Evolutionary dynamics of nitrogen fixation in the legume-rhizobia symbiosis

Unveiling the potential of A. fabrum and γ-aminobutyric acid for mitigation of nickel toxicity in fenugreek

Nickel (Ni) is a heavy metal that adversely affects the growth of different crops by inducing oxidative stress and nutrient imbalance. The role of rhizobacteria (RB) is vital to resolve this issue. They can promote root growth and facilitate the uptake of water and nutrients, resulting in better crop growth. On the other hand, γ-aminobutyric acid (GABA) can maintain the osmotic balance and scavenge the reactive oxygen species under stress conditions. However, the combined effect of GABA and RB has not been thoroughly explored to alleviate Ni toxicity, especially in fenugreek plants. Therefore, in the current pot study, four treatments, i.e., control, A. fabrum (RB), 0.40 mM GABA, and 0.40 mM GABA + RB, were applied under 0Ni and 80 mg Ni/kg soil (80Ni) stress. Results showed that RB + 0.40 mM GABA caused significant improvements in shoot length (~ 13%), shoot fresh weight (~ 47%), shoot dry weight (~ 47%), root length (~ 13%), root fresh weight (~ 60%), and root dry weight (~ 15%) over control under 80 Ni toxicity. A significant enhancement in total chlorophyll (~ 14%), photosynthetic rate (~ 17%), stomatal CO2 concentration (~ 19%), leaves and roots N (~ 10 and ~ 37%), P (~ 18 and ~ 7%) and K (~ 11 and ~ 30%) concentrations, while a decrease in Ni (~ 83 and ~ 49%) concentration also confirmed the effectiveness of RB + 0.40 mM GABA than control under 80Ni. In conclusion, fabrum + 0.40 mM GABA can potentially alleviate the Ni toxicity in fenugreek plants. The implications of these findings extend to agricultural practices, environmental remediation efforts, nutritional security, and ecological impact. Further research is recommended to elucidate the underlying mechanisms, assess long-term effects, and determine the practical feasibility of using A. fabrum + 0.40GABA to improve growth in different crops under Ni toxicity.

Effects of Soil Rhizobia Abundance on Interactions between a Vector, Pathogen, and Legume Plant Host

Soil rhizobia promote nitrogen fixation in legume hosts, maximizing their tolerance to different biotic stressors, plant biomass, crop growth, and yield. While the presence of soil rhizobia is considered beneficial for plants, few studies have assessed whether variation in rhizobia abundance affects the tolerance of legumes to stressors. To address this, we assessed the effects of variable soil rhizobia inoculum concentrations on interactions between a legume host (Pisum sativum), a vector insect (Acyrthosiphon pisum), and a virus (Pea enation mosaic virus, PEMV). We showed that increased rhizobia abundance reduces the inhibitory effects of PEMV on the nodule formation and root growth in 2-week-old plants. However, these trends were reversed in 4-week-old plants. Rhizobia abundance did not affect shoot growth or virus prevalence in 2- or 4-week-old plants. Our results show that rhizobia abundance may indirectly affect legume tolerance to a virus, but effects varied based on plant age. To assess the mechanisms that mediated interactions between rhizobia, plants, aphids, and PEMV, we measured the relative expression of gene transcripts related to plant defense signaling. Rhizobia concentrations did not strongly affect the expression of defense genes associated with phytohormone signaling. Our study shows that an abundance of soil rhizobia may impact a plant's ability to tolerate stressors such as vector-borne pathogens, as well as aid in developing sustainable pest and pathogen management systems for legume crops. More broadly, understanding how variable rhizobia concentrations can optimize legume-rhizobia symbiosis may enhance the productivity of legume crops.

The role of microbial interactions on rhizobial fitness

Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.

Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms

Simple Summary

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. We detected chemical exchanges between intracellular bacteria and plant cells. We found that endophytic bacteria that show evidence of the transfer of nitrogen to plants are present in non-photosynthetic cells of leaves and bracts of diverse plant species. Nitrogen transfer from bacteria was observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. The most efficient of the nitrogen-transfer endosymbioses were seen to involve glandular trichomes, as seen in hops (Humulus lupulus) and hemp (Cannabis sativa). Trichome chemistry is hypothesized to function to scavenge oxygen around bacteria to facilitate nitrogen fixation.

Abstract

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

Legume-rhizobium specificity effect on nodulation, biomass production and partitioning of faba bean (Vicia faba L.)

