The value of biodiversity in legume symbiotic nitrogen fixation and nodulation for biofuel and food production

Bacterial community drives soil organic carbon transformation in vanadium titanium magnetite tailings through remediation using Pongamia pinnata

With continuous mine exploitation, regional ecosystems have been damaged, resulting in a decline in the carbon sink capacity of mining areas. There is a global shortage of effective soil ecological restoration techniques for mining areas, especially for vanadium (V) and titanium (Ti) magnetite tailings, and the impact of phytoremediation techniques on the soil carbon cycle remains unclear. Therefore, this study aimed to explore the effects of long-term Pongamia pinnata remediation on soil organic carbon transformation of V-Ti magnetite tailing to reveal the bacterial community driving mechanism. In this study, it was found that four soil active organic carbon components (ROC, POC, DOC, and MBC) and three carbon transformation related enzymes (S-CL, S-SC, and S-PPO) in vanadium titanium magnetite tailings significantly (P < 0.05) increased with P. pinnata remediation. The abundance of carbon transformation functional genes such as carbon degradation, carbon fixation, and methane oxidation were also significantly (P < 0.05) enriched. The network nodes, links, and modularity of the microbial community, carbon components, and carbon transformation genes were enhanced, indicating stronger connections among the soil microbes, carbon components, and carbon transformation functional genes. Structural equation model (SEM) analysis revealed that the bacterial communities indirectly affected the soil organic carbon fraction and enzyme activity to regulate the soil total organic carbon after P. pinnata remediation. The soil active organic carbon fraction and free light fraction carbon also directly regulated the soil carbon and nitrogen ratio by directly affecting the soil total organic carbon content. These results provide a theoretical reference for the use of phytoremediation to drive soil carbon transformation for carbon sequestration enhancement through the remediation of degraded ecosystems in mining areas.

Underrated aspects of a true Mediterranean diet: understanding traditional features for worldwide application of a "Planeterranean" diet

Over the last decades, the Mediterranean diet gained enormous scientific, social, and commercial attention due to proven positive effects on health and undeniable taste that facilitated a widespread popularity. Researchers have investigated the role of Mediterranean-type dietary patterns on human health all around the world, reporting consistent findings concerning its benefits. However, what does truly define the Mediterranean diet? The myriad of dietary scores synthesizes the nutritional content of a Mediterranean-type diet, but a variety of aspects are generally unexplored when studying the adherence to this dietary pattern. Among dietary factors, the main characteristics of the Mediterranean diet, such as consumption of fruit and vegetables, olive oil, and cereals should be accompanied by other underrated features, such as the following: (i) specific reference to whole-grain consumption; (ii) considering the consumption of legumes, nuts, seeds, herbs and spices often untested when exploring the adherence to the Mediterranean diet; (iii) consumption of eggs and dairy products as common foods consumed in the Mediterranean region (irrespectively of the modern demonization of dietary fat intake). Another main feature of the Mediterranean diet includes (red) wine consumption, but more general patterns of alcohol intake are generally unmeasured, lacking specificity concerning the drinking occasion and intensity (i.e., alcohol drinking during meals). Among other underrated aspects, cooking methods are rather simple and yet extremely varied. Several underrated aspects are related to the quality of food consumed when the Mediterranean diet was first investigated: foods are locally produced, minimally processed, and preserved with more natural methods (i.e., fermentation), strongly connected with the territory with limited and controlled impact on the environment. Dietary habits are also associated with lifestyle behaviors, such as sleeping patterns, and social and cultural values, favoring commensality and frugality. In conclusion, it is rather reductive to consider the Mediterranean diet as just a pattern of food groups to be consumed decontextualized from the social and geographical background of Mediterranean culture. While the methodologies to study the Mediterranean diet have demonstrated to be useful up to date, a more holistic approach should be considered in future studies by considering the aforementioned underrated features and values to be potentially applied globally through the concept of a "Planeterranean" diet.

