, plant colonization, and nitrogen fixation in R. leguminosarum. In this study, we present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or to a prioritized list of genes for further study. [ABSTRACT FROM AUTHOR]

We reported nucleation mechanisms of InP directly on Si (8% lattice mismatch) under confined structures, called micro-crucibles, at ultra-high vacuum (UHV) by chemical beam epitaxy. These micro-crucibles are used to induce lateral growth in the presence of a micro-scale Au catalyst. It is found that at this UHV condition, the kinetics is dictated predominantly by adatom surface diffusion. Using a two-step growth process ((1) In-only exposure, then, (2) simultaneous In and P exposures), InP islands have been successfully nucleated on Si substrates under micro-crucible structures. The nucleation of these InP islands strongly depends on the metal catalyst location relative to the micro-crucible opening with metal catalysts residing closer to the opening having a higher chance to get incorporated with In and P atoms. Importantly, we found that using smaller micro-crucibles with double openings can increase the possibility of having metal catalysts reside near either opening and nucleate InP under micro-crucibles. [ABSTRACT FROM AUTHOR]

Summary: Legume nodulation requires the detection of flavonoids in the rhizosphere by rhizobia to activate their production of Nod factor countersignals. Here we investigated the flavonoids involved in nodulation of Medicago truncatula.We biochemically characterized five flavonoid‐O‐methyltransferases (OMTs) and a lux‐based nod gene reporter was used to investigate the response of Sinorhizobium medicae NodD1 to various flavonoids.We found that chalcone‐OMT 1 (ChOMT1) and ChOMT3, but not OMT2, 4, and 5, were able to produce 4,4′‐dihydroxy‐2′‐methoxychalcone (DHMC). The bioreporter responded most strongly to DHMC, while isoflavones important for nodulation of soybean (Glycine max) showed no activity. Mutant analysis revealed that loss of ChOMT1 strongly reduced DHMC levels. Furthermore, chomt1 and omt2 showed strongly reduced bioreporter luminescence in their rhizospheres. In addition, loss of both ChOMT1 and ChOMT3 reduced nodulation, and this phenotype was strengthened by the further loss of OMT2.We conclude that: the loss of ChOMT1 greatly reduces root DHMC levels; ChOMT1 or OMT2 are important for nod gene activation in the rhizosphere; and ChOMT1/3 and OMT2 promote nodulation. Our findings suggest a degree of exclusivity in the flavonoids used for nodulation in M. truncatula compared to soybean, supporting a role for flavonoids in rhizobial host range. [ABSTRACT FROM AUTHOR]

Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays. Plants secrete root exudates into the rhizosphere to attract beneficial microbes. This study shows that barley genotype exerts multi-level selective pressure on the soil Pseudomonas population, affecting overall abundance, genotype and individual genetic features as well as expression of specific genes. [ABSTRACT FROM AUTHOR]

An on-demand source of bright entangled photon pairs is desirable for quantum key distribution (QKD) and quantum repeaters. The leading candidate to generate such pairs is based on spontaneous parametric down-conversion (SPDC) in non-linear crystals. However, its pair extraction efficiency is limited to 0.1% when operating at near-unity fidelity due to multiphoton emission at high brightness. Quantum dots in photonic nanostructures can in principle overcome this limit, but the devices with high entanglement fidelity (99%) have low pair extraction efficiency (0.01%). Here, we show a measured peak entanglement fidelity of 97.5% ± 0.8% and pair extraction efficiency of 0.65% from an InAsP quantum dot in an InP photonic nanowire waveguide. We show that the generated oscillating two-photon Bell state can establish a secure key for peer-to-peer QKD. Using our time-resolved QKD scheme alleviates the need to remove the quantum dot energy splitting of the intermediate exciton states in the biexciton-exciton cascade. Spontaneous parametric down-conversion, the standard technique for generating entangled photons, is limited by low pair extraction efficiencies at near-unity fidelity. The authors show quantum dots in nanowires efficiently emit an oscillating state with near-unity entanglement fidelity and propose a time-resolved quantum key distribution protocol. [ABSTRACT FROM AUTHOR]

Motility and chemotaxis are crucial processes for soil bacteria and plant–microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free‐living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism‐based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free‐living cell in the rhizosphere, and at different stages of the symbiosis. [ABSTRACT FROM AUTHOR]

