We've all heard this paradoxical claim: If we want tangible, scientific solutions to society's urgent problems, then we need to invest in basic, curiosity-driven research that’s not motivated by its potential for practical applications. As Vannevar Bush, director of the United States government's chief science agency during World War II famously put it: "Basic research is scientific capital." By investing in basic research— research that is "performed without thought of practical ends"—we create "the fund from which the practical applications of knowledge must be drawn."
It's easy to pay lip service to this idea, but harder to put it into practice, especially when we have to choose how to spend a limited budget. Basic research can seem terribly inefficient. Its practical results are hard to predict, and they often have little to do with the original research goals. Vannevar Bush argued that the best way to support basic research is to give federal funding to academic scientists, who are not under pressure to produce immediately practical results and are “free to pursue the truth wherever it may lead." But this approach is often hard for many to accept because scientists sometimes undertake what seem like wasteful projects with no practical benefits. This leads to accusations that scientists are making poor decisions—in a recent op-ed written with Senator Rand Paul (R-Kentucky), Congressman Lamar Smith (R-Texas), chair of the House Science Committee, complained that, "The academic community forgets that federal science funding should be in the national interest."
When aiming to increase plants' nitrogen (N) budget, special attention is given to the microbial inoculum's capacity to perform biological N₂ fixation. However, we consider that other approaches can be explored. Here, we report initial results of plant growth promoting rhizobacteria (Azospirillum brasilense strains Sp245 and ARG2) capacity to scavenge atmospheric ammonia (NH₃). Using a bipartite Petri dish system, we grew the two A. brasilense strains with the appropriate controls, and with atmospheric NH₃ as a N source. By increasing the atmospheric NH₃ concentration, the growth rate of both A. brasilense strains increased almost 4 times in relation to the controls. By creating a gradient of atmospheric NH₃ concentrations we changed the growth rate of both A. brasilense strains, but its effect differed between the two bacterial strains, i.e., the Sp245 strain increased its growth rates up to pH 9.0, while the ARG2 strain reached maximum growth rates at pH 9.5. The fact that these two plant growth promoting rhizobacteria scavenge atmospheric NH₃, instead of fixing N₂, suggests that this overlooked microbial trait can be an interesting tool to mitigate atmospheric NH₃ concentrations, especially in farming environments.
Jean-Michel Ané's insight:
Well, that's not so surprising. It's less energetically expensive to use ammonium than fixing nitrogen.
Glomalin-related soil protein (GRSP) extracted from soil is considered crucial for the formation and stability of soil aggregates. However, due to limitations in extraction purity and interference from co-extracted products, the actual contribution of pure glomalin produced by arbuscular mycorrhizal fungi (AMF) to soil structure improvement and its specific mechanism of action remain elusive. Here, genetic engineering and cryo-electron microscopy (cryo-EM) are introduced to obtain purified glomalin and to determine its homo-tetradecamer structure. This allowed investigations of the effect of pure glomalin on soil aggregate stability and the specific glomalin-mineral interaction mechanism. The results showed that addition of glomalin significantly enhanced the formation of soil water-stable aggregates and soil macroaggregates. This enhancement was primarily attributed to the strong binding of glomalin to soil minerals, as evidenced by single molecule force spectroscopy (SMFS) and attenuated total reflectance-Fourier transform infrared spectrum (ATR-FTIR) experiments. Glomalin structural analysis, comparison of its amino sequence alignment with that of Escherichia coli heat shock protein 60 (E. coli Hsp60) and mineral binding experiments with several glomalin related mutants highlighted that the N-terminus disordered tail of glomalin composed of ∼39 amino acids were crucial for the glomalin super binding ability. These findings advance the understanding of glomalin's intrinsic mechanism for improving soil structure and open the opportunity for mass production of this ecologically important protein as a soil amendment.
Jean-Michel Ané's insight:
I'm really puzzled by this article. We cloned and used the exact same RiHSP60 sequence, including the N-terminal tail, but we did not obtain any signal with the MAb32B11 antibody. This finding seems difficult to reconcile with the paper we published earlier this year.