Bacillus paralicheniformis 2R5 and its impact on canola growth and N-cycle genes in the rhizosphere

Chemical fertilization has a negative impact on the natural environment. Plant growth-promoting (PGP) rhizobacterial biofertilizers can be a safer alternative to synthetic agrochemicals. In this research, a culture-based method was used to assess the population size of rhizobacteria at the vegetative, flowering, and maturity stages of canola. Rhizobacteria were then isolated from each of the canola growth stages, and their seven PGP traits were determined. The highest abundance of culturable bacteria was found at the vegetative stage of the plants. Furthermore, four out of seven PGP traits were produced by the highest % of isolates at the vegetative stage. In the greenhouse experiment that included six rhizobacterial strains with best PGP traits, the greatest canola growth promotion ability under sterile conditions was observed after the introduction of Bacillus paralicheniformis 2R5. Moreover, under nonsterile conditions, 2R5 significantly increased canola growth. The presence of the trpA, B, C, D, E, F and pstA, and S genes in the 2R5 genome could be associated with canola growth promotion abilities. The chiA and mbtH genes could contribute to 2R5 antifungal activity against fungal pathogens. Moreover, the introduction of 2R5 significantly increased the abundance of the narG, nosZ, nifH, and nirS genes, which can prove that the 2R5 strain may be an important member of the soil bacterial community.

Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System

Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.

A critical review of Pongamia pinnata multiple applications: From land remediation and carbon sequestration to socioeconomic benefits

Pongamia pinnata (L.) Pierre (Pongamia) is a tree native to Southeast Asia. Recently, interest in Pongamia focused on its potential as a biofuel source as its seeds contain around 40% oil. However, Pongamia has multiple applications beyond biofuel production. It is a legume, can form symbiotic associations with mycorrhizal fungi, has been shown to be tolerant to drought, salinity, and heavy metals in soil, and has potential to mitigate climate change. Additionally, Pongamia oil has medicinal properties, can be used as biopesticide, insect repellent, to produce soap, and as a source of edible grade vegetable oil. The seed cake can be used as a source of bioenergy, food and feed protein, and organic fertiliser, and the flowers are a good source of pollen and nectar. Pongamia can also bring socio-economic benefits as its ability to restore degraded and contaminated land provides opportunities for local communities through novel valorisation pathways. These multiple applications have potential to form part of a circular bioeconomy in line with sustainable development goals. Although research on the multiple applications of Pongamia has grown considerably, knowledge gaps remain and these need to be addressed so that the full potential of Pongamia can be achieved. Further understanding of the mechanisms underlying its resilience to abiotic stresses, phytoremediation potential and biotic interactions should be a priority, and co-ordinated breeding efforts will be key. Here, we critically review the available literature on Pongamia and highlight gaps in knowledge in which future research should focus on to ensure that the full potential of this versatile tree can be achieved. We conclude that Pongamia can potentially form part of a circular bioeconomy and that harnessing the multiple applications of Pongamia in a holistic manner, with collaboration among key stakeholders, is crucial for the successful application of its benefits far beyond biofuel production.

Legume Protein Extracts: The Relevance of Physical Processing in the Context of Structural, Techno-Functional and Nutritional Aspects of Food Development

Legumes are sustainable protein-rich crops with numerous industrial food applications, which give them the potential of a functional food ingredient. Legume proteins have appreciable techno-functional properties (e.g., emulsification, foaming, water absorption), which could be affected along with its digestibility during processing. Extraction and isolation of legumes’ protein content makes their use more efficient; however, exposure to the conditions of further use (such as temperature and pressure) results in, and significantly increases, changes in the structural, and therefore functional and nutritional, properties. The present review focuses on the quality of legume protein concentrates and their changes under the influence of different physical processing treatments and highlights the effect of processing techniques on the structural, functional, and some of the nutritional, properties of legume proteins.

Genome-wide identification and characterization of legume T2 Ribonuclease gene family and analysis of GmaRNS9, a soybean T2 Ribonuclease gene, function in nodulation

T2 ribonuclease family (RNaseT2) proteins are secretory and nonspecific endoribonucleases that have a large conserved biological role. Family members of RNaseT2 are found in every organism and carry out important biological functions. However, little is known about the functions of these proteins in legumes, including potential roles in symbiotic nodulation. This study aimed to characterize and perform bioinformatic analysis of RNaseT2 genes in four legume species that their genome was sequenced. In total, 60 RNaseT2 genes were identified and characterized. By analyzing their phylogeny, we divided these RNaseT2 into five clades. Expression analysis of RNaseT2 genes indicated that these genes are expressed in various tissues, and the most expression level was related to the pod, flower, and root. Moreover, GmaRNS9 expression analysis in soybean was consistent with in silico studies and demonstrated that this gene usually has high root tip expression. GmaRNS9 expression was reduced by Bradyrhizobium japonicum inoculation and nodule formation. Reduced expression of this gene was possibly controlled by the GmNARK gene either directly or pleiotropically through increased phosphorus requirements during increased nodulation. However, the nutrient stress (phosphate and nitrate starvation) led to an increase in the expression level of GmRNS9. In silico and quantitative gene expression analyses showed that RNaseT2 genes could play important roles in the growth and development of legumes as well as nodulation.