Greenhouse and multi-location experiments were conducted for two consecutive years to investigate the effects of rhizobium on nodulation, biomass production and partitioning of faba bean. Split-plot in randomized complete block design was used for field experiments. Treatments consisted of six rhizobium strains and three faba bean varieties. Peat carrier-based inoculant of each strain was applied at the rate of 10 g kg^-1 seed. Non-inoculated plants without N fertilizer and with N fertilizer served as -N and + N controls, respectively. Data on nodulation, shoot dry weight and root dry weight were collected and analyzed. Inoculation of rhizobium significantly increased nodulation of faba bean under greenhouse and field conditions. Location x strain x variety interaction had significant effects on nodulation, dry matter production and partitioning. Rhizobium inoculation increased nodulation, shoot and root dry weights of faba bean across locations. For example, inoculation with rhizobium strains NSFBR-15 and NSFBR-12 to variety Moti resulted in 206.9 and 99.3% shoot dry weight increase at Abala Gase and Hankomolicha, respectively and 133.3 and 70.7% root dry weight increase on the same variety at the same sites, respectively. Nodulation and biomass production depend on the compatibility between faba bean genotype and rhizobium strain and its interaction with soil bio-physical conditions.

Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity

Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.

Legume-Rhizobium Strain Specificity Enhances Nutrition and Nitrogen Fixation in Faba Bean (Vicia faba L.)

This study reports the effectiveness of some selected rhizobium strains in enhancing nitrogen fixation and nutrient uptake in Vicia faba L. Multi-location field experiments were conducted for two years (2016 and 2017) using a split-plot in randomized complete block design. Treatments comprised six rhizobium strains as the main plot factor and three varieties of Vicia faba as the sub-plot factor. Non-inoculated plants with or without N fertilizer served as +N and −N controls, respectively. Peat carrier-based inoculant of each strain was applied at the rate of 10 g kg−1 seed. Data on nodulation were taken at the late-flowering stage, whereas nitrogen and phosphorus concentrations in plant parts were analyzed at physiological maturity. The total nitrogen difference method was employed to quantify nitrogen fixation. Location x rhizobium strain x variety interaction had a significant effect on nodule dry weight plant−1. Rhizobium strains significantly enhanced nodulation, nitrogen fixation, nutrient uptake and soil nitrogen balance. Inoculation with NSFBR-12 and NSFBR-15 resulted in the highest nitrogen fixed, nutrient uptake and soil nitrogen balance. Vicia faba inoculated with the two top performing strains, NSFBR-12 and NSFBR-15 fixed respectively 87.7% and 85.5% of the total nitrogen uptake. Non-inoculated plants fulfilled proportionately more of the total nitrogen uptake through nitrogen derived from the soil rather than fixed nitrogen. Soil available phosphorus and pH had appreciable influences on nitrogen and phosphorus uptake of inoculated Vicia faba. Inoculation with competitive and effective rhizobium strains can improve soil nitrogen balance, nitrogen fixation and nutrient uptake of Vicia faba.

A microfluidic co-cultivation platform to investigate microbial interactions at defined microenvironments

Interspecies interactions inside microbial communities bear a tremendous diversity of complex chemical processes that are by far not understood. Even for simplified, often synthetic systems, the interactions between two microbes are barely revealed in detail. Here, we present a microfluidic co-cultivation platform for the analysis of growth and interactions inside microbial consortia with single-cell resolution. Our device allows the spatial separation of two different microbial organisms inside adjacent microchambers facilitating sufficient exchange of metabolites via connecting nanochannels. Inside the cultivation chambers cell growth can be observed with high spatio-temporal resolution by live-cell imaging. In contrast to conventional approaches, in which single-cell activity is typically fully masked by the average bulk behavior, the small dimensions of the microfluidic cultivation chambers enable accurate environmental control and observation of cellular interactions with full spatio-temporal resolution. Our method enables one to study phenomena in microbial interactions, such as gene transfer or metabolic cross-feeding. We chose two different microbial model systems to demonstrate the wide applicability of the technology. First, we investigated commensalistic interactions between an industrially relevant l-lysine-producing Corynebacterium glutamicum strain and an l-lysine auxotrophic variant of the same species. Spatially separated co-cultivation of both strains resulted in growth of the auxotrophic strain due to secreted l-lysine supplied by the producer strain. As a second example we investigated bacterial conjugation between Escherichia coli S17-1 and Pseudomonas putida KT2440 cells. We could show that direct cell contact is essential for the successful gene transfer via conjugation and was hindered when cells were spatially separated. The presented device lays the foundation for further studies on contactless and contact-based interactions of natural and synthetic microbial communities.

Co-inoculation of a Pea Core-Collection with Diverse Rhizobial Strains Shows Competitiveness for Nodulation and Efficiency of Nitrogen Fixation Are Distinct traits in the Interaction

Pea forms symbiotic nodules with Rhizobium leguminosarum sv. viciae (Rlv). In the field, pea roots can be exposed to multiple compatible Rlv strains. Little is known about the mechanisms underlying the competitiveness for nodulation of Rlv strains and the ability of pea to choose between diverse compatible Rlv strains. The variability of pea-Rlv partner choice was investigated by co-inoculation with a mixture of five diverse Rlv strains of a 104-pea collection representative of the variability encountered in the genus Pisum. The nitrogen fixation efficiency conferred by each strain was determined in additional mono-inoculation experiments on a subset of 18 pea lines displaying contrasted Rlv choice. Differences in Rlv choice were observed within the pea collection according to their genetic or geographical diversities. The competitiveness for nodulation of a given pea-Rlv association evaluated in the multi-inoculated experiment was poorly correlated with its nitrogen fixation efficiency determined in mono-inoculation. Both plant and bacterial genetic determinants contribute to pea-Rlv partner choice. No evidence was found for co-selection of competitiveness for nodulation and nitrogen fixation efficiency. Plant and inoculant for an improved symbiotic association in the field must be selected not only on nitrogen fixation efficiency but also for competitiveness for nodulation.

Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical, Noninfective, Ineffective Isolates

Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that were isolated from root nodules but are unable to reinfect actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively.

A legume genetic framework controls infection of nodules by symbiotic and endophytic bacteria

Legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules. For the symbionts, a complex genetic mechanism that allows mutual recognition and plant infection has emerged from genetic studies under axenic conditions. In contrast, little is known about the mechanisms controlling the endophytic infection. Here we investigate the contribution of both the host and the symbiotic microbe to endophyte infection and development of mixed colonised nodules in Lotus japonicus. We found that infection threads initiated by Mesorhizobium loti, the natural symbiont of Lotus, can selectively guide endophytic bacteria towards nodule primordia, where competent strains multiply and colonise the nodule together with the nitrogen-fixing symbiotic partner. Further co-inoculation studies with the competent coloniser, Rhizobium mesosinicum strain KAW12, show that endophytic nodule infection depends on functional and efficient M. loti-driven Nod factor signalling. KAW12 exopolysaccharide (EPS) enabled endophyte nodule infection whilst compatible M. loti EPS restricted it. Analysis of plant mutants that control different stages of the symbiotic infection showed that both symbiont and endophyte accommodation within nodules is under host genetic control. This demonstrates that when legume plants are exposed to complex communities they selectively regulate access and accommodation of bacteria occupying this specialized environmental niche, the root nodule.

Plants have evolved elaborated mechanisms to monitor microbial presence and to control their infection, therefore only particular microbes, so called “endophytes,” are able to colonise the internal tissues with minimal or no host damage. The legume root nodule is a unique environmental niche induced by symbiotic bacteria, but where multiple species, symbiotic and endophytic co-exist. Genetic studies of the binary interaction legume-symbiont led to the discovery of key components evolved in the two partners allowing mutual recognition and nodule infection. In contrast, there is limited knowledge about the endophytic nodule infection, the role of the legume host, or the symbiont in the process of nodule colonisation by endophytes. Here we focus on the early stages of nodule infection in order to identify which molecular signatures and genetic components favour/allow endophyte accommodation, and multiple species co-existence inside nodules. We found that colonisation of Lotus japonicus nodules by endophytic bacteria is a selective process, that endophyte nodule occupancy is host-controlled, and that exopolysaccharides are key bacterial features for chronic infection of nodules. Our strategy based on model legume genetics and co-inoculation can thus be used for identifying mechanisms operating behind host-microbes compatibility in environments where multiple species co-exist.

Diversity of nitrogen fixation strategies in Mediterranean legumes

Symbiotic N2 fixation (SNF) brings nitrogen into ecosystems, fuelling much of the world's agriculture(1) and sustaining carbon storage(2,3). However, it can also cause nitrogen saturation, exacerbating eutrophication and greenhouse warming(4-7). The balance of these effects depends on the degree to which N2-fixing plants adjust how much N2 they fix based on their needs (their SNF 'strategies')(5,6). Genetic, biochemical and physiological details of SNF are well known for certain economically important species(8,9), but the diversity of N2-fixing plants(10) and bacteria(11) is enormous, and little is known about most N2-fixing symbioses in natural ecosystems(12). Here, we show that co-occurring, closely related herbs exhibit diverse SNF strategies. In response to a nitrogen supply gradient, four species fixed less N2 than they needed (over-regulation), two fixed what they needed (facultative) and two did not downregulate SNF (obligate). No species downregulated but fixed more N2 than it needed (under-regulation or incomplete downregulation), but some species under-regulated or incompletely downregulated structural allocation to SNF. In fact, most species maintained nodules (the root structures that house symbionts) when they did not fix N2, suggesting decoupling of SNF activity and structure. Simulations showed that over-regulation of SNF activity is more adaptive than under-regulation or incomplete downregulation, and that different strategies have wildly different effects on ecosystem-level nitrogen cycling.

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game

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We fully analyze continuous snowdrift games with quadratic payoff functions in diversified populations.

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It is well known that classical snowdrift games maintain the coexistence of cooperators and cheaters.

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We clarify that the continuous snowdrift games often lead to assimilation of cooperators and cheaters.

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Allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures.

It is well known that in contrast to the Prisoner’s Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness.