Common Bean: A Legume Model on the Rise for Unraveling Responses and Adaptations to Iron, Zinc, and Phosphate Deficiencies

ABA as a downstream signal actively participates in phthalanilic acid mediated cold tolerance of common beans (Phaseolus vulgaris)

Although the reaction of plants to various stresses can be regulated by phthalanilic acid (PPA), the regulation mechanism in the cold resistance of common beans was still unclear. The study showed that the ABA content of common bean seedlings was significantly increased by PPA application under low-temperature stress, the growth of common bean seedlings was effectively protected, and the yield loss was reduced. Importantly, the regulation of PPA on cold resistance of common bean seedlings depended on ABA pathway. It was further revealed that the ABA receptor pathway was observably activated by knocking down the ABA catabolic gene CYP707As, and the cold resistance of common bean seedlings was considerably enhanced. At the same time, the regulation of PPA on the low-temperature resistance of common bean seedlings was visibly weakened, which was also proved by gene over-expression and virus induced gene silence of CYP707As. In addition, combining exogenous treatment of ABA biosynthesis inhibitor (fluridone) with endogenous gene knock-down, over-expression and virus induced gene silence of phospholipase D coding gene (PLD1), it was found that PPA could obviously enhance cold resistance of common bean seedlings by promoting phospholipase D to produce phosphatidic acid, increasing the antioxidant enzyme activity to reduce oxidative damage and improve the stability of the photosynthetic system. In summary, the molecular and physiological basis was firstly elucidated that phthalanilic acid enhanced cold resistance of common bean seedlings by phospholipid metabolism, photosynthetic system, and antioxidant status through the ABA pathway in the present study.

Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress

Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully factorial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines (Phaseolus vulgaris L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each generation. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change.IMPORTANCESeed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implications for durable plant microbiome maintenance in agriculture on the changing planet.

Chitosan, Methyl Jasmonate, and Silicon Induce Resistance to Angular Leaf Spot in Common Bean, Caused by Pseudocercospora griseola, with Expression of Defense-Related Genes and Enzyme Activities

This study assessed the efficacy of chitosan, methyl jasmonate, and silicon in the reduction of disease severity and the induction of defense responses in common bean plants against angular leaf spot caused by Pseudocercospora griseola. The expression level of several pathogenesis-related (PR) proteins, PR1, PR2 (β-1,3-glucanase), and PR3 (chitinase), and defense-related enzymes, phenylalanine ammonia-lyase, peroxidase, and lipoxygenase, was analyzed at different time points in common bean plants after different treatments. Elicitor treatments significantly reduced disease severity 21 days after inoculation, with silicon at a 2 mM concentration proving most effective with 38.93% disease control, followed by 1 mM MeJA and 2% chitosan, respectively. Treatments with chitosan, methyl jasmonate, and silicon, regardless of pathogen infection, significantly elevated PR1, PR2, and PR3 gene expressions at 48 h after inoculation (hpi). PAL and POD activities were similarly increased following elicitor treatments and pathogen infection, especially at 48 hpi. Chemical elicitors applied post-inoculation induced PR proteins, PAL, and POD enzyme activities at 48 hpi, while LOX activity exhibited a variable fluctuation with treatments. These findings suggested that chemical elicitors, especially silicon, were effective in reducing ALS disease severity in common beans, with improved resistance associated with the expression of pathogen-responsive genes. This study is the first to analyze the expression profiles of defense-related genes in common beans treated with chemical elicitors prior to P. griseola infection.

Suppression of Root Rot Fungal Diseases in Common Beans (Phaseolus vulgaris L.) through the Application of Biologically Synthesized Silver Nanoparticles

The biosynthesis of silver nanoparticles (AgNPs) using plant extracts has become a safe replacement for conventional chemical synthesis methods to fight plant pathogens. In this study, the antifungal activity of biosynthesized AgNPs was evaluated both in vitro and under greenhouse conditions against root rot fungi of common beans (Phaseolus vulgaris L.), including Macrophomina phaseolina, Pythium graminicola, Rhizoctonia solani, and Sclerotium rolfsii. Among the eleven biosynthesized AgNPs, those synthesized using Alhagi graecorum plant extract displayed the highest efficacy in suppressing those fungi. The findings showed that using AgNPs made with A. graecorum at a concentration of 100 μg/mL greatly slowed down the growth of mycelium for R. solani, P. graminicola, S. rolfsii, and M. phaseolina by 92.60%, 94.44%, 75.93%, and 79.63%, respectively. Additionally, the minimum inhibitory concentration (75 μg/mL) of AgNPs synthesized by A. graecorum was very effective against all of these fungi, lowering the pre-emergence damping-off, post-emergence damping-off, and disease percent and severity in vitro and greenhouse conditions. Additionally, the treatment with AgNPs led to increased root length, shoot length, fresh weight, dry weight, and vigor index of bean seedlings compared to the control group. The synthesis of nanoparticles using A. graecorum was confirmed using various physicochemical techniques, including UV spectroscopy, Fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDS) analysis. Collectively, the findings of this study highlight the potential of AgNPs as an effective and environmentally sustainable approach for controlling root rot fungi in beans.

Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses

Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.

Phaseolus vulgaris mutants reveal variation in the nuclear genome

Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.

Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype

We analyzed the changes in the volatilome, proteome, stomatal conductance, salicylic and jasmonic acid contents of a susceptible and a moderately resistant genotype of common bean, Phaseoulus vulgaris L., challenged with Colletotrichum lindemuthianum, the causal agent of fungal anthracnose. Our results indicate differences at both proteome and volatilome levels between the two genotypes, before and after the infection, and different defense strategies. The moderately resistant genotype hindered pathogen infection, invasion, and replication mainly by maintaining epidermal and cell wall structure. The susceptible genotype was not able to limit the early stages of pathogen infection. Rather, stomatal conductance increased in the infected susceptible genotype, and enhanced synthesis of Green Leaf Volatiles and salicylic acid was observed, together with a strong hypersensitive response. Proteomic investigation provided a general framework for physiological changes, whereas observed variations in the volatilome suggested that volatile organic compounds may principally represent stress markers rather than defensive compounds per se.

Biofortification of common bean (Phaseolus vulgaris L.) with iron and zinc: Achievements and challenges

Micronutrient deficiencies (hidden hunger), particularly in iron (Fe) and zinc (Zn), remain one of the most serious public health challenges, affecting more than three billion people globally. A number of strategies are used to ameliorate the problem of micronutrient deficiencies and to improve the nutritional profile of food products. These include (i) dietary diversification, (ii) industrial food fortification and supplements, (iii) agronomic approaches including soil mineral fertilisation, bioinoculants and crop rotations, and (iv) biofortification through the implementation of biotechnology including gene editing and plant breeding. These efforts must consider the dietary patterns and culinary preferences of the consumer and stakeholder acceptance of new biofortified varieties. Deficiencies in Zn and Fe are often linked to the poor nutritional status of agricultural soils, resulting in low amounts and/or poor availability of these nutrients in staple food crops such as common bean. This review describes the genes and processes associated with Fe and Zn accumulation in common bean, a significant food source in Africa that plays an important role in nutritional security. We discuss the conventional plant breeding, transgenic and gene editing approaches that are being deployed to improve Fe and Zn accumulation in beans. We also consider the requirements of successful bean biofortification programmes, highlighting gaps in current knowledge, possible solutions and future perspectives.

Biochemical and proteomic insights revealed selenium priming induced phosphorus stress tolerance in common bean (Phaseolus vulgaris L.)

BACKGROUND

Mineral stress is one of the dominating abiotic stresses, which leads to decrease in crop production. Selenium (Se) seed priming is a recent approach to mitigate the plant's mineral deficiency stress. Although not an essential element, Se has beneficial effects on the plants in terms of growth, quality, yield and plant defense system thus, enhancing plant tolerance to mineral deficiency.

METHODS AND RESULTS

The present research was accomplished to find out the effect of Se priming on common bean plant (SFB-1 variety) under phosphorus (P) stress. The seeds were grown invitro on four different MGRL media which are normal MGRL media as control with non-Se primed seeds (Se^- P⁺), non -Se primed seeds grown on P deficient MGRL media (Se^- P^-), Se primed seeds grown on normal MGRL media (Se⁺P⁺) and Se primed seeds grown on P deficient MGRL media (Se⁺P ^-). The various morphological and biochemical parameters such as proline content, total sugar content, polyphenols and expression of proteins were analyzed under P stress. The results showed that Se priming has significantly (p ≤ 0.05) affected the morphological as well as biochemical parameters under normal and P stress conditions. The morphological parameters-length, weight, number of nodes and leaves of Se⁺P⁺, Se⁺P^- root and shoot tissue showed significant increase as compared to Se^-P⁺, Se^-P^-. Similarly various biochemical parameters such as total chlorophyll content, proline, total sugar content and polyphenols of Se⁺P⁺, Se⁺P^- increased significantly as compared to Se^-P⁺, Se^-P^-. The differential protein expression in both Se⁺P⁺, Se⁺P^- and Se^-P⁺, Se^-P^- plants were determined using MALDI-MS/MS. The differentially expressed proteins in Se⁺P⁺, Se⁺P^- plants were identified as caffeic acid-3-O-methyltransferase (COMT) and SecA protein (a subunit of Protein Translocan transporter), and are found responsible for lignin synthesis in root cell walls and ATP dependent movement of thylakoid proteins across the membranes in shoot respectively. The differential expression of proteins in plant tissues, validated morphological and biochemical responses such as maintaining membrane integrity, enhanced modifications in cellular metabolism, improved polyphenol activities and expression of defensive proteins against mineral deficiency.

CONCLUSIONS

The study provided an understanding of Se application as a potential approach increasing tolerance and yield in crop plants against mineral deficiency.

Plant-growth-promoting bacteria from rhizosphere of Chilean common bean ecotype (Phaseolus vulgaris L.) supporting seed germination and growth against salinity stress

Salinity abiotic stress is increasing day by day due to continuous global warming and climate change. This is also becoming one of the major causes behind the reduction in crop production. Plant-bacteria interaction plays an essential role in improving crop yield without using any chemical fertilizers. The present study aims to characterize the interaction between plant-growth-promoting bacteria (PGPB) and their role in mitigating salinity stress for local variety crops. Therefore, in this work, two PGPB, namely, Bacillus proteolyticus Cyn1 and Bacillus safensis Cyn2, were isolated from rhizospheric soil of the Chilean common bean ecotype "Sapito" (Phaseolus vulgaris L.), and their PGPB traits were analyzed. Cyn1 can produce NH₃ and HCN and also secrete siderophores, whereas Cyn2 produced NH₃ and siderophores but responded negatively to HCN production. Both the isolated bacteria have shown a positive result for ACC deaminase production, phosphate solubilization, and catalase enzyme secretion. Under all three tested abiotic stresses, i.e., temperature, water, and salinity, both the bacteria and their consortium have demonstrated positive responses. Cyn1 under temperature stress and water stress can produce a biofilm network to combat the stress. While under salinity stress, both the PGPB isolates indicated the production of stress components and cytoplasmic inclusion bodies. Based on the response, among all other abiotic stresses, salinity stress was chosen for further plant-bacteria interaction study and growth. Visible root colonization of the bacteria has been observed in comparison to the control. The germination index was 100% for all experimental setups of seed bacterization, both under control conditions and salinity stress. Both bacteria responded with good PGP traits that helped in the growth of healthy plants after the bacterial treatment in final pot experiments. Additionally, the consortium and the plants treated with Cyn1 have demonstrated high production of photosynthetic pigments in both experimental setups. Both B. proteolyticus Cyn1 and B. safensis Cyn2 have shown promising PGP characters and efficient response against toxicity related to salinity. Hence, both of these bacteria and consortium can be used for improved agricultural production of Chilean native common beans in the near future.

Regulation of the Zinc Deficiency Response in the Legume Model Medicago truncatula

The zinc deficiency response in Arabidopsis thaliana is regulated by F-group basic region leucine-zipper (F-bZIP) transcription factors, and there is evidence of evolutionary conservation of this regulatory network in land plants. Fundamental knowledge on the zinc homeostasis regulation in crop species will contribute to improving their zinc nutritional value. Legumes are protein-rich crops, used worldwide as part of traditional diets and as animal forage, being therefore a good target for micronutrient biofortification. Here, we identified F-bZIP transcription factors in representative legume species and functionally characterized the two F-bZIPs from Medicago truncatula. Results indicate that MtFbZIP1 is the functional homolog of A. thaliana bZIP19 and bZIP23, while MtFbZIP2 does not play a role in the zinc deficiency response. Additionally, analysis of M. truncatula genes from the Zrt/Irt-like protein (ZIP) family of zinc transporters or encoding nicotianamine synthase enzymes that produce the zinc ligand nicotianamine, support the conservation of the F-bZIP-regulated zinc deficiency response in M. truncatula. Phylogenetic analysis of F-bZIP homologs enriched in legume species reinforces the branching into two groups, with MtFbZIP1 and MtFbZIP2 mapping in Groups 1 and 2, respectively. This phylogeny combined with the functional characterization of MtFbZIPs supports the suggested conservation of the zinc deficiency response associated with Group 1 F-bZIPs, and the more variable evolutionary paths associated with Group 2. Overall, we provide novel insight on the mechanisms of response to zinc deficiency in M. truncatula, which contributes to developing strategies for improving zinc content in legume crops.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.

The effect of ENSO on common bean production in Colombia: a time series approach

The common bean is an important staple food in Colombia with diverse nutritional content and environmental benefits. The most important climatic risk confronted by common bean production in Colombia is El Niño Southern Oscillation (ENSO) since its two extreme phases -El Niño and La Niña- increase the intensity and variety of abiotic and biotic stresses in the region. Using information from the Food and Agricultural Organization (FAO) for the period 1991-2018, we test whether pre-2030 ENSO has had a negative impact on common bean production in Colombia using a Prais-Winsten regression model. We find that common beans' yields have been negatively affected by El Niño, but not by La Niña. Moreover, short-run ENSO-induced deviations in the growth rate of precipitation with respect to its long-run value reduce yields and increase farmers' income from common bean production. These results have two important implications. From a modelling standpoint, we find that precipitation has a non-linear relationship with yields and incomes, implying that second-order effects should be incorporated in any analysis of the effects of climatic variables on agricultural production. From a policy perspective, our results suggest a need for countercyclical polices to counteract price spikes of common beans in the Colombian market since, when they occur, they tend to over-compensate the reduction in yields, which reduce common bean consumers' purchasing power and food security.

Zinc deficiency responses: bridging the gap between Arabidopsis and dicotyledonous crops

Zinc (Zn) deficiency is a widespread phenomenon in agricultural soils worldwide and has a major impact on crop yield and quality, and hence on human nutrition and health. Although dicotyledonous crops represent >30% of human plant-based nutrition, relatively few efforts have been dedicated to the investigation of Zn deficiency response mechanisms in dicotyledonous, in contrast to monocotyledonous crops, such as rice or barley. Here, we describe the Zn requirement and impact of Zn deficiency in several economically important dicotyledonous crops, Phaseolus vulgaris, Glycine max, Brassica oleracea, and Solanum lycopersicum. We briefly review our current knowledge of the Zn deficiency response in Arabidopsis and outline how this knowledge is translated in dicotyledonous crops. We highlight commonalities and differences between dicotyledonous species (and with monocotyledonous species) regarding the function and regulation of Zn transporters and chelators, as well as the Zn-sensing mechanisms and the role of hormones in the Zn deficiency response. Moreover, we show how the Zn homeostatic network intimately interacts with other nutrients, such as iron or phosphate. Finally, we outline how variation in Zn deficiency tolerance and Zn use efficiency among cultivars of dicotyledonous species can be leveraged for the design of Zn biofortification strategies.

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

Common bean blight (CBB), primarily caused by Xanthomonas axonopodis pv. phaseoli (Xap), is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). The tepary bean genotype PI 319443 displays high resistance to Xap, and the common bean genotypes HR45 and Bilu display high resistance and susceptibility to Xap, respectively. To identify candidate genes related to Xap resistance, transcriptomic analysis was performed to compare gene expression levels with Xap inoculation at 0, 24, and 48 h post inoculation (hpi) among the three genotypes. A total of 1,146,009,876 high-quality clean reads were obtained. Differentially expressed gene (DEG) analysis showed that 1,688 DEGs responded to pathogen infection in the three genotypes. Weighted gene coexpression network analysis (WGCNA) was also performed to identify three modules highly correlated with Xap resistance, in which 334 DEGs were likely involved in Xap resistance. By combining differential expression analysis and WGCNA, 139 DEGs were identified as core resistance-responsive genes, including 18 genes encoding resistance (R) proteins, 19 genes belonging to transcription factor families, 63 genes encoding proteins with oxidoreductase activity, and 33 plant hormone signal transduction-related genes, which play important roles in the resistance to pathogen infection. The expression patterns of 20 DEGs were determined by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-seq results.

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Iron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris. The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.

The determinants of common bean variety selection and diversification in Colombia

Variety selection and diversification are climate change adaptation practices pursued by Colombian common bean producers. We investigate the drivers behind common bean variety selection and diversification in one of the most important common bean production regions in Colombia -Santander. The effects of climate change on this region are expected to be elevation driven. Exploiting the relationship between elevation-driven weather variations and climate change perception in Santander, we estimate an alternative-specific conditional logistic regression model to identify the determinants of common bean variety selection from a survey of producers. Using an ordered-logistic regression model, we also investigate the drivers behind common bean variety diversification within this farming community. We find that farms' elevation, household composition, and seed certification are some of the most important drivers behind farmers' common bean variety selection in Santander. We also find that varieties that sell at higher prices and have shorter vegetative cycles tend to be more preferred by farmers. Finally, farmers who receive more help from family members and own a tractor tend to grow more than one variety in the same production cycle. Common bean breeding programmes can exploit these drivers to design communication strategies to maximize uptake of newly developed common bean phenotypes.

DISTRIBUTION AND BIOLOGY OF INVASIVE SPECIES OF BEAN BRUCHID <i>ACANTHOSCELIDES OBTECTUS</i> (INSECTA, COLEOPTERA, BRUCHIDAE)

The review of literary sources on ecology, biology, distribution of bean bruchid ( Acanthoscelides obtectus ) and its main food plant - Phaseolus vulgaris in North and South America; Europe, Africa, Asia, Australia and more details in Russia; the influence of abiotic, biotic and anthropogenic factors on the invasive process, phytosanitary condition of common bean crops in Russia is presented. Some aspects of the invader management are shown. The main stages and areas of cultivation of common bean and invasion of bean bruchid from their primary habitat in South America and in the south of North America are traced; the vectors and reasons causing them are considered. In Russia, the economic importance of bean bruchid has increased since the mid-1980s, which coincided with the climate warming; there was an expansion of its distribution in the eastern and north-western directions. At the last decades of the 20th century, it had penetrated in Smolensk and in the south part of the Tver and the Tomsk regions. With the increase in production of beans in Russia, the lack of systemic protection from bean bruchid and further increase of climate warming will contribute to the extension of its range to the north in the European part of Russia and the Urals to 57-58° N. Lat., where the conditions of the summer period are favorable for development of common bean and bean bruchid. To the east, it may spread to Tyva, Buryatia, the Trans-Baikal territory, the Amur region, the Jewish Autonomous region, and the southern part of the Khabarovsk territory. With the introduction of strict internal quarantine and a system of protection of common bean from this pest, which prevents the spread of infected dry bean, on the contrary, it is possible to reduce the distribution range of the bean bruchid, with its disappearance in the Siberian, Ural districts, Bashkortostan and Tatarstan.

Short Term Elevated CO2 Interacts with Iron Deficiency, Further Repressing Growth, Photosynthesis and Mineral Accumulation in Soybean (Glycine max L.) and Common Bean (Phaseolus vulgaris L.)

Elevated CO2 (eCO2) has been reported to cause mineral losses in several important food crops such as soybean (Glycine max L.) and common bean (Phaseolus vulgaris L.). In addition, more than 30% of the world’s arable land is calcareous, leading to iron (Fe) deficiency chlorosis and lower Fe levels in plant tissues. We hypothesize that there will be combinatorial effects of eCO2 and Fe deficiency on the mineral dynamics of these crops at a morphological, biochemical and physiological level. To test this hypothesis, plants were grown hydroponically under Fe sufficiency (20 μM Fe-EDDHA) or deficiency (0 μM Fe-EDDHA) at ambient CO2 (aCO2, 400 ppm) or eCO2 (800 ppm). Plants of both species exposed to eCO2 and Fe deficiency showed the lowest biomass accumulation and the lowest root: shoot ratio. Soybean at eCO2 had significantly higher chlorophyll levels (81%, p < 0.0001) and common bean had significantly higher photosynthetic rates (60%, p < 0.05) but only under Fe sufficiency. In addition, eCO2 increased ferric chelate reductase acivity (FCR) in Fe-sufficient soybean by 4-fold (p < 0.1) and in Fe-deficient common bean plants by 10-fold (p < 0.0001). In common bean, an interactive effect of both environmental factors was observed, resulting in the lowest root Fe levels. The lowering of Fe accumulation in both crops under eCO2 may be linked to the low root citrate accumulation in these plants when grown with unrestricted Fe supply. No changes were observed for malate in soybean, but in common bean, shoot levels were significantly lower under Fe deficiency (77%, p < 0.05) and Fe sufficiency (98%, p < 0.001). These results suggest that the mechanisms involved in reduced Fe accumulation caused by eCO2 and Fe deficiency may not be independent, and an interaction of these factors may lead to further reduced Fe levels.

Morphological, Biochemical, and Proteomic Studies Revealed Impact of Fe and P Crosstalk on Root Development in Phaseolus vulgaris L

Mineral stress is one of the major abiotic stresses faced by crop plants. The present study was undertaken to investigate the impact of mineral stress (iron (Fe) and phosphorus (P)) on various morphological and biochemical responses of the shoot and root tissues and root architecture of common bean (Phaseolus vulgaris L.). This study also leads us to the identification of P stress responsive proteins. The study was conducted under in vitro conditions, in which seeds of Shalimar French Bean-1 (SFB-1) variety were cultured on four different MGRL medium (control (P₁Fe₁), iron deficient (P₁Fe₀), phosphorus deficient (P₀Fe₁), and phosphorus and iron deficient (P₀Fe₀)). Chlorophyll content of leaves, Fe/P content of root tissues, total sugars, proline, length, and weight of shoot and root tissues were assessed and compared within and between the treatments. The analyzed data revealed significant difference between control and other three treatments. Chlorophyll content of shoots was found significantly decreased under mineral stress treatments P₀Fe₁, P₁Fe₀, and P₀Fe₀ than control. Length and weight of shoot and root were also observed significantly decreased under P₀Fe₁, P₁Fe₀, and P₀Fe₀ as compared to control. Total sugar was significantly higher in P₀Fe₁ of roots in comparison to control. Proline content was significantly higher in both tissues of shoots and roots of plants grown under P₁Fe₀, P₀Fe₁, and P₀Fe₀ than control condition. Furthermore, we unexpectedly observed the recovery of roots (mainly primary roots) under P₀Fe₀ as compared to P₁Fe₀ and P₀Fe₁^. Interestingly higher concentration of Fe was also observed in P₀Fe₁ compared to other treatments and also higher concentration of P was observed in P₁Fe₁. These findings suggested that there is a crosstalk between Fe and P and also revealed that there is a disruption in the ability of PR (primary root) to sense local P deficiency in the absence of Fe. Furthermore, proteomics analysis (SDS-PAGE followed by MALDI MS) helped in identification of defensive proteins in P stress condition compared to control.

Isolation and Characterization of High-Efficiency Rhizobia From Western Kenya Nodulating With Common Bean

Common bean is one of the primary protein sources in third-world countries. They form nodules with nitrogen-fixing rhizobia, which have to be adapted to the local soils. Commercial rhizobial strains such as Rhizobium tropici CIAT899 are often used in agriculture. However, this strain failed to significantly increase the common bean yield in many places, including Kenya, due to the local soils' low pH. We isolated two indigenous rhizobial strains from the nodules of common bean from two fields in Western Kenya that have never been exposed to commercial inocula. We then determined their ability to fix nitrogen in common beans, solubilize phosphorus, and produce indole acetic acid. In greenhouse experiments, common bean plants inoculated with two isolates, B3 and S2 in sterile vermiculite, performed better than those inoculated with CIAT899 or plants grown with nitrogen fertilizer alone. In contrast to CIAT899, both isolates grew in the media with pH 4.8. Furthermore, isolate B3 had higher phosphate solubilization ability and produced more indole acetic acid than the other two rhizobia. Genome analyses revealed that B3 and S2 are different strains of Rhizobium phaseoli. We recommend fieldwork studies in Kenyan soils to test the efficacy of the two isolates in the natural environment in an effort to produce inoculants specific for these soils.

Context-Dependent Effects of Trichoderma Seed Inoculation on Anthracnose Disease and Seed Yield of Bean (Phaseolus vulgaris): Ambient Conditions Override Cultivar-Specific Differences

Root colonizing Trichoderma fungi can stimulate plant immunity, but net effects are strain × cultivar-specific and changing ambient conditions further contribute to variable outcomes. Here, we used four Trichoderma spp. to inoculate seeds of four common bean (Phaseolus vulgaris) cultivars and explored in three different experimental setups the effects on fungal anthracnose after leaf inoculation with Colletotrichum lindemuthianum. Plants growing in pots with field soil under greenhouse conditions exhibited the highest and those in the open field the lowest overall levels of disease. Among 48 Trichoderma strain × bean cultivar × setup combinations, Trichoderma-inoculation enhanced disease in six and decreased disease in ten cases, but with the exception of T. asperellum B6-inoculated Negro San Luis beans, the strain × cultivar-specific effects on anthracnose severity differed among the setups, and anthracnose severity did not predict seed yield in the open field. In the case of Flor de Mayo beans, Trichoderma even reduced yield in anthracnose-free field plots, although this effect was counterbalanced in anthracnose-infected plots. We consider our work as a case study that calls for stronger emphasis on field experiments in the early phases of screenings of Trichoderma inoculants as plant biostimulants.

Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans

Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.

Genetic Variability of Mineral Content in Different Grain Structures of Bean Cultivars from Mesoamerican and Andean Gene Pools

Beans (Phaseolus vulgaris L.) are an important source of proteins, carbohydrates, and micronutrients in the diets of millions of people in Latin America and Africa. Studies related to genetic variability in the accumulation and distribution of nutrients are valuable for biofortification programs, as there is evidence that the seed coat and embryo differ in the bioavailability of essential nutrients. In this study, we sought to evaluate the genetic variability of total mineral content in the grain and its constituent parts (seed coat, cotyledon, and embryonic axis) of bean genotypes from Mesoamerican and Andean centers of origin. Grain samples of 10 bean cultivars were analyzed for the content of proteins and minerals (Mg, Ca, K, P, Mn, S, Cu, B, Fe, and Zn) in the whole grains and seed coat, cotyledons, and embryonic axis tissues. Genetic variability was observed among the cultivars for protein content and all evaluated minerals. Moreover, differential accumulation of minerals was observed in the seed coat, cotyledons, and embryonic axis. Except for Ca, which accumulated predominantly in the seed coat, higher percentages of minerals were detected in the cotyledons. Furthermore, 100-grain mass values showed negative correlations with the contents of Ca, Mg, P, Zn, Fe, and Mn in whole grains or in the different grain tissues. In general, the Mesoamerican cultivars showed a higher concentration of minerals in the grains, whereas Andean cultivars showed higher concentrations of protein.

Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors

Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.

Comparative Study between Exogenously Applied Plant Growth Hormones versus Metabolites of Microbial Endophytes as Plant Growth-Promoting for Phaseolus vulgaris L

Microbial endophytes organize symbiotic relationships with the host plant, and their excretions contain diverse plant beneficial matter such as phytohormones and bioactive compounds. In the present investigation, six bacterial and four fungal strains were isolated from the common bean (Phaseolus vulgaris L.) root plant, identified using molecular techniques, and their growth-promoting properties were reviewed. All microbial isolates showed varying activities to produce indole-3-acetic acid (IAA) and different hydrolytic enzymes such as amylase, cellulase, protease, pectinase, and xylanase. Six bacterial endophytic isolates displayed phosphate-solubilizing capacity and ammonia production. We conducted a field experiment to evaluate the promotion activity of the metabolites of the most potent endophytic bacterial (Bacillus thuringiensis PB2 and Brevibacillus agri PB5) and fungal (Alternaria sorghi PF2 and, Penicillium commune PF3) strains in comparison to two exogenously applied hormone, IAA, and benzyl adenine (BA), on the growth and biochemical characteristics of the P. vulgaris L. Interestingly, our investigations showed that bacterial and fungal endophytic metabolites surpassed the exogenously applied hormones in increasing the plant biomass, photosynthetic pigments, carbohydrate and protein contents, antioxidant enzyme activity, endogenous hormones and yield traits. Our findings illustrate that the endophyte Brevibacillus agri (PB5) provides high potential as a stimulator for the growth and productivity of common bean plants.

Priming of seeds with INA and its transgenerational effect in common bean (Phaseolus vulgaris L.) plants

Priming is a mechanism of defense that prepares the plant's immune system for a faster and/or stronger activation of cellular defenses against future exposure to different types of stress. This enhanced resistance can be achieved by using inorganic and organic compounds which imitate the biological induction of systemic acquired resistance. INA (2,6 dichloro-isonicotinic acid) was the first synthetic compound created as a resistance inducer for plant-pathogen interactions. However, the use of INA to activate primed resistance in common bean, at the seed stage and during germination, remains experimentally unexplored. Here, we test the hypothesis that INA-seed treatment would induce resistance in common bean plants to Pseudomonas syringae pv. phaseolicola, and that the increased resistance is not accompanied by a tradeoff between plant defense and growth. Additionally, it was hypothesized that treating seeds with INA has a transgenerational priming effect. We provide evidence that seed treatment activates a primed state for disease resistance, in which low nucleosome enrichment and reduced histone activation marks during the priming phase, are associated with a defense-resistant phenotype, characterized by symptom appearance, pathogen accumulation, yield, and changes in gene expression. In addition, the priming status for induced resistance can be inherited to its offspring.

Contrasting Expression of Rhizobial Phytase in Nodules of Two Soybean Cultivars Grown Under Low Phosphorus Availability

Phosphorus deficiency can be a major limitation to legume growth when plant nitrogen nutrition depends on symbiotic nitrogen fixation. One possible approach to overcome this constraint is the selection of plant and rhizobial genotypes capable of metabolizing complex forms of phosphorus in the nodules. The aim of this research was to study the rhizobial phytase transcript abundance in nodules of two soybean cultivars (Glycine max (L.) Merr.) grown under two different phosphorus conditions in hydroaeroponic conditions. An in situ RT-PCR of a rhizobial phytase was performed in microtome sections of soybean nodules of two cultivars growing under phosphorus sufficiency vs. phosphorus deficiency. The results showed that the plant cultivar may influence the level of transcript abundance of the bacterial phytase and in consequence affect the phosphorus use efficiency of nitrogen-dependent Bradyrhizobium spp.-soybean symbioses. Thus, the selection of a good combination of plant and rhizobial genotypes should be a priority when breeding for phosphorus deficiency is performed.