Soil phosphorus (P) deficiency can severely limit crop and forage productivity. With limited P resources, breeding programs to select high-P efficiency (HPE) genotypes have been developed, but the role of arbuscular mycorrhizal fungi (AMF) in altering root morphology and physiology to increase P use efficiency and production remains poorly understood. In this study, we compared mycorrhizal responsiveness, and plasticity of root morphological and physiological traits between two low-P efficiency (LPE) and two HPE alfalfa genotypes under low- and high-P treatments. Plants were grown either in soil with naturally occurring AMF or in sterilized soil with added AMF-free bacteria. The results indicated that the AMF symbiosis significantly increased alfalfa productivity and physiological P use efficiency by enhancing total root length and root surface area while reducing carboxylate release. Under low-P conditions, HPE genotypes with AMF symbiosis showed higher shoot DW, greater mycorrhizal responsiveness, thicker and more robust roots, as well as increased carboxylate release compared with LPE genotypes. We conclude that exploitation of the dominant species in indigenous AMF populations and breeding of crop genotypes with high mycorrhizal responsiveness show promising avenues with which to improve forage productivity and alleviate P limitation in modern agricultural ecosystems.
• Root mucilage and border cells act together in shaping rhizosphere functions. • The ‘mucicell’ concept unites mucilage with its metabolically active border cells. • Border cells alter mucilage properties, impacting hydraulic and microbial dynamics. • Many effects attributed to mucilage alone may stem from the mucicell complex. • Adopting the mucicell concept refines rhizosphere research and data interpretation.
Jean-Michel Ané's insight:
I don't find this concept personally very helpful but the term is hilarious.
Bacterial volatile compounds play important roles in intra- and interkingdom interactions but very little is known about their effects on soil and plant microbiomes. The legume symbiont Sinorhizobium meliloti (Sm) releases volatile methylketones (MKs), one of which acts as an infochemical in bacteria and hampers plant-bacteria interactions. MK production in Sm is modestly increased in the absence of the long-chain-fatty-acyl-coenzyme-A (CoA) synthetase FadD. To explore further the ecological role of MKs on soil and plant bacterial communities, we aimed at obtaining an MK-overproducer Sm strain by deleting the 3-oxo-acyl-CoA-thiolase-encoding fadA gene. Analyses of the Sm wild type (wt), and fad mutant volatilomes identified seventeen compounds consisting mostly of MKs and fatty acid methyl esters (FAMEs) and revealed that the fadA mutant produced more MKs than the fadD mutant and much more than the wt, while in the fadD mutant FAME emission was increased. When natural soil or the rhizosphere of Medicago truncatula were exposed to wt and fadA volatilomes or synthetic MKs, bacterial alpha- or beta-diversity were not strongly affected but specific genera were identified which responded differentially to each condition. Interestingly, Sm volatilomes had a significant effect on root endosphere Ensifer/Sinorhizobium populations by maintaining their abundance over time in contrast to control conditions or exposure to synthetic MKs. This study provides new insights on the synthesis of rhizobial volatile compounds and represents the first exploration of the effects of bacterial volatilomes on plant bacterial communities, contributing to increase our knowledge on the complex molecular bases underlying plant-bacteria interactions.
Arbuscular mycorrhizal (AM) symbiosis is an ancient association that played a key role in the adaptation of plants to terrestrial environments. Originating over 400 million years ago at the dawn of land plants, this interaction depends on a core set of conserved genes that enable hosts to establish and maintain symbiotic relationships with AM fungi. The AM symbiotic program includes distinct genetic components for each stage of development, from signal perception to nutrient exchange. While AM-host plants have retained key genes dedicated to symbiosis, non-host lineages have independently lost these genes multiple times over evolutionary history. Recent studies in the liverwort Marchantia paleacea demonstrate that core mechanisms underlying AM symbiosis are conserved from bryophytes to angiosperms. Comparative genomic studies continue to uncover how symbiosis-specific genes are integrated with broadly conserved cellular machinery to sustain this interaction. Understanding these deeply conserved genetic modules is essential for uncovering the evolutionary foundations of plant–microbe associations and for harnessing their potential in sustainable agriculture.
In this series of time-lapse movies we are zooming in on the root nodule formation of Barrel Clover (Medicago truncatula). This type of endosymbioses between the plant and Rhizobia bacteria is typical for legumes and plays a very important role in a healthy soil. Bacteria of the genus Rhizobium are capable of nitrogen fixing. The bacteria fix atmospheric nitrogen into ammonium. In a sense making fertiliser out of thin air.
The plant secretes chemical signals (flavonoids) to attract rhizobia. The bacteria respond by producing a response signal (LCO (lipo-chitooligosaccharide) aka nodulation (Nod) factor). Upon perception of this return signal root nodules are initiated. This only occurs near the tip of the root. Region where root hairs are present. The susceptible zone. These hairs are needed for the infection. Medicago truncatula nodules are so called indeterminant nodules. Which means they keep on growing.