Single photon sources operating on-demand at telecom wavelengths are required in fiber-based quantum secure communication technologies. In this work, we demonstrate single photon emission from position-controlled nanowire quantum dots emitting at λ > 1530 nm. Emission in the C-band is achieved by composition engineering of an InAsxP1−x dot-in-a-rod structure. Using above-band pulsed excitation, we obtain single photon purities of g (2) (0) = 0.062. These results represent an important step toward the scalable manufacture of high efficiency, high rate single photon emitters in the telecom C-band. [ABSTRACT FROM AUTHOR]

The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [ 1,2 ]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control, the microbiome is still able to adapt and thrive. The molecular knowledge behind these interactions and microbial ‘-omic’ technologies are developing to the point of enabling holobiont engineering. For a long time microorganisms were in the background of plant biology but new multidisciplinary approaches have led to an appreciation of the importance of the holobiont, where plants and microbes are interdependent. [ABSTRACT FROM AUTHOR]

Symbioticrhizobia in legumes account for a large portion of nitrogen fixation in the biosphere. Nitrogen fixation is an energy-demanding process requiring tight control of metabolism and redox state. It is of great interest to understand the bacteroid differentiation process and the roles of energy storage molecules, such as glycogen and polyhydroxybutyrate(PHB), in maintaining the Rhizobium-legume symbioses. Traditional biochemical assays for checking phenotypic changes of mutants require a large volume of starting materials, which is difficult for unculturable, terminally differentiated bacteroids. Here we present a label-free technique that allows the identification and characterization of phenotypic changes of bacteria at the single-cell level. This work demonstrates the application of single-cell Raman spectra (SCRS) to differentiate Rhizobium leguminosarum bv. viciae wild-type and mutants under differentconditions.We found symbiotically differentiated bacteroids and free-living bacteria differed primarily at a Raman biomarker, cytochrome c, corresponding to a bacteroid-specific terminal oxidase. We demonstrated that, for the first time, SCRS were able to link phenotypic changes and specific genetic mutants, in this case, single and double mutations in synthesis of carbon storage molecules glycogen and polyhydroxybutyrate (PHB). By analyzing SCRS of these mutants, it provides insights into metabolite production and carbon regulatory network of rhizobia. [ABSTRACT FROM AUTHOR]

Controlling the morphology and composition of semiconductor nano- and micro-structures is crucial for fundamental studies and applications. Here, Si-Ge semiconductor nanostructures were fabricated using photolithographically defined micro-crucibles on Si substrates. Interestingly, the nanostructure morphology and composition of these structures are strongly dependent on the size of the liquid–vapour interface (i.e., the opening of the micro-crucible) in the CVD deposition step of Ge. In particular, Ge crystallites nucleate in micro-crucibles with larger opening sizes (3.74–4.73 μm2), while no such crystallites are found in micro-crucibles with smaller openings of 1.15 μm2. This interface area tuning also results in the formation of unique semiconductor nanostructures: lateral nano-trees (for smaller openings) and nano-rods (for larger openings). Further TEM imaging reveals that these nanostructures have an epitaxial relationship with the underlying Si substrate. This geometrical dependence on the micro-scale vapour–liquid–solid (VLS) nucleation and growth is explained within a dedicated model, where the incubation time for the VLS Ge nucleation is inversely proportional to the opening size. The geometric effect on the VLS nucleation can be used for the fine tuning of the morphology and composition of different lateral nano- and micro-structures by simply changing the area of the liquid–vapour interface. [ABSTRACT FROM AUTHOR]

Engineering signalling between plants and microbes could be exploited to establish host‐specificity between plant‐growth‐promoting bacteria and target crops in the environment. We previously engineered rhizopine‐signalling circuitry facilitating exclusive signalling between rhizopine‐producing (RhiP) plants and model bacterial strains. Here, we conduct an in‐depth analysis of rhizopine‐inducible expression in bacteria. We characterize two rhizopine‐inducible promoters and explore the bacterial host‐range of rhizopine biosensor plasmids. By tuning the expression of rhizopine uptake genes, we also construct a new biosensor plasmid pSIR05 that has minimal impact on host cell growth in vitro and exhibits markedly improved stability of expression in situ on RhiP barley roots compared to the previously described biosensor plasmid pSIR02. We demonstrate that a sub‐population of Azorhizobium caulinodans cells carrying pSIR05 can sense rhizopine and activate gene expression when colonizing RhiP barley roots. However, these bacteria were mildly defective for colonization of RhiP barley roots compared to the wild‐type parent strain. This work provides advancement towards establishing more robust plant‐dependent control of bacterial gene expression and highlights the key challenges remaining to achieve this goal. [ABSTRACT FROM AUTHOR]

