The Symbiotic Performance of Chickpea Rhizobia Can Be Improved by Additional Copies of the clpB Chaperone Gene

'Friend versus foe'-does autophagy help regulate symbiotic plant-microbe interactions and can it be manipulated to improve legume cultivation?

Autophagy is a genetically regulated, eukaryotic catabolic pathway that responds to internal and external cellular signals. In plants, it plays crucial roles in development, and responses to abiotic and biotic stresses. Due to its role in limiting the hypersensitive response, research on the molecular mechanisms of autophagic signalling pathways in plant-microbe interactions has primarily focused on plant-pathogen responses. Although there is substantially less information on the role of autophagy signalling in symbiotic plant-microbe interactions, there is accumulating evidence that it is also a key regulator of mutualistic plant-microbe interactions. Here, we review recent progress on the roles of autophagy in symbiotic plant interactions and discuss potential future research directions. Once understood, the central role that autophagy plays within pathogenic and symbiotic plant-microbe interactions has significant potential application for crop improvement. Manipulating autophagy in legume crops could help support crop growth with reduced levels of fertiliser application while maintaining yields with increased protein content in the harvest.

Rhizosphere microbiome influence on tomato growth under low-nutrient settings

Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.

An overview of heat stress in Chickpea (Cicer arietinum L.): effects, mechanisms and diverse molecular breeding approaches for enhancing resilience and productivity

Chickpea (Cicer arietinum. L) holds the esteemed position of being the second most cultivated and consumed legume crop globally. Nevertheless, both biotic and abiotic constraints limit chickpea production. This legume is sensitive to heat stress at its reproductive stage leading to reduced flowering, flower abortion, and lack of pod formation, therefore emerging as a major limiting factor for yield. Chickpea, predominantly cultivated in semi-arid regions, is frequently subjected to high-temperature stress, which adversely affects its growth and yield. Given the escalating impacts of climate change, the development of heat-tolerant chickpea genotypes is imperative and can be achieved through the integration of advanced biotechnological approaches. The appropriate solution devised by some researchers is the modification of genetic architecture by targeting specific genes associated with tolerance to heat stress and harnessing them in the development of more robust chickpea varieties. Besides this, multi-omics strategies (Genomics, Transcriptomics, Proteomics, and Metabolomics) have made it easier to reveal the distinct genes / quantitative trait loci (QTLs) / markers, proteins, and metabolites correlated with heat tolerance. This review compiles noteworthy revelations and different tactics to boost chickpea tolerance under heat temperatures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01538-4.

Challenges to rhizobial adaptability in a changing climate: Genetic engineering solutions for stress tolerance

Rhizobia interact with leguminous plants in the soil to form nitrogen fixing nodules in which rhizobia and plant cells coexist. Although there are emerging studies on rhizobium-associated nitrogen fixation in cereals, the legume-rhizobium interaction is more well-studied and usually serves as the model to study rhizobium-mediated nitrogen fixation in plants. Rhizobia play a crucial role in the nitrogen cycle in many ecosystems. However, rhizobia are highly sensitive to variations in soil conditions and physicochemical properties (i.e. moisture, temperature, salinity, pH, and oxygen availability). Such variations directly caused by global climate change are challenging the adaptive capabilities of rhizobia in both natural and agricultural environments. Although a few studies have identified rhizobial genes that confer adaptation to different environmental conditions, the genetic basis of rhizobial stress tolerance remains poorly understood. In this review, we highlight the importance of improving the survival of rhizobia in soil to enhance their symbiosis with plants, which can increase crop yields and facilitate the establishment of sustainable agricultural systems. To achieve this goal, we summarize the key challenges imposed by global climate change on rhizobium-plant symbiosis and collate current knowledge of stress tolerance-related genes and pathways in rhizobia. And finally, we present the latest genetic engineering approaches, such as synthetic biology, implemented to improve the adaptability of rhizobia to changing environmental conditions.

Cyclic Isothiocyanate Goitrin Impairs Lotus japonicus Nodulation, Affects the Proteomes of Nodules and Free Mesorhizobium loti, and Induces the Formation of Caffeic Acid Derivatives in Bacterial Cultures

The continuous release of glucosinolates into the soil by Brassicaceae root exudation is a prerequisite to maintaining toxic levels of breakdown products such as isothiocyanates (ITCs). ITCs influence plant and microbial diversity in ecosystems, while fungi and Rhizobiaceae are particularly injured. Studies explaining the molecular mechanisms of the negative effects are presently limited. Therefore, we investigated the early effects of cyclic ITC goitrin on proteomes of the host and symbiotic Mesorhizobium loti in the nodules of Lotus japonicus and of free-living bacteria. In the nodules, many host proteins had a higher abundance, among them, peroxidases and pathogenesis-related PR-10 proteins functioning in the abscisic-acid-activated signaling pathway. In the microsymbiont, transporter proteins as a prominent group are enhanced; some proteins involved in N-fixation decreased. The proteomes give a report about the loss of immunity suppression resulting in the termination of symbiosis, which initiates nodule senescence. Free-living M. loti are severely damaged, indicated, i.a., by a decrease in transporter proteins, the assumed candidates for goitrin protein complex formation, and high proteolysis. The production of chicoric acid by the accompanying bacteria is inhibitory for M. loti but connected to goitrin elimination, as confirmed by mass spectrometric (MS) analysis. In summary, the nodulation process is severely affected by goitrin, causing nodule dysfunction and failed nodule development. N deficiency conditions leads to yellowish leaves and leaf abscission.