Nod factor receptor complex phosphorylates GmGEF2 to stimulate ROP signaling during nodulation

The establishment of the symbiotic interaction between rhizobia and legumes involves the Nod factor signaling pathway. Nod factor recognition occurs through two plant receptors, NFR1 and NFR5. However, the signal transduction mechanisms downstream of NFR1-NFR5-mediated Nod factor perception remain largely unknown. Here, we report that a small guanosine triphosphatase (GTPase), GmROP9, and a guanine nucleotide exchange factor, GmGEF2, are involved in the soybean-rhizobium symbiosis. We show that GmNFR1α phosphorylates GmGEF2a at its N-terminal S86, which stimulates guanosine diphosphate (GDP)-to-GTP exchange to activate GmROP9 and that the active form of GmROP9 can associate with both GmNFR1α and GmNFR5α. We further show that a scaffold protein, GmRACK1, interacts with active GmROP9 and contributes to root nodule symbiosis. Collectively, our results highlight the symbiotic role of GmROP9-GmRACK1 and support the hypothesis that rhizobial signals promote the formation of a protein complex comprising GmNFR1, GmNFR5, GmROP9, and GmRACK1 for symbiotic signal transduction in soybean.

Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling

Legumes include several major crops that can fix atmospheric nitrogen in symbiotic root nodules, thus reducing the demand for nitrogen fertilizers and contributing to sustainable agriculture. Global change models predict increases in temperature and extreme weather conditions. This scenario might increase plant exposure to abiotic stresses and negatively affect crop production. Regulation of whole plant physiology and nitrogen fixation in legumes during abiotic stress is complex, and only a few mechanisms have been elucidated. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are key players in the acclimation and stress tolerance mechanisms of plants. However, the specific redox-dependent signaling pathways are far from understood. One mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification (PTM) of proteins. Redox-based PTMs occur in the cysteine thiol group (oxidation, S-nitrosylation, S-glutathionylation, persulfidation), and also in methionine (oxidation), tyrosine (nitration), and lysine and arginine (carbonylation/glycation) residues. Unraveling PTM patterns under different types of stress and establishing the functional implications may give insight into the underlying mechanisms by which the plant and nodule respond to adverse conditions. Here, we review current knowledge on redox-based PTMs and their possible consequences in legume and nodule biology.

miR169c-NFYA-C-ENOD40 modulates nitrogen inhibitory effects in soybean nodulation

Legume crops contribute a great portion of clean nitrogen (N) to agro-ecosystems through symbiotic N2 fixation in the nodule; however, the nodulation is always inhibited by high N availability which is known as the N inhibitory effect through largely unknown mechanisms. We functionally investigated miR169c-GmNFYA-C-GmENOD40 under multiple N conditions in soybean (Glycine max) (ENOD, Early Nodulin; NFYA, Nuclear Factor-Y Subunit A). We elucidated their regulatory roles in soybean nodulation through analyzing expression patterns, micro-messenger RNA (miRNA-mRNA) interactions, phenotypes of transgenic soybean plants and genetic interactions. We found that miR169c expression was induced by high N, whereas its target GmNFYA-C was preferentially expressed in nodules and induced by rhizobium inoculation. Overexpression of miR169c inhibited nodulation through targeting 3'-UTR of GmNFYA-C, whereas knockout miR169c through CRISPR-cas9 promoted nodulation. However, overexpression of GmNFYA-C promoted soybean nodulation through facilitating rhizobium infection and increasing the expression of symbiotic signaling gene GmENOD40. Besides, GmNFYA-C directly induced the expression of GmENOD40. In addition, overexpression of GmNFYA-C without the target site of miR169c partially attenuated the inhibitory effect of high N on soybean nodulation. We discovered a new regulatory pathway involving the miR169c-NFYA-C-ENOD40 module that regulates soybean nodulation in response to N availability. This pathway provides substantial new insights into the mechanisms underlying the N inhibitory effect on nodulation.