The plant common symbiosis signalling (SYM) pathway has shared function between interactions with rhizobia and arbuscular mycorrhizal fungi, the two most important symbiotic interactions between plants and microorganisms that are crucial in plant and agricultural yields. Here, we determine the role of the plant SYM pathway in the structure and abundance of the microbiota in the model legume Medicago truncatula and whether this is controlled by the nitrogen or phosphorus status of the plant. We show that SYM mutants (dmi3) differ substantially from the wild type (WT) in the absolute abundance of the root microbiota, especially under nitrogen limitation. Changes in the structure of the microbiota were less pronounced and depended on both plant genotype and nutrient status. Thus, the SYM pathway has a major impact on microbial abundance in M. truncatula and also subtly alters the composition of the microbiota. [ABSTRACT FROM AUTHOR]

We have combined ultrasensitive force-based spin detection with high-fidelity spin control to achieve NMR diffraction (NMRd) measurement of ∼2 million 31P spins in a (50 nm)³ volume of an indium-phosphide (InP) nanowire. NMRd is a technique originally proposed for studying the structure of periodic arrangements of spins, with complete access to the spectroscopic capabilities of NMR. We describe two experiments that realize NMRd detection with subangstrom precision. In the first experiment, we encode a nanometer-scale spatial modulation of the z -axis magnetization of 31P spins and detect the period and position of the modulation with a precision of <0.8 ˚ A. In the second experiment, we demonstrate an interferometric technique, utilizing NMRd, to detect an angstrom-scale displacement of the InP sample with a precision of 0.07 ˚ A. The diffraction-based techniques developed in this work extend the Fourier-encoding capabilities of NMR to the angstrom scale and demonstrate the potential of NMRd as a tool for probing the structure and dynamics of nanocrystalline materials. [ABSTRACT FROM AUTHOR]

We report on the far field emission profile of pure wurtzite InP nanowires in comparison to InP nanowires with predominantly zincblende crystal structure. The emission profile is measured on individual nanowires using Fourier microscopy. The most intense photoluminescence of wurtzite nanowires is collected at small angles with respect to the nanowire growth axis. In contrast, zincblende nanowires present a minimum of the collected light intensity in the direction of the nanowire growth. Results are explained by the orientation of electric dipoles responsible for the photoluminescence, which is different from wurtzite to zincblende. Wurtzite nanowires have dipoles oriented perpendicular to the nanowire growth direction, whereas zincblende nanowires have dipoles oriented along the nanowire axis. This interpretation is confirmed by both numerical simulations and polarization dependent photoluminescence spectroscopy. Knowledge of the dipole orientation in nanostructures is crucial for developing a wide range of photonic devices such as light-emitting diodes, photodetectors, and solar cells. [ABSTRACT FROM AUTHOR]

Salicylic acid is an important signalling molecule in plant-microbe defence and symbiosis. We analysed the transcriptional responses of the nitrogen fixing plant symbiont, Rhizobium leguminosarum bv viciae 3841 to salicylic acid. Two MFS-type multicomponent efflux systems were induced in response to salicylic acid, rmrAB and the hitherto undescribed system salRAB. Based on sequence similarity salA and salB encode a membrane fusion and inner membrane protein respectively. salAB are positively regulated by the LysR regulator SalR. Disruption of salA significantly increased the sensitivity of the mutant to salicylic acid, while disruption of rmrA did not. A salA/rmrA double mutation did not have increased sensitivity relative to the salA mutant. Pea plants nodulated by salA or rmrA strains did not have altered nodule number or nitrogen fixation rates, consistent with weak expression of salA in the rhizosphere and in nodule bacteria. However, BLAST analysis revealed seventeen putative efflux systems in Rlv3841 and several of these were highly differentially expressed during rhizosphere colonisation, host infection and bacteroid differentiation. This suggests they have an integral role in symbiosis with host plants. [ABSTRACT FROM AUTHOR]

Due to the costly energy demands of nitrogen (N) fixation, diazotrophic bacteria have evolved complex regulatory networks that permit expression of the catalyst nitrogenase only under conditions of N starvation, whereas the same condition stimulates upregulation of high-affinity ammonia (NH3) assimilation by glutamine synthetase (GS), preventing excess release of excess NH3 for plants. Diazotrophic bacteria can be engineered to excrete NH3 by interference with GS, however control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target plants. Here, we tested two strategies to control GS regulation and NH3 excretion in our model cereal symbiont Azorhizobium caulinodans AcLP, a derivative of ORS571. We first attempted to recapitulate previous work where mutation of both PII homologues glnB and glnK stimulated GS shutdown but found that one of these genes was essential for growth. Secondly, we expressed unidirectional adenylyltransferases (uATs) in a ΔglnE mutant of AcLP which permitted strong GS shutdown and excretion of NH3 derived from N2 fixation and completely alleviated negative feedback regulation on nitrogenase expression. We placed a uAT allele under control of the NifA-dependent promoter PnifH, permitting GS shutdown and NH3 excretion specifically under microaerobic conditions, the same cue that initiates N2 fixation, then deleted nifA and transferred a rhizopine nifAL94Q/D95Q-rpoN controller plasmid into this strain, permitting coupled rhizopine-dependent activation of N2 fixation and NH3 excretion. This highly sophisticated and multi-layered control circuitry brings us a step closer to the development of a "synthetic symbioses" where N2 fixation and NH3 excretion could be specifically activated in diazotrophic bacteria colonising transgenic rhizopine producing cereals, targeting delivery of fixed N to the crop while preventing interaction with non-target plants. Author summary: Inoculation of cereal crops with associative diazotrophic bacteria that convert atmospheric nitrogen (N2) into ammonia (NH3) could be used to sustainably improve delivery of nitrogen to crops. However, due to the costly energy demands of N2 fixation, bacteria restrict excess production of NH3 and release to the plants. Diazotrophs can be engineered for excess NH3 production and release, however genetic control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target weed species. Here, we engineer coupled control of N2 fixation and NH3 release in response to the signalling molecule rhizopine supplemented in vitro. This control circuitry represents a prototype for the future development of a "synthetic symbiosis" where bacterial N2 fixation and NH3 excretion could be specifically activated following colonisation of transgenic rhizopine producing cereals in the field, minimising bacterial energy requirements and preventing provision of NH3 to non-target plants. [ABSTRACT FROM AUTHOR]

Resonant excitation of the biexciton state in an InAsP quantum dot by a phase-coherent pair of picosecond pulses allows preparing time-bin entangled pairs of photons via the biexciton–exciton cascade. We show that this scheme can be implemented for a dot embedded in an InP nanowire. The underlying physical mechanisms can be represented and quantitatively analyzed by an effective three-level open system master equation. Simulation parameters including decay and intensity dependent dephasing rates are extracted from experimental data, which in turn let us predict the resulting entanglement and optimal operating conditions. [ABSTRACT FROM AUTHOR]

Rhizobial bacteria enter a symbiotic association with leguminous plants, resulting in differentiated bacteria enclosed in intracellular compartments called symbiosomes within nodules on the root. The nodules and associated symbiosomes are structured for efficient nitrogen fixation. Although the interaction is beneficial to both partners, it comes with rigid rules that are strictly enforced by the plant. Entry into root cells requires appropriate recognition of the rhizobial Nod factor signaling molecule, and this recognition activates a series of events, including polarized root-hair tip growth, invagination associated with bacterial infection, and the promotion of cell division in the cortex leading to the nodule meristem. The plant's command of the infection process has been highlighted by its enforcement of terminal differentiation upon the bacteria within nodules of some legumes, and this can result in a loss of bacterial viability while permitting effective nitrogen fixation. Here, we review the mechanisms by which the plant allows bacterial infection and promotes the formation of the nodule, as well as the details of how this intimate association plays out inside the cells of the nodule where a complex interchange of metabolites and regulatory peptides force the bacteria into a nitrogen-fixing organelle-like state. [ABSTRACT FROM AUTHOR]

Engineering N2-fixing symbioses between cereals and diazotrophic bacteria represents a promising strategy to sustainably deliver biologically fixed nitrogen (N) in agriculture. We previously developed novel transkingdom signaling between plants and bacteria, through plant production of the bacterial signal rhizopine, allowing control of bacterial gene expression in association with the plant. Here, we have developed both a homozygous rhizopine producing (RhiP) barley line and a hybrid rhizopine uptake system that conveys upon our model bacterium Azorhizobium caulinodans ORS571 (Ac) 10 improved sensitivity for rhizopine perception. Using this improved genetic circuitry, we established tight rhizopine-dependent transcriptional control of the nitrogenase master regulator nifA and the N metabolism s-factor rpoN, which drove nitrogenase expression and activity in vitro and in situ by bacteria colonizing RhiP barley roots. Although in situ nitrogenase activity was suboptimally effective relative to the wild-type strain, activation was specific to RhiP barley and was not observed on the roots of wild-type plants. This work represents a key milestone toward the development of a synthetic plant-controlled symbiosis in which the bacteria fix N2 only when in contact with the desired host plant and are prevented from interaction with nontarget plant species. [ABSTRACT FROM AUTHOR]

Summary: Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore‐space, and models of AMF‐enhanced P‐uptake are poorly validated.We used synchrotron X‐ray computed tomography to visualize mycorrhizas in soil and synchrotron X‐ray fluorescence/X‐ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co‐locate with areas of high P and low Al, and preferentially associate with organic‐type P species over Al‐rich inorganic P.We discovered that AMF avoid Al‐rich areas as a source of P. Sulphur‐rich regions were found to be correlated with higher hyphal density and an increased organic‐associated P‐pool, whilst oxidized S‐species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome‐related. Our experimentally‐validated model led to an estimate of P‐uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated – a result with significant implications for the modelling of plant–soil–AMF interactions. [ABSTRACT FROM AUTHOR]

We study experimentally and theoretically the in-plane magnetic field dependence of the coupling between dots forming a vertically stacked double dot molecule. The InAsP molecule is grown epitaxially in an InP nanowire and interrogated optically at millikelvin temperatures. The strength of interdot tunneling, leading to the formation of the bonding-antibonding pair of molecular orbitals, is investigated by adjusting the sample geometry. For specific geometries, we show that the interdot coupling can be controlled in-situ using a magnetic field-mediated redistribution of interdot coupling strengths. This is an important milestone in the development of qubits required in future quantum information technologies. [ABSTRACT FROM AUTHOR]

Examines the identification of Rhizobium leguminosarum bv. viciae VF39 gene encoding a gamma-aminobutyrate (GABA) aminotransferase. Involvement of the gene in GABA metabolism; Bacterial strains and plasmids; Preparation of cell extracts.

We present a compact, fibre-coupled single photon source using gradient-index (GRIN) lenses and an InAsP semiconductor quantum dot embedded within an InP photonic nanowire waveguide. A GRIN lens assembly is used to collect photons close to the tip of the nanowire, coupling the light immediately into a single mode optical fibre. The system provides a stable, high brightness source of fibre-coupled single photons. Using pulsed excitation, we demonstrate on-demand operation with a single photon purity of 98.5% when exciting at saturation in a device with a source-fibre collection efficiency of 35% and an overall single photon collection efficiency of 10%. We also demonstrate "plug and play" operation using room temperature photoluminescence from the InP nanowire for room temperature alignment. [ABSTRACT FROM AUTHOR]

Summary: Bacterial colonization of the rhizosphere is critical for the establishment of plant–bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria–bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration. [ABSTRACT FROM AUTHOR]

Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs that host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate the global reprogramming of physiological processes and the rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and, more recently, computational modeling. Here, we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship. [ABSTRACT FROM AUTHOR]

Motivation Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information. Results We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods, such as Pearson correlation and mutual information. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson correlation or mutual information. Availability and implementation Code is available online (https://github.com/javier-pardodiaz/sdcorGCN). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

We report on the design, growth, fabrication, and performance of InAs/InP quantum dash (QD) multi-wavelength lasers (MWLs) developed by the National Research Council (NRC) Canada. The key technical specifications investigated include optical and RF beating spectra, relative intensity noise (RIN), and optical phase noise of each individual wavelength channel. Data bandwidth transmission capacity of 5.376 Tbit/s and 10.8 Tbit/s respectively in the PAM-4 and 16-QAM modulation formats are demonstrated using only a single C-band QD 34.2-GHz MWL chip. We have also developed a monolithic InAs/InP QD dual-wavelength (DW) DFB laser as a compact optical beat source to generate millimeter-wave (MMW) signals. Due to the common cavity, highly coherent and correlated optical modes with optical linewidth as low as 15.83 kHz, spectrally pure MMW signals around 46.8 GHz with a linewidth down to 26.1 kHz were experimentally demonstrated. By using this QD DW-DFB laser, a one GBaud (2 Gbps) MMW over-fiber transmission link is demonstrated with PAM-4 signals. The results show that the demonstrated device is suitable for high speed high capacity MMW fiber-wireless integrated fronthaul of 5G networks. [ABSTRACT FROM AUTHOR]

