An increasing opine carbon bias in artificial exudation systems and genetically modified plant rhizospheres leads to an increasing reshaping of bacterial populations

Evolutionary Fate of the Opine Synthesis Genes in the Arachis L. Genomes

Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of "Agrobacterium". In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts.

Synthetic microbe-to-plant communication channels

Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.

Application of plant specialized metabolites to modulate soil microbiota

Plant specialized metabolites (PSMs) are considerably diverse compounds with multifaceted roles in the adaptation of plants to various abiotic and biotic stresses. PSMs are frequently secreted into the rhizosphere, a small region around the roots, where they facilitate interactions between plants and soil microorganisms. PSMs shape the host-specific rhizosphere microbial communities that potentially influence plant growth and tolerance to adverse conditions. Plant mutants defective in PSM biosynthesis contribute to reveal the roles of each PSM in plant-microbiota interactions in the rhizosphere. Recently, various approaches have been used to directly supply PSMs to soil by in vitro methods or through addition in pots with plants. This review focuses on the feasibility of the direct PSM application methods to reveal rhizospheric plant-microbiota interactions and discusses the possibility of applying the knowledge gained to future engineering of rhizospheric traits.

Rhizopine biosensors for plant-dependent control of bacterial gene expression

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.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Engineered plant control of associative nitrogen fixation

Inoculation of cereals with diazotrophic (N₂-fixing) bacteria offers a sustainable alternative to the application of nitrogen fertilizers in agriculture. While natural diazotrophs have evolved multilayered regulatory mechanisms that couple N₂ fixation with assimilation of the product NH₃ and prevent release to plants, genetic modifications can permit excess production and excretion of NH₃. However, a lack of stringent host-specificity for root colonization by the bacteria would allow growth promotion of target and nontarget plants species alike. Here, we exploit synthetic transkingdom signaling to establish plant host-specific control of the N₂-fixation catalyst nitrogenase in Azorhizobium caulinodans occupying barley roots. This work demonstrates how partner-specific interactions can be established to avoid potential growth promotion of nontarget plants.

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) 10³-fold 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 σ-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.

Identification and Quantitation of Taste-Active Compounds in Dried Scallops by Combined Application of the Sensomics and a Quantitative NMR Approach

Application of the sensomics concept on dried scallops, a Japanese specialty produced from the adductor muscle of scallops, revealed after activity-guided fractionation with subsequent (comparative) taste dilution analyses besides nucleotides, amino acids, organic acids, and inorganic ions, the presence of taste-modulating quaternary ammonium compounds and opines in highly taste-active fractions. In order to recreate the taste of dried scallops, two independent quantitation approaches were applied and compared. The first approach used multiple targeted UHPLC-MS/MS and high-performance ion chromatography methods. Besides already established quantitation methods for basic taste compounds, a new HILIC-UHPLC-MS/MS_MRM method for the quantitation of chromatographically challenging opines, using synthesized stable isotope-labeled standards, was developed. Furthermore, a qHNMR approach was applied, enabling a direct identification and quantitation of organic taste compounds in a food extract without prior fractionation using a reference ¹H NMR database. Both methods yielded similar quantitative results of taste-active compounds in dried scallop extracts and subsequent taste recombination experiments based on these data were able to recreate the taste of dried scallops.

Opine biosynthesis in naturally transgenic plants: Genes and products

The plant pathogen Agrobacterium transfers DNA into plant cells by a specific transfer mechanism. Expression of this transferred DNA or T-DNA leads to crown gall tumors or abnormal, hairy roots and the synthesis of specific compounds, called opines. Opines are produced from common plant metabolites like sugars, amino acids and α-keto acids, which are combined into different low molecular weight structures by T-DNA-encoded opine synthase enzymes. Opines can be converted back by Agrobacterium into the original metabolites and used for agrobacterial growth. Recently it has been discovered that about 7% of Angiosperms carry T-DNA-like sequences. These result from ancient Agrobacterium transformation events, followed by spontaneous regeneration of transformed cells into natural genetically transformed organisms (nGMOs). Nearly all nGMOs identified up to date carry opine synthesis genes, several of these are intact and potentially encode opine synthesis. So far, only tobacco and cuscuta have been demonstrated to contain opines. Whereas opines from crown gall and hairy root tissues have been studied for over 60 years, those from the nGMOs remain to be explored.