Inside the root nodules the Rhizobia bacteria will perform nitrogenase: Nitrogen fixing. Highly energy demanding, bacteria do this in return for energy from the plant. Bacteria have a protein complex called nitrogenase, responsible to produce ammonium. This complex is unstable and easily damaged by O2. The pink colour you see in the nodules is leghaemoglobin (the plants equivalent of what is in our blood). Leghaemoglobin binds O2 but can release it when needed. This ensures the conditions for nitrogenase and the cell to survive together.
The time-lapese were shot over a period of many months. The speed varies between 24 hours in one second for the roots and 24 hours in 4 seconds for the above ground shots.
This video is part of the Soil Life in Action project. The movie can be used for education in classrooms and for lectures. For other use please contact: egmond(at)tip.nl
Plants interact with a plethora of organisms in the rhizosphere, with outcomes that range from detrimental to beneficial. Arbuscular mycorrhizal (AM) symbiosis is the most ubiquitous beneficial plant interaction in terrestrial ecosystems and involves soil borne fungi of the Glomeromycotina. It is believed that plants detect diagnostic signals for the discrimination between beneficial arbuscular mycorrhizal (AM) fungi and parasitic fungi during the pre-symbiotic molecular crosstalk. Here, we investigated the transcriptome of rice roots upon exposure to the complete cocktail of fungal exudates from either beneficial Rhizophagus irregularis or pathogenic Magnaporthe oryzae. We report that regardless of the exudate donor species, the transcriptional response lacked diagnostic differences. Instead, the profiles were marked by the common suppression of symbiosis signalling components, accompanied by the induction of a generic stress response (GSR) and defense-related signature, which was retained in a suite of symbiosis signalling mutants impaired at different stages of symbiosis development. However, upon permitting physical engagement with AM fungi, a striking reversion in the transcriptional responses occurred marked by the simultaneous relaxation of symbiosis signalling suppression and down-regulation of defense-related and GSR markers, overall comparable between wild-type and mutants. Our data therefore reveal that rather than specific recognition in the rhizosphere, a sequence of signals orchestrates stress, immunity and symbiosis, pivoting towards symbiosis potentially at the stage of plant-fungal contact formation.
Jean-Michel Ané's insight:
Yes... most fungi make COs and LCOs. They are important signals for plants to recognize fungi but more contact signals are required to differentiate symbiotic and pathogenic fungi. Cool preprint!
Most terrestrial plants establish symbiotic relationships with microorganisms to acquire nutrients and simultaneously restrict pathogen infection. In rice, the receptor-like kinase OsARK1 is essential for the colonization and development of arbuscular mycorrhizal (AM) fungi. However, whether OsARK1 participates in plant–pathogen interactions remain unknown. Here, we demonstrate that OsARK1 is involved in the transcriptional reprogramming of immune defense-related genes prior to and following AM colonization. Mutation of OsARK1 resulted in increased susceptibility to Magnaporthe oryzae (blast fungus) and Xanthomonas oryzae (bacterial blight). Transcriptomic profiling during blast infection demonstrated OsARK1 coordinates early immune responses; particularly, the upregulation of genes encoding lectin receptor-like kinases (LecRLKs), nucleotide-binding leucine-rich repeat (NLR) immune receptors and secondary metabolism-related genes was significantly impaired in Osark1 mutant. Collectively, OsARK1 acts as a positive regulator of rice immunity against pathogens while fine-tuning defense suppression during beneficial AM symbiosis.
The spatial variation and underlying mechanisms of pattern formation in the rhizosphere microbiome are not well understood. We demonstrate that specific patterns in the distribution of recently fixed carbon within the plant root system influence the spatial organization of the rhizosphere microbiota. Non-invasive analysis of carbon allocation in the maize root system by 11C tracer-based positron emission tomography combined with magnetic resonance imaging reveals high spatial heterogeneity with highest 11C-signal accumulations at root tips and differences between root types. Strong correlations exist between root internal carbon allocation and rhizodeposition as evident from 13CO2 labeling. These patterns are reflected in the bacterial, fungal and protistan community structure in rhizosphere soil with differences depending on root structure and related spatial heterogeneities in carbon allocation. Especially the active consumers of 13C-labeled rhizodeposits are responsive to photosynthate distribution with differences in 13C-labeling according to their spatial localization within the root system. Thus, root photosynthate allocation supports distinct habitats in the plant root system and is a key determinant of microbial food web development, evident from 13C-labeling of diverse bacterial and protistan predators, especially at root bases, resulting in characteristic spatiotemporal patterns in the rhizosphere microbiome.