A Minimal Genetic Passkey to Unlock Many Legume Doors to Root Nodulation by Rhizobia

In legume crops, formation of developmentally mature nodules is a prerequisite for efficient nitrogen fixation by populations of rhizobial bacteroids established inside nodule cells. Development of root nodules, and concomitant microbial colonization of plant cells, are constrained by sets of recognition signals exchanged by infecting rhizobia and their legume hosts, with much of the specificity of symbiotic interactions being determined by the flavonoid cocktails released by legume roots and the strain-specific nodulation factors (NFs) secreted by rhizobia. Hence, much of Sinorhizobium fredii strain NGR234 symbiotic promiscuity was thought to stem from a family of >80 structurally diverse NFs and associated nodulation keys in the form of secreted effector proteins and rhamnose-rich surface polysaccharides. Here, we show instead that a mini-symbiotic plasmid (pMiniSym2) carrying only the nodABCIJ, nodS and nodD1 genes of NGR234 conferred promiscuous nodulation to ANU265, a derivative strain cured of the large symbiotic plasmid pNGR234a. The ANU265::pMiniSym2 transconjugant triggered nodulation responses on 12 of the 22 legumes we tested. On roots of Macroptilium atropurpureum, Leucaena leucocephala and Vigna unguiculata, ANU265::pMiniSym2 formed mature-like nodule and successfully infected nodule cells. While cowpea and siratro responded to nodule colonization with defense responses that eventually eliminated bacteria, L. leucocephala formed leghemoglobin-containing mature-like nodules inside which the pMiniSym2 transconjugant established persistent intracellular colonies. These data show seven nodulation genes of NGR234 suffice to trigger nodule formation on roots of many hosts and to establish chronic infections in Leucaena cells.

Novel rhizobia exhibit superior nodulation and biological nitrogen fixation even under high nitrate concentrations

Legume-rhizobium symbiosis leads to the formation of nitrogen-fixing root nodules. However, externally applied chemical nitrogen fertilizers (nitrate and ammonia) strongly inhibit nodule formation and nitrogen fixation. Here, we isolated several rhizobial strains exhibiting a superior nodulation and nitrogen fixation with soybean at high nitrate concentrations. The nodulation of soybean symbiont Bradyrhizobium diazoefficiens USDA110 was significantly inhibited at 12.5 mM nitrate; however, three isolates (NKS4, NKM2 and NKTG2) were capable of forming nitrogen-fixing nodules, even at 20 mM nitrate. These isolates exhibited higher nodulation competitiveness and induced larger nodules with higher nitrogen-fixation activity than USDA110 at 5 mM nitrate. Furthermore, these isolates induced more nodules than USDA110 even in nitrate-free conditions. These isolates had a distant lineage within the Bradyrhizobium genus; though they were relatively phylogenetically close to Bradyrhizobium japonicum, their morphological and growth characteristics were significantly different. Notably, in the presence of nitrate, expression of the soybean symbiosis-related genes (GmENOD40 and GmNIN) was significantly higher and expression of GmNIC1 that is involved in nitrate-dependent nodulation inhibition was lower in the roots inoculated with these isolates in contrast with inoculation of USDA110. These novel rhizobia serve as promising inoculants for soybeans cultivated in diverse agroecosystems, particularly on nitrate-applied soils.

Hypernodulating soybean mutant line nod4 lacking 'Autoregulation of Nodulation' (AON) has limited root-to-shoot water transport capacity

BACKGROUND AND AIMS

Although hypernodulating phenotype mutants of legumes, such as soybean, possess a high leaf N content, the large number of root nodules decreases carbohydrate availability for plant growth and seed yield. In addition, under conditions of high air vapour pressure deficit (VPD), hypernodulating plants show a limited capacity to replace water losses through transpiration, resulting in stomatal closure, and therefore decreased net photosynthetic rates. Here, we used hypernodulating (nod4) (282.33 ± 28.56 nodules per plant) and non-nodulating (nod139) (0 nodules per plant) soybean mutant lines to determine explicitly whether a large number of nodules reduces root hydraulic capacity, resulting in decreased stomatal conductance and net photosynthetic rates under high air VPD conditions.

METHODS

Plants were either inoculated or not inoculated with Bradyrhizobium diazoefficiens (strain BR 85, SEMIA 5080) to induce nitrogen-fixing root nodules (where possible). Absolute root conductance and root conductivity, plant growth, leaf water potential, gas exchange, chlorophyll a fluorescence, leaf 'greenness' [Soil Plant Analysis Development (SPAD) reading] and nitrogen content were measured 37 days after sowing.

KEY RESULTS

Besides the reduced growth of hypernodulating soybean mutant nod4, such plants showed decreased root capacity to supply leaf water demand as a consequence of their reduced root dry mass and root volume, which resulted in limited absolute root conductance and root conductivity normalized by leaf area. Thereby, reduced leaf water potential at 1300 h was observed, which contributed to depression of photosynthesis at midday associated with both stomatal and non-stomatal limitations.