Engineering the plant microbiota in the context of the theory of ecological communities

Crop-associated microorganisms are known to have a determining influence on crop growth and resistance to stresses. Indeed, microorganisms can deter pathogens, reduce stress levels, improve nutrition, and stimulate growth. However, the microbial communities associated with a plant are rarely optimal for agricultural needs. But how can we engineer crops-associated microbial communities? An interesting framework to address this question is the theory of ecological communities that stipulates four processes by which communities can change: 1) selection, 2) dispersal, 3) speciation and 4) ecological drift. Of these, speciation and dispersal can result in the addition of new species to the plant microbiota, whereas selection and drift can lead to the loss of species. We believe that if these mechanisms are sufficiently understood, they could be harnessed to purposefully engineer the crop microbiota. Here, we will discuss the recent efforts to modify the phenotype of plants that are aligned with these ecological processes.

Engineering Posttranslational Regulation of Glutamine Synthetase for Controllable Ammonia Production in the Plant Symbiont Azospirillum brasilense

Nitrogen requirements for modern agriculture far exceed the levels of bioavailable nitrogen in most arable soils. As a result, the addition of nitrogen fertilizer is necessary to sustain productivity and yields, especially for cereal crops, the planet's major calorie suppliers. Given the unsustainability of industrial fertilizer production and application, engineering biological nitrogen fixation directly at the roots of plants has been a grand challenge for biotechnology. Here, we designed and tested a potentially broadly applicable metabolic engineering strategy for the overproduction of ammonia in the diazotrophic symbiont Azospirillum brasilense. Our approach is based on an engineered unidirectional adenylyltransferase (uAT) that posttranslationally modifies and deactivates glutamine synthetase (GS), a key regulator of nitrogen metabolism in the cell. We show that this circuit can be controlled inducibly, and we leveraged the inherent self-contained nature of our posttranslational approach to demonstrate that multicopy redundancy can improve strain evolutionary stability. uAT-engineered Azospirillum is capable of producing ammonia at rates of up to 500 μM h-1 unit of OD600 (optical density at 600 nm)-1. We demonstrated that when grown in coculture with the model monocot Setaria viridis, these strains increase the biomass and chlorophyll content of plants up to 54% and 71%, respectively, relative to the wild type (WT). Furthermore, we rigorously demonstrated direct transfer of atmospheric nitrogen to extracellular ammonia and then plant biomass using isotopic labeling: after 14 days of cocultivation with engineered uAT strains, 9% of chlorophyll nitrogen in Setaria seedlings was derived from diazotrophically fixed dinitrogen, whereas no nitrogen was incorporated in plants cocultivated with WT controls. This rational design for tunable ammonia overproduction is modular and flexible, and we envision that it could be deployable in a consortium of nitrogen-fixing symbiotic diazotrophs for plant fertilization. IMPORTANCE Nitrogen is the most limiting nutrient in modern agriculture. Free-living diazotrophs, such as Azospirillum, are common colonizers of cereal grasses and have the ability to fix nitrogen but natively do not release excess ammonia. Here, we used a rational engineering approach to generate ammonia-excreting strains of Azospirillum. Our design features posttranslational control of highly conserved central metabolism, enabling tunability and flexibility of circuit placement. We found that our strains promote the growth and health of the model grass S. viridis and rigorously demonstrated that in comparison to WT controls, our engineered strains can transfer nitrogen from 15N2 gas to plant biomass. Unlike previously reported ammonia-producing mutants, our rationally designed approach easily lends itself to further engineering opportunities and has the potential to be broadly deployable.

Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and 'Crack-Entry' Legume Groundnut (Arachis hypogaea L.)

Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as "crack-entry'' mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges.

Current Progress in Nitrogen Fixing Plants and Microbiome Research

In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.