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops

Minor grain crops are widely cultivated in northwest China and played important roles in local economic. Soil microbes play a central role in ecological function and biological stability and related to soil quality. In order to uncover the soil microbial composition differences and the factors under 5-year continuous monocropping of three minor crops (Proso millet, Common bean and Common buckwheat) in Guan-Zhong Plain, six soil nutrimental parameters, soil pH, soil moisture content, and four soil enzyme activities were analyzed and soil microbial composition were sequenced. The results showed that after 5-years of continuous monocropping, different cover crops influenced most of soil physicochemical properties, expect soil moisture content (P < 0.05), the available nutrients were significant higher in proso millet soil, and the pH was significantly higher in common buckwheat soil. soil ALP, catalase and urease activities were significantly different between soils (P< 0.01), in which soil catalase activities were significantly lower and soil ALP and urease activities were significantly higher than that of proso millet and common buckwheat. A total of 171439 sequences, 9468 OTUs and 29 phylum for bacteria, 128920 sequences, 544 OTUs and 27 phylum for fungi were obtained. In addition, no significantly difference obtained in diversity and richness between soils (P < 0.05). According to relative abundance, Proteobacteria, Chloroflexi, Gemmatimonadetes and Acidobacteria were the dominant bacterial phylum in all samples, moreover, the relative abundance of Caldiserica was significantly different between soils (P < 0.05). Ascomycota (79.04%-90.21%) was dominant phylum in fungal community and phylum Phragmoplastophyta (P < 0.01) and Glomeromycota (P < 0.05) were significantly different between soils. Redundancy analysis indicated that available nutrients Nitrogen and Potassium are the strongest predictors in both bacterial and fungal community. In conclusion, different cover crops influenced soil nutrient properties, soil pH and soil microbial composition, and continuous monocropping decreased soil fertility condition. Moreover, Common bean and Common buckwheat were more sensitive to monocropping treatment.

Inhibition of legume nodulation by Pi deficiency is dependent on the autoregulation of nodulation (AON) pathway

Inhibition of nodule development is one of the main adverse effects of phosphate (Pi) deficiency in legumes. Despite all of the efforts made over the last decades to understand how root nodules cope with Pi deficiency, the molecular mechanisms leading to the reduction in nodule number under Pi deficiency remain elusive. In the present study, we provide experimental evidence indicating that Pi deficiency activates the autoregulation of nodulation (AON) pathway, leading to a reduction in nodule numbers in both common bean and soybean. A transcriptional profile analysis revealed that the expression of the AON-related genes PvNIN, PvRIC1, PvRIC2, and PvTML is upregulated under Pi deficiency conditions. The downregulation of the MYB transcription factor PvPHR1 in common bean roots significantly reduced the expression of these four AON-related genes. Physiological analyses indicated that Pi deficiency does not affect the establishment of the root nodule symbiosis in the supernodulation mutant lines Pvnark and Gmnark. Reciprocal grafting and split-roots analyses determined that the activation of the AON pathway was required for the inhibitory effect of Pi deficiency. Altogether, these data improve our understanding of the genetic mechanisms controlling the establishment of the root nodule symbiosis under Pi deficiency.

Genotypic variation for cadmium tolerance in common bean (Phaseolus vulgaris L.)

Given the limitation of crop production in Cd-polluted areas, the identification and selection of plant genotypes tolerant to Cd stress are of great significance. In the present work, we show the existence of genotypic variation for Cd tolerance in common bean. The laboratory screening of 25 bean genotypes indicated a significant positive correlation of the mean productivity (MP) and the geometric mean productivity (GMP) with plant fresh weight both in control and Cd-treated plants. A principal component analysis further confirmed this variation and, together with other analyses, led to the selection of genotypes G-11867, Taylor, Emerson, and D-81083 as tolerant genotypes. A total of six bean genotypes with different degrees of Cd tolerance were selected, and their long-term physiological responses to Cd (0, 45, and 90 mg/kg soil) were evaluated. Increasing Cd concentrations led to higher Cd accumulation both in roots and shoots, and to significant rises in the levels of the oxidative stress biomarkers malondialdehyde (MDA), dityrosine (D-T), and 8-hydroxy-2'-deoxyguanosine (8-OH-2'-dG). Remarkable reductions in plant hormone levels and chlorophyll contents, as well as in dry and fresh weight, were observed in Cd-treated plants. Among the examined genotypes, Emerson, Taylor, and G-11867 were found to be more tolerant to Cd owing to lower Cd accumulation and lower oxidative stress levels, as well as higher chlorophyll and hormone contents. Our results contribute to the understanding of the physiological and biochemical basis of Cd tolerance in bean plants and may therefore, be useful for breeding programs directed towards obtaining bean varieties showing low Cd accumulation.

Comparative transcriptome provides molecular insight into defense-associated mechanisms against spider mite in resistant and susceptible common bean cultivars

Common bean (Phaseolus vulgaris L.) is a major source of proteins and one of the most important edible foods for more than three hundred million people in the world. The common bean plants are frequently attacked by spider mite (Tetranychus urticae Koch), leading to a significant decrease in plant growth and economic performance. The use of resistant cultivars and the identification of the genes involved in plant-mite resistance are practical solutions to this problem. Hence, a comprehensive study of the molecular interactions between resistant and susceptible common bean cultivars and spider mite can shed light into the understanding of mechanisms and biological pathways of resistance. In this study, one resistant (Naz) and one susceptible (Akhtar) cultivars were selected for a transcriptome comparison at different time points (0, 1 and 5 days) after spider mite feeding. The comparison of cultivars in different time points revealed several key genes, which showed a change increase in transcript abundance via spider mite infestation. These included genes involved in flavonoid biosynthesis process; a conserved MYB-bHLH-WD40 (MBW) regulatory complex; transcription factors (TFs) TT2, TT8, TCP, Cys2/His2-type and C2H2-type zinc finger proteins; the ethylene response factors (ERFs) ERF1 and ERF9; genes related to metabolism of auxin and jasmonic acid (JA); pathogenesis-related (PR) proteins and heat shock proteins.

Common bean protein hydrolysate modulates lipid metabolism and prevents endothelial dysfunction in BALB/c mice fed an atherogenic diet

BACKGROUND AND AIMS

Common beans (Phaseolus vulgaris L.) protein hydrolysate is a source of bioactive peptides with known health benefits. The aim of this study was to evaluate the effect of common bean protein hydrolysate on lipid metabolism and endothelial function in male adult BALB/c mice fed an atherogenic diet for nine weeks.

METHODS AND RESULTS

Male adult mice were divided into three experimental groups (n = 12) and fed with normal control diet; atherogenic diet and atherogenic diet added with bean protein hydrolysate (700 mg/kg/day) for nine weeks. Food intake, weight gain, lipid profile, Atherogenic Index of Plasma, inflammation biomarkers and endothelial function were evaluated. APH group presented reduced feed intake, weight gain, lipid profile, tumor necrosis factor-α, angiotensin II (94% and 79%, respectively) and increased endothelial nitric oxide synthase (62%).

CONCLUSIONS

Protein hydrolysate showed hypocholesterolemic activity preventing inflammation and dysfunction of vascular endothelium, in addition to decreasing oxidative stress, indicating an adjuvant effect on reducing atherogenic risk.

Argonaute Proteins: Why Are They So Important for the Legume-Rhizobia Symbiosis?

Unlike most other land plants, legumes can fulfill their nitrogen needs through the establishment of symbioses with nitrogen-fixing soil bacteria (rhizobia). Through this symbiosis, fixed nitrogen is incorporated into the food chain. Because of this ecological relevance, the genetic mechanisms underlying the establishment of the legume-rhizobia symbiosis (LRS) have been extensively studied over the past decades. During this time, different types of regulators of this symbiosis have been discovered and characterized. A growing number of studies have demonstrated the participation of different types of small RNAs, including microRNAs, in the different stages of this symbiosis. The involvement of small RNAs also indicates that Argonaute (AGO) proteins participate in the regulation of the LRS. However, despite this obvious role, the relevance of AGO proteins in the LRS has been overlooked and understudied. Here, we discuss and hypothesize the likely participation of AGO proteins in the regulation of the different steps that enable the establishment of the LRS. We also briefly review and discuss whether rhizobial symbiosis induces DNA damages in the legume host. Understanding the different levels of LRS regulation could lead to the development of improved nitrogen fixation efficiency to enhance sustainable agriculture, thereby reducing dependence on inorganic fertilizers.

A Novel Positive Regulator of the Early Stages of Root Nodule Symbiosis Identified by Phosphoproteomics

Signals and signaling pathways underlying the symbiosis between legumes and rhizobia have been studied extensively over the past decades. In a previous phosphoproteomic study on the Medicago truncatula-Sinorhizobium meliloti symbiosis, we identified plant proteins that are differentially phosphorylated upon the perception of rhizobial signals, called Nod factors. In this study, we provide experimental evidence that one of these proteins, Early Phosphorylated Protein 1 (EPP1), is required for the initiation of this symbiosis. Upon inoculation with rhizobia, MtEPP1 expression was induced in curled root hairs. Down-regulation of MtEPP1 in M. truncatula roots almost abolished calcium spiking, reduced the expression of essential symbiosis-related genes (MtNIN, MtNF-YB1, MtERN1 and MtENOD40) and strongly decreased nodule development. Phylogenetic analyses revealed that orthologs of MtEPP1 are present in legumes and specifically in plant species able to host arbuscular mycorrhizal fungi, suggesting a possible role in this association too. Short chitin oligomers induced the phosphorylation of MtEPP1 like Nod factors. However, the down-regulation of MtEPP1 affected the colonization of M. truncatula roots by arbuscular mycorrhizal fungi only moderately. Altogether, these findings indicate that MtEPP1 is essential for the establishment of the legume-rhizobia symbiosis but might plays a limited role in the arbuscular mycorrhizal symbiosis.

Legume biofortification is an underexploited strategy for combatting hidden hunger

Legumes are the world's primary source of dietary protein and are particularly important for those in developing economies. However, the biofortification potential of legumes remains underexploited. Legumes offer a diversity of micronutrients and amino acids, exceeding or complementing the profiles of cereals. As such, the enhancement of legume nutritional composition presents an appealing target for addressing the "hidden hunger" of global micronutrient malnutrition. Affecting ~2 billion people, micronutrient malnutrition causes severe health effects ranging from stunted growth to reduced lifespan. An increased availability of micronutrient-enriched legumes, particularly to those in socio-economically deprived areas, would serve the dual functions of ameliorating hidden hunger and increasing the positive health effects associated with legumes. Here, we give an updated overview of breeding approaches for the nutritional improvement of legumes, and crucially, we highlight the importance of considering nutritional improvement in a wider ecological context. Specifically, we review the potential of the legume microbiome for agronomic trait improvement and highlight the need for increased genetic, biochemical, and environmental data resources. Finally, we state that such resources should be complemented by an international and multidisciplinary initiative that will drive crop improvement and, most importantly, ensure that research outcomes benefit those who need them most.

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, which are genes controlling the nodulation process were significantly reduced in Pi-deficient common bean seedlings. In addition, whole-genome transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Moreover, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule numbers, was higher in Pi-deficient seedlings compared to control seedlings. The data presented in this study provides a mechanistic model to better understand how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia.

Metabolomics and Transcriptomics in Legumes Under Phosphate Deficiency in Relation to Nitrogen Fixation by Root Nodules

Phosphate (Pi) deficiency is a critical environmental constraint that affects the growth and development of several legume crops that are usually cultivated in semi-arid regions and marginal areas. Pi deficiency is known to be a significant limitation for symbiotic nitrogen (N2) fixation (SNF), and variability in SNF is strongly interlinked with the concentrations of Pi in the nodules. To deal with Pi deficiency, plants trigger various adaptive responses, including the induction and secretion of acid phosphatases, maintenance of Pi homeostasis in nodules and other organs, and improvement of oxygen (O2) consumption per unit of nodule mass. These molecular and physiological responses can be observed in terms of changes in growth, photosynthesis, and respiration. In this mini review, we provide a brief introduction to the problem of Pi deficiency in legume crops. We then summarize the current understanding of how Pi deficiency is regulated in legumes by changes in the transcriptomes and metabolomes found in different plant organs. Finally, we will provide perspectives on future directions for research in this field.

Genetic resistance against viruses in Phaseolus vulgaris L.: State of the art and future prospects

Viruses are obligate parasites that replicate intracellularly in many living organisms, including plants. Consequently, no chemicals are available that target only the virus without impacting host cells or vector organisms. The use of natural resistant varieties appears as the most reliable control strategy and remains the best and cheapest option in managing virus diseases, especially in the current ecological context of preserving biodiversity and environment in which the use of phytosanitary products becomes limited. Common bean is a grain legume cultivated mainly in Africa and Central-South America. Virus diseases of common bean have been extensively studied both by breeders to identify natural resistance genes in existing germplasms and by pathologists to understand the molecular bases of plant-virus interactions. Here we present a critical review in which we synthesize previous and recent information concerning 1) main viruses causing diseases in common bean, 2) genetic resistance to viruses in common bean, 3) the different resistance phenotypes observed and more particularly the effect of temperature, 4) the molecular bases of resistance genes to viruses in common bean, and 5) future prospects using transgenic-engineered resistant lines.

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.

The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought

Recent studies have identified microRNAs as post-transcriptional regulators involved in stress responses. miR1514a is a legume microRNA that is induced in response to drought stress in Phaseolus vulgaris (common bean) and shows differential accumulation levels in roots during water deficit in two cultivars with different drought tolerance phenotypes. A recent degradome analysis revealed that miR1514a targets the transcripts of two NAC transcription factors (TFs), Phvul.010g121000 and Phvul.010g120700. Furthermore, expression studies and small RNA-seq data indicate that only Phvul.010g120700 generates phasiRNAs, which also accumulate under water deficit conditions. To confirm these results, we over-expressed miR1514a in transgenic hairy roots, and observed a reduced accumulation of Phvul.010g120700 and an increase in NAC-derived phasiRNAs; inhibition of miR1514a activity resulted in the opposite effect. Moreover, we determined that a NAC-derived phasiRNA associates with ARGONAUTE 1 (AGO1), suggesting that it is functional. In addition, a transcriptome analysis of transgenic hairy roots with reduced miR1514a levels revealed several differentially expressed transcripts, mainly involved in metabolism and stress responses, suggesting they are regulated by the NAC TF and/or by phasiRNAs. This work therefore demonstrates the participation of miR1514 in the regulation of a NAC transcription factor transcript through phasiRNA production during the plant response to water deficit.

Visualisation of abscisic acid and 12-oxo-phytodienoic acid in immature Phaseolus vulgaris L. seeds using desorption electrospray ionisation-imaging mass spectrometry

The plant hormone abscisic acid (ABA) and the jasmonic acid related-compound 12-oxo-phytodienoic acid (OPDA) play crucial roles in seed development, dormancy, and germination. However, a lack of suitable techniques for visualising plant hormones has restricted the investigation of their biological mechanisms. In the present study, desorption electrospray ionisation-imaging mass spectrometry (DESI-IMS), a powerful tool for visualising metabolites in biological tissues, was used to visualise ABA and OPDA in immature Phaseolus vulgaris L. seed sections. The mass spectra, peak values and chemical formulae obtained from the analysis of seed sections were consistent with those determined for ABA and OPDA standards, as were the precursor and major fragment ions observed in tandem mass spectrometry (MS/MS) imaging. Furthermore, the precursor and fragment ion images showed similar distribution patterns. In addition, the localisation of ABA and OPDA using DESI-IMS was confirmed using liquid chromatography-MS/MS (LC-MS/MS). The results indicated that ABA was mainly distributed in the radical and cotyledon of the embryo, whereas OPDA was distributed exclusively in external structures, such as the hilum and seed coat. The present study is the first to report the visualisation of plant hormones using IMS, and demonstrates that DESI-IMS is a promising technique for future plant hormone research.

Dietary arsenic exposure in Brazil: The contribution of rice and beans

The human health risk associated with arsenic in food in Southeast Brazil was quantified. Based on the most commonly consumed food types in the Brazilian diet, the maximum inorganic As (iAs) daily intake from food (0.255 μg kg^-1 body weight per day) is approximately 9% of the Benchmark Dose Lower Limit (BMDL_0.5) of 3 μg kg^-1 body weight per day set by the World Health Organization (WHO) and Food and Agriculture Organization (FAO) Joint Expert Committee in Food Additives (JECFA). When water is included, the contribution of food to the total intake varies from 96.9% to 39.7%. Rice and beans, the main Brazilian staple food, contribute between 67 and 90% of the total As intake from food (46-79% from rice and 11-23% from beans). The substantial contribution of beans to total As food intake is reported for the first time. The broad range of As concentrations in rice and beans highlights the variable and potentially large contribution of both to As food intake in places where diet consists largely of these two food categories.

Zinc and selenium accumulation and their effect on iron bioavailability in common bean seeds

Common beans (Phaseolus vulgaris) are the most important legume crops. They represent a major source of micronutrients and a target for essential trace mineral enhancement (i.e. biofortification). To investigate mineral accumulation during seed maturation and to examine whether it is possible to biofortify seeds with multi-micronutrients without affecting mineral bioavailability, three common bean cultivars were treated independently with zinc (Zn) and selenium (Se), the two critical micronutrients that can be effectively enhanced via fertilization. The seed mineral concentrations during seed maturation and the seed Fe bioavailability were analyzed. Common bean seeds were found to respond positively to Zn and Se treatments in accumulating these micronutrients. While the seed pods showed a decrease in Zn and Se along with Fe content during pod development, the seeds maintained relatively constant mineral concentrations during seed maturation. Selenium treatment had minimal effect on the seed accumulation of phytic acid and polyphenols, the compounds affecting Fe bioavailability. Zinc treatment reduced phytic acid level, but did not dramatically affect the concentrations of total polyphenols. Iron bioavailability was found not to be greatly affected in seeds biofortified with Se and Zn. In contrast, the inhibitory polyphenol compounds in the black bean profoundly reduced Fe bioavailability. These results provide valuable information for Se and Zn enhancement in common bean seeds and suggest the possibility to biofortify with these essential nutrients without greatly affecting mineral bioavailability to increase the food quality of common bean seeds.