When did plants begin their symbiotic relationships with microorganisms? It is hypothesized that plant-microbe symbiosis began around 450 million years ago, when fungi known as endomycorrhizal fungi formed mutually beneficial interactions with early terrestrial plants [25]. At the time when early terrestrial plants evolved from aquatic photosynthetic organisms to adapt to life on land, nutrients were scarce, making symbiosis with nutrient-supplying microorganisms crucial for their survival. The symbiosis between plants and nitrogen-fixing bacteria emerged later, approximately 100 million years ago, and developed independently multiple times. For microorganisms, plants provided a convenient and safe habitat, while plants benefited by internalizing them, as this made it easier to manage and utilize microorganisms effectively.
Low nitrogen availability is the number one limitation to plant growth in most ecosystems. Farmers compensate by adding nitrogen-rich fertilizers to their crops, which is expensive and harmful to the environment. Plants in the bean family and other closely related families evolved a symbiotic relationship with bacteria capable of acquiring nitrogen from the air, where it is abundant. Scientists want to genetically engineer crop plants to do the same, but there are several obstacles in their way. The open question of how many times this type of symbiosis evolved is one such obstacle. In a new study funded by the U.S. Department of Energy, scientists show that chemical receptors that plants use to recognize nitrogen-fixing bacteria have developed the same function independently on at least three separate occasions through a process called convergent evolution.
Understanding the contributions of arbuscular mycorrhizal fungi (AMF) to plant nutrition is essential for sustainable agriculture. We hypothesised that soil phosphorus (P) availability modulates the diversity and functionality of wheat root-associated AMF community, particularly the mycorrhizal nutrition.
Wheat plants were sampled over two campaigns (2019 and 2022) in a long-term P fertilisation trial. The expression of the wheat transporters involved in the mycorrhizal nutrition was assessed by RT-qPCR, and AMF community composition by metabarcoding. Complementary experiments under controlled conditions were performed to further study the interaction between nitrogen (N) and P availability on AM.
Different effects of P on AMF colonisation and transporter expression were observed in field-grown wheat depending on the campaigns, which differed in wheat N status. Controlled experiments confirmed that AMF colonisation depends on the limitation of either P or N, but that regulation of peri-arbuscular phosphate, ammonium and nitrate transporters depends on the nature of the limiting soil nutrients. Additionally, AMF communities varied according to the soil P availability, with the Funneliformis genus becoming more dominant under high P conditions for both years.
Together, our findings show that N and P availability jointly shape root AMF communities and AM functioning. Combining community profiling and molecular markers of colonisation and nutrition offers a framework to better understand AMF contributions to plant nutrition across agroecosystems.
•Bacteria strains altered roots, biomass, pigments, and K⁺ concentration •CJND1 and LN3BA improved root traits and foliar K⁺ in L. purpureus •Proline and Na⁺ blockage are the main salt tolerance mechanisms in L. purpureus •Active K⁺ transport helps L. purpureus retain leaf potassium under stress •L. purpureus is a promising climate-resilient crop for Mediterranean farmers
Microalgal biomass is increasingly valued in industrial and agricultural sectors due to its bioactive compounds. However, large-scale production remains costly, mainly due to nitrogen fertilizer expenses. A promising sustainable alternative is co-cultivation with N2-fixing bacteria, capable of supplying biologically available nitrogen. In this study, Chlorella vulgaris was grown in synthetic medium with and without nitrogen, as well as in co-culture with three different N2-fixing bacteria in nitrogen-free medium. Microalgal growth was assessed by dry weight, Fv/Fm ratio, and flow cytometry, which also allowed evaluation of population dynamics and cell viability. Biomass composition (proteins, carbohydrates, lipids, chlorophyll, and carotenoids) was analyzed under all conditions. Co-cultures in nitrogen-free medium showed comparable biomass productivity to nitrogen-supplemented controls, although Fv/Fm values indicated physiological stress in some cases. Moreover, the agricultural potential of the resulting biomass and supernatants was evaluated through germination bioassays using lettuce seeds. All cultures tested at 0.2 g·L−1 significantly improved the germination index. Also, applying the culture supernatant (biomass removed) also yielded positive effects, with GI increases exceeding 40 %. These results suggest that co-cultivation with N2-fixing bacteria can support efficient microalgal production while generating biomass and supernatants with biostimulant potential, contributing to sustainable agriculture and circular bioeconomy strategies.