Harnessing chickpea bacterial endophytes for improved plant health and fitness

Endophytic bacteria live asymptomatically inside the tissues of host plants without inflicting any damage. Endophytes can confer several beneficial traits to plants, which can contribute to their growth, development, and overall health. They have been found to stimulate plant growth by enhancing nutrient uptake and availability. They can produce plant growth-promoting substances such as auxins, cytokinins, and gibberellins, which regulate various aspects of plant growth and development. Endophytes can also improve root system architecture, leading to increased nutrient and water absorption. Some endophytes possess the ability to solubilize nutrients, such as phosphorus and potassium, making them more available for plant uptake, and fixing atmospheric nitrogen. Chickpea (Cicer arietinum) is a major legume crop that has mutualistic interactions with endophytes. These endophytes can benefit the chickpea plant in various ways, including higher growth, improved nutrient uptake, increased tolerance to abiotic and biotic stressors, and disease suppression. They can produce enzymes and metabolites that scavenge harmful reactive oxygen species, thus reducing oxidative stress. Moreover, several studies reported that endophytes produce antimicrobial compounds, lytic enzymes, and volatile organic compounds that inhibit the growth of fungal pathogens and trigger systemic defense responses in plants, leading to increased resistance against a broad range of pathogens. They can activate plant defense pathways, including the production of defense-related enzymes, phytoalexins, and pathogenesis-related proteins, thereby providing long-lasting protection. It is important to note that the diversity and function of chickpea-associated endophytes can vary depending on factors such as variety, geographical location, and environmental conditions. The mechanisms behind the plant-beneficial interactions are still being intensively explored. In this review, new biotechnologies in agricultural production and ecosystem stability were presented. Thus, harnessing chickpea endophytes could be exploited in developing drought-resistant cultivars that can maintain productivity in arid and semi-arid environments, crucial for meeting the global demand for chickpeas.

Chickpea tolerance to temperature stress: Status and opportunity for improvement

Chickpea is a globally important commercial crop and a key source of protein for vegetarian populations. Though chickpea was domesticated at least 3000 years ago, research into abiotic stress tolerance has been limited compared to cereal crops such as wheat. This review investigates the impacts of heat stress on chickpea, focusing on reproductive development. The fertilisation process is particularly sensitive to environmental stress, such as drought and heat that can reduce yields by up to 70%. Current research has largely focused on breeding cultivars that reach maturity faster to avoid stress rather than true thermotolerance and little is known of the impact of heat on cellular processes. This review suggests that there is ample variation within the chickpea gene pool for selective breeding to achieve improved abiotic stress tolerance. Rates of genetic progress will improve once key QTL are identified and the link between thermotolerance and pollen viability confirmed. Other benefits may arise from better understanding of heat shock proteins and molecular chaperones and their role in the protection of reproductive processes.

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

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

Mediterranean Native Leguminous Plants: A Reservoir of Endophytic Bacteria with Potential to Enhance Chickpea Growth under Stress Conditions

Bacterial endophytes, a subset of a plant’s microbiota, can facilitate plant growth by a number of different mechanisms. The aims of this study were to assess the diversity and functionality of endophytic bacterial strains from internal root tissues of native legume species grown in two distinct sites in South of Portugal and to evaluate their ability to promote plant growth. Here, 122 endophytic bacterial isolates were obtained from 12 different native legume species. Most of these bacteria possess at least one of the plant growth-promoting features tested in vitro, with indole acetic acid production being the most common feature among the isolates followed by the production of siderophores and inorganic phosphate solubilization. The results of in planta experiments revealed that co-inoculation of chickpea plants with specific endophytic bacteria along with N₂-fixing symbionts significantly improved the total biomass of chickpea plants, in particular when these plants were grown under saline conditions. Altogether, this study revealed that Mediterranean native legume species are a reservoir of plant growth-promoting bacteria, that are also tolerant to salinity and to toxic levels of Mn. Thus, these bacterial endophytes are well adapted to common constraints present in soils of this region which constitutes important factors to consider in the development of bacterial inoculants for stressful conditions in the Mediterranean region.

Can stress response genes be used to improve the symbiotic performance of rhizobia?

Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.