Legumes are high in protein and form a valuable part of human diets due to their interaction with symbiotic nitrogen-fixing bacteria known as rhizobia. Plants house rhizobia in specialized root nodules and provide the rhizobia with carbon in return for nitrogen. However, plants usually housemultiple rhizobial strains that vary in their fixation ability, so the plant faces an investment dilemma. Plants are known to sanction strains that do not fix nitrogen, but nonfixers are rare in field settings, while intermediate fixers are common. Here, we modeled how plants should respond to an intermediate fixer that was otherwise isogenic and tested model predictions using pea plants. Intermediate fixers were only tolerated when a better strain was not available. In agreement with model predictions, nodules containing the intermediate-fixing strain were large and healthy when the only alternative was a nonfixer, but nodules of the intermediate-fixing strain were small and white when the plant was coinoculated with a more effective strain. The reduction in nodule size was preceded by a lower carbon supply to the nodule even before differences in nodule size could be observed. Sanctioned nodules had reduced rates of nitrogen fixation, and in later developmental stages, sanctioned nodules contained fewer viable bacteria than nonsanctioned nodules. This indicates that legumes can make conditional decisions, most likely by comparing a local nodule-dependent cue of nitrogen output with a global cue, giving them remarkable control over their symbiotic partners. [ABSTRACT FROM AUTHOR]

A systematic study of the emission spectra of single InAsP nanowire quantum dots in position-controlled InP photonic nanowire waveguides is presented. Using excitation power-dependent photoluminescence and correlation measurements, we distinguish between the different excitonic complexes responsible for s-shell emission. From measurements of over 40 nominally identical devices, we obtain a standard deviation of ∼ 5 meV in the emission energy of excitons, biexcitons, and charged exciton photons. The mean biexciton binding energy was 1.9 meV with a standard deviation of ∼ 0.8 meV. The experimental spectra are understood using atomistic multi-million atom theory of neutral and charged multi-exciton complexes implemented in the design tool QNANO. [ABSTRACT FROM AUTHOR]

Regulation by oxygen (O2) in rhizobia is essential for their symbioses with plants and involves multiple O2 sensing proteins. Three sensors exist in the pea microsymbiont Rhizobium leguminosarum Rlv3841: hFixL, FnrN and NifA. At low O2 concentrations (1%) hFixL signals via FxkR to induce expression of the FixK transcription factor, which activates transcription of downstream genes. These include fixNOQP, encoding the high-affinity cbb3-type terminal oxidase used in symbiosis. In free-living Rlv3841, the hFixL-FxkR-FixK pathway was active at 1% O2, and confocal microscopy showed hFixL-FxkR-FixK activity in the earliest stages of Rlv3841 differentiation in nodules (zones I and II). Work on Rlv3841 inside and outside nodules showed that the hFixL-FxkR-FixK pathway also induces transcription of fnrN at 1% O2 and in the earliest stages of Rlv3841 differentiation in nodules. We confirmed past findings suggesting a role for FnrN in fixNOQP expression. However, unlike hFixL-FxkR-FixK, Rlv3841 FnrN was only active in the near-anaerobic zones III and IV of pea nodules. Quantification of fixNOQP expression in nodules showed this was driven primarily by FnrN, with minimal direct hFixL-FxkR-FixK induction. Thus, FnrN is key for full symbiotic expression of fixNOQP. Without FnrN, nitrogen fixation was reduced by 85% in Rlv3841, while eliminating hFixL only reduced fixation by 25%. The hFixL-FxkR-FixK pathway effectively primes the O2 response by increasing fnrN expression in early differentiation (zones I-II). In zone III of mature nodules, near-anaerobic conditions activate FnrN, which induces fixNOQP transcription to the level required for wild-type nitrogen fixation activity. Modelling and transcriptional analysis indicates that the different O2 sensitivities of hFixL and FnrN lead to a nuanced spatiotemporal pattern of gene regulation in different nodule zones in response to changing O2 concentration. Multi-sensor O2 regulation is prevalent in rhizobia, suggesting the fine-tuned control this enables is common and maximizes the effectiveness of the symbioses. Author summary: Rhizobia are soil bacteria that form a symbiosis with legume plants. In exchange for shelter from the plant, rhizobia provide nitrogen fertilizer, produced by nitrogen fixation. Fixation is catalysed by the nitrogenase enzyme, which is inactivated by oxygen. To prevent this, plants house rhizobia in root nodules, which create a low oxygen environment. However, rhizobia need oxygen, and must adapt to survive the low oxygen concentration in the nodule. Key to this is regulating their genes based on oxygen concentration. We studied one Rhizobium species which uses three different protein sensors of oxygen, each turning on at a different oxygen concentration. As the bacteria get deeper inside the plant nodule and the oxygen concentration drops, each sensor switches on in turn. Our results also show that the first sensor to turn on, hFixL, primes the second sensor, FnrN. This prepares the rhizobia for the core region of the nodule where oxygen concentration is lowest and most nitrogen fixation takes place. If both sensors are removed, the bacteria cannot fix nitrogen. Many rhizobia have several oxygen sensing proteins, so using multiple sensors is likely a common strategy enabling rhizobia to adapt to low oxygen precisely and in stages during symbiosis. [ABSTRACT FROM AUTHOR]

Malonyl-coenzyme A (CoA) decarboxylase, malonyl-CoA synthetase, and malonate transporter mutants of Rhizobium leguminosarum bv. viciae and trifolii fixed N2 at wild-type rates on pea and clover, respectively. Thus, malonate does not drive N2 fixation in legume nodules. [ABSTRACT FROM AUTHOR]

A method to fine-tune photonic crystal defect cavities is developed based on successive oxidation and wet etching cycles. Photonic crystal microcavities based on InP membranes are oxidized using an ultraviolet (UV)/ozone treatment, and the oxide is subsequently removed using a hydrofluoric acid solution. Each oxidation/etch cycle consumes a thin layer of InP directly exposed to the UV/ozone, enlarging the radius of holes in the photonic crystal and decreasing the membrane thickness. The method is applied to single missing air-hole defect cavities with embedded InAs quantum dots, permitting measurement of the resonant frequency tuning in emission. Defect mode energies were found to blueshift 1.74 meV per cycle, consistent with finite-difference time-domain simulations. A tuning range of 33 meV was obtained after 20 cycles. [ABSTRACT FROM AUTHOR]

Deletion of both alanine dehydrogenase genes (aldA) in Mesorhizobium loti resulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of Lotus corniculatus plants. Thus, neither indeterminate pea nodules nor determinate L. corniculatus nodules export alanine as the sole nitrogen secretion product. [ABSTRACT FROM AUTHOR]

By analyzing successive lifestyle stages of a model Rhizobium– legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N2-fixing bacteroids, and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 transfer RNAs, and 5 RNA features) are required for the competitive ability to nodulate pea and fix N2. Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphere progressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signaling, N2 fixation, and metabolic adaptation. Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism, and glutamine synthesis (GlnII). There are 17 separate lifestyle adaptations specific to rhizosphere growth and 23 to root colonization, distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium–legume symbiosis. [ABSTRACT FROM AUTHOR]

Background and aims: Plant and bacteria are able to synthesise proline, which acts as a compound to counteract the negative effects of osmotic stresses. Most methodologies rely on the extraction of compounds using destructive methods. This work describes a new proline biosensor that allows the monitoring of proline levels in a non-invasive manner in root exudates and nodules of legume plants. Methods: The proline biosensor was constructed by cloning the promoter region of pRL120553, a gene with high levels of induction in the presence of proline, in front of the lux cassette in Rhizobium leguminosarum bv. viciae. Results: Free-living assays show that the proline biosensor is sensitive and specific for proline. Proline was detected in both root exudates and nodules of pea plants. The luminescence detected in bacteroids did not show variations during osmotic stress treatments, but significantly increased during recovery. Conclusions: This biosensor is a useful tool for the in vivo monitoring of proline levels in root exudates and bacteroids of symbiotic root nodules, and it contributes to our understanding of the metabolic exchange occurring in nodules under abiotic stress conditions. [ABSTRACT FROM AUTHOR]

The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells “blind” to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance. [ABSTRACT FROM AUTHOR]