Plant Symbionts Are Engineers of the Plant-Associated Microbiome

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria

The root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N₂. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants.

The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.

Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant

Agrobacterium tumefaciens constructs an ecological niche in its host plant by transferring the T-DNA from its Ti plasmid into the host genome and by diverting the host metabolism. We combined transcriptomics and genetics for understanding the A. tumefaciens lifestyle when it colonizes Arabidopsis thaliana tumors. Transcriptomics highlighted: a transition from a motile to sessile behavior that mobilizes some master regulators (Hfq, CtrA, DivK and PleD); a remodeling of some cell surface components (O-antigen, succinoglucan, curdlan, att genes, putative fasciclin) and functions associated with plant defense (Ef-Tu and flagellin pathogen-associated molecular pattern-response and glycerol-3-phosphate and nitric oxide signaling); and an exploitation of a wide variety of host resources, including opines, amino acids, sugars, organic acids, phosphate, phosphorylated compounds, and iron. In addition, construction of transgenic A. thaliana lines expressing a lactonase enzyme showed that Ti plasmid transfer could escape host-mediated quorum-quenching. Finally, construction of knock-out mutants in A. tumefaciens showed that expression of some At plasmid genes seemed more costly than the selective advantage they would have conferred in tumor colonization. We provide the first overview of A. tumefaciens lifestyle in a plant tumor and reveal novel signaling and trophic interplays for investigating host-pathogen interactions.

Niche Construction and Exploitation by Agrobacterium: How to Survive and Face Competition in Soil and Plant Habitats

Agrobacterium populations live in different habitats (bare soil, rhizosphere, host plants), and hence face different environmental constraints. They have evolved the capacity to exploit diverse resources and to escape plant defense and competition from other microbiota. By modifying the genome of their host, Agrobacterium populations exhibit the remarkable ability to construct and exploit the ecological niche of the plant tumors that they incite. This niche is characterized by the accumulation of specific, low molecular weight compounds termed opines that play a critical role in Agrobacterium 's lifestyle. We present and discuss the functions, advantages, and costs associated with this niche construction and exploitation.

Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate

Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.

Natural Agrobacterium Transformants: Recent Results and Some Theoretical Considerations

Agrobacterium rhizogenes causes hairy root growth on a large number of plant species. It does so by transferring specific DNA fragments (T-DNA) from its root-inducing plasmid (pRi) into plant cells. Expression of T-DNA genes leads to abnormal root growth and production of specific metabolites (opines) which are taken up by the bacterium and used for its growth. Recent work has shown that several Nicotiana, Linaria, and Ipomoea species contain T-DNA genes from A. rhizogenes in their genomes. Plants carrying such T-DNAs (called cellular T-DNA or cT-DNA) can be considered as natural transformants. In the Nicotiana genus, seven different T-DNAs are found originating from different Agrobacterium strains, and in the Tomentosae section no <4 successive insertion events took place. In several cases cT-DNA genes were found to be expressed. In some Nicotiana tabacum cultivars the opine synthesis gene TB-mas2' is expressed in the roots. These cultivars were found to produce opines. Here we review what is known about natural Agrobacterium transformants, develop a theoretical framework to analyze this unusual phenomenon, and provide some outlines for further research.

Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities

Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.

Fitness costs restrict niche expansion by generalist niche-constructing pathogens

We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.

Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.

Engineering the Rhizosphere

All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.

Use of plant colonizing bacteria as chassis for transfer of N₂-fixation to cereals

Engineering cereal crops that are self-supported by nitrogen fixation has been a dream since the 1970s when nitrogenase was transferred from Klebsiella pneumoniae to Escherichia coli. A renewed interest in this area has generated several new approaches with the common aim of transferring nitrogen fixation to cereal crops. Advances in synthetic biology have afforded the tools to rationally engineer microorganisms with traits of interest. Nitrogenase biosynthesis has been a recent target for the application of new synthetic engineering tools. Early successes in this area suggest that the transfer of nitrogenase and other supporting traits to microorganisms that already closely associate with cereal crops is a logical approach to deliver nitrogen to cereal crops.