Jean-Michel Ané's insight:
What about all the other nutrients, such as phosphorus, required for these co-cultures? I am skeptical that this is truly an "eco-friendly" and sustainable approach.
Plants form mycorrhizal symbioses to enhance nutrient acquisition, yet the biophysical principles governing carbon and nutrient exchange remain unclear. Here, we develop a theory of bi-directional carbon–nutrient transfer that integrates root anatomy, energetic costs, and mycorrhizal positioning. We show that nutrient uptake per unit carbon or energy investment declines with increasing root diameter due to higher carbon demands across thicker cortical tissues. Mycorrhizal fungi mitigate this constraint by enabling more carbon-efficient nutrient uptake, particularly when arbuscules are positioned in inner cortical layers. This spatial optimization minimizes the carbon cost of transporting nutrients to the stele. Our framework reconciles anatomical variation, symbiotic structure, and functional efficiency across root types and mycorrhizal strategies and offers a new lens for understanding the coevolution between roots and mycorrhizal fungi.
Jean-Michel Ané's insight:
I never thought about this... Very interesting model.
Root nodule symbiosis (RNS) is a mutualistic association formed between nitrogen-fixing rhizobia or Frankia and host plants limited to four orders within Rosid I—Fabales, Fagales, Cucurbitales and Rosales—which comprise the so-called ‘Nitrogen Fixing Nodulation Clade’ (NFNC). The majority of nodulation studies have focused on Leguminosae, given their agricultural and environmental importance, as well as the widespread occurrence of nodulation among members of this family. Endowing cereal crops with nitrogen fixation, like Leguminosae, presents a strategy to reduce the detrimental effects of synthetic fertilizer overuse. Different hypotheses on the origin of RNS have been proposed, however key genetic innovations underlying the evolution of RNS, even in Leguminsoae, have been rarely reported. In this review, we begin by examining current knowledge of genetic innovations—including gene gain, gene loss, and the acquisition or loss of conserved noncoding sequences (CNS) in preexisting genes. We explore the available evidence supporting these genetic innovations underlying the evolution of RNS in Leguminosae and offer the phylogenomics approach that could be applied to uncover these genetic innovations. Finally, we conclude by proposing a model of genetic innovations underlying the evolution of RNS in Leguminsoae and consider the potential implications for the development of nitrogen-fixing crops.
Legume symbiosis with nitrogen-fixing bacteria is controlled by a cascade of signaling events leading to root nodule development. While plant cell-surface receptors initiate this process, the link between receptors and cytoplasmic signaling components remains unclear. Here we identify Early Phosphorylated Protein 1 (EPP1) as a central mediator of this pathway. EPP1 is recruited to the activated SYMRK receptor, where it is phosphorylated on a key serine residue, an event essential and sufficient to propagate symbiotic signaling. We provide structural and functional validation of the SYMRK-EPP1 signaling complex and demonstrate that EPP1 is required for root nodule formation. Synthetic engineering of the SYMRK-EPP1 interaction bypasses the need for symbiotic bacteria to initiate the pathway and triggers nodule organogenesis. These findings establish EPP1 as a crucial cytoplasmic component between receptor activation and intracellular signaling, advancing our understanding of nitrogen-fixing symbiosis.
Given climate-related drought and temperature extremes, declining soil quality, and a decrease in arable land, endophytes, argue Pankaj Trivedi, Chakradhar Mattupalli, Kellye Eversole, and Jan E. Leach, might undergird a sustainable “green revolution” to improve agricultural productivity while lessening reliance on environmentally damaging and health-threatening agricultural chemicals. Endophytes can have an impact, says plant biotechnologist Julissa Ek-Ramos, on “climate change, recovering the soil, and having more healthy food to eat.”
Arbuscular mycorrhizal symbiosis (AMS) is a ubiquitous and ancient interaction between plant root systems and fungi of the Glomeromycotina subphylum. The resulting relationship is mutually beneficial and deeply intimate where the fungus intracellularly colonises root cortex cells to receive organic carbon and deliver minerals and water to the plant. Fungal colonisation of plant roots and cells is extremely dynamic and asynchronous across the root system. Symbiosis development must therefore result from spatio-temporally fine-tuned molecular control mechanisms of plant and fungus. Although the plant genetic program underpinning AMS has been extensively studied, little is known about its dynamic regulation across root cell layers and developmental stages of the association. Thus, many questions remain outstanding: how do different cell-types transcriptionally respond to AMS, how are distinct cell-type specific regulatory states coordinated, and what are the transcriptional activities in the fungus associated with discrete stages of root colonisation? The advent of single cell-based techniques now enables the high-resolution analysis to address these questions. In this review, we recapitulate the current knowledge on the spatio-temporal control of AMS, we evaluate the relevance of existing spatial datasets to AMS research and provide new perspectives for future study.