CONCLUSIONS

Hypernodulated plants were more vulnerable to VPD increases due to their limited root-to-shoot water transport capacity. However, greater CO2 uptake caused by the high N content can be partly compensated by the stomatal limitation imposed by increased VPD conditions.

Unravelling the MicroRNA-Mediated Gene Regulation in Developing Pongamia Seeds by High-Throughput Small RNA Profiling

Pongamia (Millettia pinnata syn. Pongamia pinnata) is a multipurpose biofuel tree which can withstand a variety of abiotic stresses. Commercial applications of Pongamia trees may substantially benefit from improvements in their oil-seed productivity, which is governed by complex regulatory mechanisms underlying seed development. MicroRNAs (miRNAs) are important molecular regulators of plant development, while relatively little is known about their roles in seed development, especially for woody plants. In this study, we identified 236 conserved miRNAs within 49 families and 143 novel miRNAs via deep sequencing of Pongamia seeds sampled at three developmental phases. For these miRNAs, 1327 target genes were computationally predicted. Furthermore, 115 differentially expressed miRNAs (DEmiRs) between successive developmental phases were sorted out. The DEmiR-targeted genes were preferentially enriched in the functional categories associated with DNA damage repair and photosynthesis. The combined analyses of expression profiles for DEmiRs and functional annotations for their target genes revealed the involvements of both conserved and novel miRNA-target modules in Pongamia seed development. Quantitative Real-Time PCR validated the expression changes of 15 DEmiRs as well as the opposite expression changes of six targets. These results provide valuable miRNA candidates for further functional characterization and breeding practice in Pongamia and other oilseed plants.

Legume nodulation: The host controls the party

Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic relationship that legume plants establish with nitrogen-fixing rhizobia bacteria is central to their advantage. This plant-microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.

Modelling predicts that soybean is poised to dominate crop production across Africa

The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume-based farming is particularly important in Africa, where small-scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land-use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful "soybean bonanza" across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.

Triarabinosylation is required for nodulation-suppressive CLE peptides to systemically inhibit nodulation in Pisum sativum

Legumes form root nodules to house beneficial nitrogen-fixing rhizobia bacteria. However, nodulation is resource demanding; hence, legumes evolved a systemic signalling mechanism called autoregulation of nodulation (AON) to control nodule numbers. AON begins with the production of CLE peptides in the root, which are predicted to be glycosylated, transported to the shoot, and perceived. We synthesized variants of nodulation-suppressing CLE peptides to test their activity using petiole feeding to introduce CLE peptides into the shoot. Hydroxylated, monoarabinosylated, and triarabinosylated variants of soybean GmRIC1a and GmRIC2a were chemically synthesized and fed into recipient Pisum sativum (pea) plants, which were used due to the availability of key AON pathway mutants unavailable in soybean. Triarabinosylated GmRIC1a and GmRIC2a suppressed nodulation of wild-type pea, whereas no other peptide variant tested had this ability. Suppression also occurred in the supernodulating hydroxyproline O-arabinosyltransferase mutant, Psnod3, but not in the supernodulating receptor mutants, Pssym29, and to some extent, Pssym28. During our study, bioinformatic resources for pea became available and our analyses identified 40 CLE peptide-encoding genes, including orthologues of nodulation-suppressive CLE peptides. Collectively, we demonstrated that soybean nodulation-suppressive CLE peptides can function interspecifically in the AON pathway of pea and require arabinosylation for their activity.

Local and Systemic Effect of Cytokinins on Soybean Nodulation and Regulation of Their Isopentenyl Transferase (IPT) Biosynthesis Genes Following Rhizobia Inoculation

Cytokinins are important regulators of cell proliferation and differentiation in plant development. Here, a role for this phytohormone group in soybean nodulation is shown through the exogenous application of cytokinins (6-benzylaminopurine, N6-(Δ2-isopentenyl)-adenine and trans-zeatin) via either root drenching or a petiole feeding technique. Overall, nodule numbers were reduced by treatment with high cytokinin concentrations, but increased with lower concentrations. This was especially evident when feeding the solutions directly into the vasculature via petiole feeding. These findings highlight the importance of cytokinin in nodule development. To further investigate the role of cytokinin in controlling nodule numbers, the IPT gene family involved in cytokinin biosynthesis was characterized in soybean. Bioinformatic analyses identified 17 IPT genes in the soybean genome and homeologous duplicate gene partners were subsequently identified including GmIPT5 and GmIPT6, the orthologs of LjIPT3. Expression of GmIPT5 was upregulated in the shoot in response to nodulation, but this was independent of a functional copy of the autoregulation of nodulation (AON) receptor, GmNARK, which suggests it is unlikely to have a role in the negative feedback system called AON. Legumes also control nodule numbers in the presence of soil nitrogen through nitrate-dependent regulation of nodulation, a locally acting pathway in soybean. Upon nitrate treatment to the root, the tandem duplicates GmIPT3 and GmIPT15 were upregulated in expression indicating a role for these genes in the plant's response to soil nitrogen, potentially including the nitrate-dependent regulation of legume nodulation pathway. Additional roles for cytokinin and their IPT biosynthetic genes in nodulation and the control of nodule numbers are discussed.

Evaluation of Alkali-Pretreated Soybean Straw for Lignocellulosic Bioethanol Production

Soybean straw is a renewable resource in agricultural residues that can be used for lignocellulosic bioethanol production. To enhance enzymatic digestibility and fermentability, the biomass was prepared with an alkali-thermal pretreatment (sodium hydroxide, 121°C, 60 min). The delignification yield was 34.1~53%, in proportion to the amount of sodium hydroxide, from 0.5 to 3.0 M. The lignin and hemicellulose contents of the pretreated biomass were reduced by the pretreatment process, whereas the proportion of cellulose was increased. Under optimal condition, the pretreated biomass consisted of 74.0±0.1% cellulose, 10.3±0.1% hemicellulose, and 10.1±0.6% lignin. During enzymatic saccharification using Cellic® CTec2 cellulase, 10% (w/v) of pretreated soybean straw was hydrolyzed completely and converted to 67.3±2.1 g/L glucose and 9.4±0.5 g/L xylose with a 90.9% yield efficiency. Simultaneous saccharification and fermentation of the pretreated biomass by Saccharomyces cerevisiae W303-1A produced 30.5±1.2 g/L ethanol in 0.5 L fermented medium containing 10% (w/v) pretreated biomass after 72 h. The ethanol productivity was 0.305 g ethanol/g dry biomass and 0.45 g ethanol/g glucose after fermentation, with a low concentration of organic acid metabolites. Also, 82% of fermentable sugar was used by the yeast for ethanol fermentation. These results show that the combination of alkaline pretreatment and biomass hydrolysate is useful for enhancing bioethanol productivity using delignified soybean straw.

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.

Oil body biogenesis and biotechnology in legume seeds

The seeds of many legume species including soybean, Pongamia pinnata and the model legume Medicago truncatula store considerable oil, apart from protein, in their cotyledons. However, as a group, legume storage strategies are quite variable and provide opportunities for better understanding of carbon partitioning into different storage products. Legumes with their ability to fix nitrogen can also increase the sustainability of agricultural systems. This review integrates the cell biology, biochemistry and molecular biology of oil body biogenesis before considering biotechnology strategies to enhance oil body biosynthesis. Cellular aspects of packaging triacylglycerol (TAG) into oil bodies are emphasized. Enhancing seed oil content has successfully focused on the up-regulation of the TAG biosynthesis pathways using overexpression of enzymes such as diacylglycerol acyltransferase1 and transcription factors such as WRINKLE1 and LEAFY COTYLEDON1. While these strategies are central, decreasing carbon flow into other storage products and maximizing the packaging of oil bodies into the cytoplasm are other strategies that need further examination. Overall there is much potential for integrating carbon partitioning, up-regulation of fatty acid and TAG synthesis and oil body packaging, for enhancing oil levels. In addition to the potential for integrated strategies to improving oil yields, the capacity to modify fatty acid composition and use of oil bodies as platforms for the production of recombinant proteins in seed of transgenic legumes provide other opportunities for legume biotechnology.

CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis

CLE peptide hormones are critical regulators of many cell proliferation and differentiation mechanisms in plants. These 12-13 amino acid glycosylated peptides play vital roles in a diverse range of plant tissues, including the shoot, root and vasculature. CLE peptides are also involved in controlling legume nodulation. Here, the entire family of CLE peptide-encoding genes was identified in Medicago truncatula (52) and Lotus japonicus (53), including pseudogenes and non-functional sequences that were identified. An array of bioinformatic techniques were used to compare and contrast these complete CLE peptide-encoding gene families with those of fellow legumes, Glycine max and Phaseolus vulgaris, in addition to the model plant Arabidopsis thaliana. This approach provided insight into the evolution of CLE peptide families and enabled us to establish putative M. truncatula and L. japonicus orthologues. This includes orthologues of nodulation-suppressing CLE peptides and AtCLE40 that controls the stem cell population of the root apical meristem. A transcriptional meta-analysis was also conducted to help elucidate the function of the CLE peptide family members. Collectively, our analyses considerably increased the number of annotated CLE peptides in the model legume species, M. truncatula and L. japonicus, and substantially enhanced the knowledgebase of this critical class of peptide hormones.