The soybean-rhizobium symbiosis plays a crucial role in sustainable agriculture, promoting biological nitrogen fixation and reducing dependence on synthetic fertilizers. This study focuses on the molecular mechanisms underlying this symbiotic relationship, with particular emphasis on the identification and characterization of key signaling genes involved in nodulation. We explore the role of nodulation factors and their perception by LysM receptor-like kinases (e.g., GmNFR1 and GmNFR5) and downstream signaling components, including calcium/calmodulin-dependent kinases and transcription factors, such as NIN and ERN1. We further discuss the functional characteristics of these genes, drawing on evidence from gene knockout, overexpression, RNAi, and CRISPR-Cas-based studies. We also highlight the integration of transcriptomics and proteomics approaches in identifying new candidate genes. Furthermore, this study explores the interplay between symbiotic signaling and other regulatory pathways, including plant hormone signaling, defense responses, and environmental cues. Using GmNARK, a key regulator of nodulation autoregulation, as an example, we delve into its negative feedback mechanism and its impact on enhancing nodulation efficiency. Finally, the biotechnological applications of these signaling genes in breeding strategies aimed at enhancing nitrogen fixation and increasing soybean yield are discussed. This study aims to comprehensively understand the signaling networks in the soybean-rhizobium symbiosis system and outline future directions for sustainable improvement of legumes using advanced genomics and synthetic biology tools.
The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using the Medicago truncatula-Sinorhizobium meliloti symbiotic system. Phenotypes were measured in the wild-type Medicago truncatula and a mutant in an ABC transporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies.
Bacteria in the soil form complex communities, and some colonize the surfaces of roots. These bacteria are not uniformly distributed, however, and exhibit precise patterning around emerging lateral roots and early root differentiation zones. Tsai et al. established that the Casparian strip, an endodermal barrier around the root vasculature, is required for normal patterning of root bacteria (see the Perspective by Kozaeva and Brophy). At locations where the Casparian strip is absent, glutamine leaks from the vasculature and serves as an attractant for soil bacteria. Using precise spatial and temporal analysis, the authors provide insight into how bacteria around the root interact both with the plant and with each other. —Madeleine Seale
Azotobacter vinelandii is a nitrogen-fixing free-living soil microbe that has been studied for decades in relation to biological nitrogen fixation (BNF). It is highly amenable to genetic manipulation, helping to unravel the intricate importance of different proteins involved in the process of BNF, including the biosynthesis of cofactors that are essential to assembling the complex metal cofactors that catalyze the difficult reaction of nitrogen fixation. Additionally, A. vinelandii accomplishes this feat while growing as an obligate aerobe, differentiating it from many of the nitrogen-fixing bacteria that are associated with plant roots. The ability to function in the presence of oxygen makes A. vinelandii suitable for application in various potential biotechnological schemes. In this study, we employed transposon sequencing (Tn-seq) to measure the fitness defects associated with disruptions of various genes under nitrogen-fixing dependent growth, versus growth with extraneously provided urea as a nitrogen source. The results allowed us to probe the importance of more than 3,800 genes, revealing that many genes previously believed to be important, can be successfully disrupted without impacting cellular fitness.
Cis-regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas for Oryza sativa from 103,911 nuclei representing 126 cell states across nine organs. Comparative genomics between O. sativa and 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum and Urochloa fusca) revealed that chromatin accessibility conservation varies with cell-type specificity. Epidermal accessible chromatin regions in the leaf were less conserved compared to other cell types, indicating accelerated regulatory evolution in the L1-derived epidermal layer of O. sativa relative to other species. Conserved accessible chromatin regions overlapping the repressive histone modification H3K27me3 were identified as potentially silencer-like CREs, as deleting these regions led to up-regulation of gene expression. This study provides a comprehensive epigenomic resource for the rice community, demonstrating the utility of a comparative genomics approach that highlights the dynamics of plant cell-type-specific CRE evolution.
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I totally agree.