Neodiversification of homeologous CLAVATA1-like receptor kinase genes in soybean leads to distinct developmental outcomes

The CLAVATA pathway that regulates stem cell numbers of the shoot apical meristem has exclusively been studied in Arabidopsis; as such insight into other species is warranted. In this study, a GmCLV1A mutant (F-S562L) with altered lateral organ development, and two mutants of GmNARK, isolated from a Forrest M2 population (EMS-mutated soybean) were studied. GmCLV1A and GmNARK encode for LRR receptor kinases, and share 92% of protein sequence. While GmNARK is critical for systemic regulation of nodulation (new organ made on the root through symbiosis), we show that GmCLV1A functions locally and has no apparent function in nodulation or root development. However, a recessive, loss-of-function mutation (S562L) in a putative S-glycosylation site of GmCLV1A causes stem nodal identity alterations as well as flower and pod abnormalities (deformed flower and pod). The mutant also exhibits a homeotic phenotype, displaying abnormal leaf development/number, vein-derived leaf emergence, and a thick, faciated stem. The mutant phenotype is also temperature-sensitive. Interestingly, a novel truncated version of GmCLV1A was identified upstream of GmCLV1A that is absent from GmNARK, but is present upstream of the GmNARK orthologues, MtSUNN and PvNARK. Taken together, our findings indicate that GmCLV1A acts on shoot architecture, whereas GmNARK, functions in controlling nodule numbers.

Novel impacts of functionalized multi-walled carbon nanotubes in plants: promotion of nodulation and nitrogenase activity in the rhizobium-legume system

The rhizobium-legume symbiosis system is critical for nitrogen-cycle balance in agriculture. However, the potential effects of carbon nanomaterials (CNMs) on this system remain largely unknown. Herein, we studied the effects of four carbon-based materials (activated carbon (AC), single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs) and graphene oxide (GO)) on the rhizobium-legume symbiosis system consisting of Lotus japonicus and Mesorhizobium loti MAFF303099. Under non-symbiotic conditions, the bacterial growth and root development of plants were both clearly inhibited by SWCNTs and GO, while the elongation of plant stems was enhanced by MWCNTs to a certain degree. More importantly, only MWCNTs could increase the number of nodules and enhance the activity of nitrogenase in the rhizobium-plant interaction. Further analyses showed that the average number of nodules in plants treated with 100 μg mL^-1 MWCNTs was significantly increased by 39% at 14 days post inoculation (dpi) and by 41% at 28 dpi. Meanwhile, the biological nitrogen fixation of the nodules was promoted by more than 10% under 100 μg mL^-1 MWCNT treatment, which enhanced the above- and below-ground fresh biomass by 14% and 25% respectively at 28 dpi. Transmission electron microscopy images further indicated that MWCNTs penetrated the cell wall, and pierced through the cell membrane to be transmitted into the cytoplasm. In addition, gene expression analysis showed that the promotion of nodulation by MWCNTs was correlated with the up-regulation of certain genes involved in this signaling pathway. In particular, the expression of NIN, a crucial gene regulating the development of nodules, was significantly elevated 2-fold by MWCNTs at an early stage of nodulation. These findings are expected to facilitate the understanding and future utilization of MWCNTs in agriculture.

Molecular Signals in Nodulation Control

Our world is facing major problems relating to food production. According to an August 30, 2015 program of LANDLINE (Australian Broadcasting Corporation, Australia),we lose 120,000,000 hectares of agricultural land per year due to population growth, associated urbanisation, and desertification.

The Regulatory Protein RosR Affects Rhizobium leguminosarum bv. trifolii Protein Profiles, Cell Surface Properties, and Symbiosis with Clover

Rhizobium leguminosarum bv. trifolii is capable of establishing a symbiotic relationship with plants from the genus Trifolium. Previously, a regulatory protein encoded by rosR was identified and characterized in this bacterium. RosR possesses a Cys2-His2-type zinc finger motif and belongs to Ros/MucR family of rhizobial transcriptional regulators. Transcriptome profiling of the rosR mutant revealed a role of this protein in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Here, we show that a mutation in rosR resulted in considerable changes in R. leguminosarum bv. trifolii protein profiles. Extracellular, membrane, and periplasmic protein profiles of R. leguminosarum bv. trifolii wild type and the rosR mutant were examined, and proteins with substantially different abundances between these strains were identified. Compared with the wild type, extracellular fraction of the rosR mutant contained greater amounts of several proteins, including Ca(2+)-binding cadherin-like proteins, a RTX-like protein, autoaggregation protein RapA1, and flagellins FlaA and FlaB. In contrast, several proteins involved in the uptake of various substrates were less abundant in the mutant strain (DppA, BraC, and SfuA). In addition, differences were observed in membrane proteins of the mutant and wild-type strains, which mainly concerned various transport system components. Using atomic force microscopy (AFM) imaging, we characterized the topography and surface properties of the rosR mutant and wild-type cells. We found that the mutation in rosR gene also affected surface properties of R. leguminosarum bv. trifolii. The mutant cells were significantly more hydrophobic than the wild-type cells, and their outer membrane was three times more permeable to the hydrophobic dye N-phenyl-1-naphthylamine. The mutation of rosR also caused defects in bacterial symbiotic interaction with clover plants. Compared with the wild type, the rosR mutant infected host plant roots much less effectively and its nodule occupation was disturbed. At the ultrastructural level, the most striking differences between the mutant and the wild-type nodules concerned the structure of infection threads, release of bacteria, and bacteroid differentiation. This confirms an essential role of RosR in establishment of successful symbiotic interaction of R. leguminosarum bv. trifolii with clover plants.

Earthworms, pesticides and sustainable agriculture: a review

The aim of this review is to generate awareness and understand the importance of earthworms in sustainable agriculture and effect of pesticides on their action. The natural resources are finite and highly prone to degradation by the misuse of land and mismanagement of soil. The world is in utter need of a healthy ecosystem that provides with fertile soil, clean water, food and other natural resources. Anthropogenic activities have led to an increased contamination of land. The intensification of industrial and agricultural practices chiefly the utilization of pesticides has in almost every way made our natural resources concave. Earthworms help in a number of tasks that support many ecosystem services that favor agrosystem sustainability but are degraded by exhaustive practices such as the use of pesticides. The present review assesses the response of earthworm toward the pesticides and also evaluates the relationship between earthworm activity and plant growth. We strictly need to refresh and rethink on the policies and norms devised by us on sustainable ecology. In an equivalent way, the natural resources should be utilized and further, essential ways for betterment of present and future livelihood should be sought.

Molecular cloning of the BLADE-ON-PETIOLE gene and expression analyses during nodule development in Lupinus luteus

The BLADE-ON-PETIOLE (BOP) genes have been recently shown to play an essential role in many physiological processes, including embryogenesis, meristem determinacy, leaf patterning and nodule development. In our research we used Lupinus luteus, a plant with great agronomic potential due to its high protein content and nitrogen fixation ability. In this work, LlBOP in L. luteus was identified for the first time and its expression during nodule development was analyzed. The high expression levels of LlBOP and LlLbI (LEGHEMOGLOBIN), essential to nitrogen-fixing symbiosis, were noted in the developing root nodules and were correlated with the occurrence of leghemoglobin. All of these data indicate that LlBOP is an important regulator of root nodule formation and functioning in L. luteus.

Bacteria and fungi controlling plant growth by manipulating auxin: balance between development and defense

Plant diseases cause huge losses by changing the quality and quantity of harvested crops. Many disease symptoms caused by bacteria or fungi rely on the involvement of plant hormones, while other plant hormones act as defense signals in the plant. In this review the role of auxins in these processes will be evaluated. Some growth promoting plant hormones cause disease symptoms. For example auxins stimulate cell division and cell elongation in a healthy plant, but tumor formation after bacterial infection. Thus, control of auxin levels and auxin signaling pathways significantly contribute to the defense network in plants. Auxin can also act directly as defense molecule with antimicrobial activity. Since much research has been done in the recent years on auxin as a pathogenicity factor for many diseases, several examples will be presented to highlight the complexity between normal plant growth, which is regulated by auxin, and processes determining resistance or susceptibility, triggered by the same class of molecules.

Implication of evolution and diversity in arbuscular and ectomycorrhizal symbioses

Being highly sensitive to ecological variations, symbiotic associations should inherently have a limited occurrence in nature. To circumvent this sensitivity and reach their universal distribution, symbioses used three strategies during their evolution, which all generated high biodiversity levels: (i) specialization to a specific environment, (ii) protection of one partner via its internalization into the other, (iii) frequent partner exchange. Mycorrhizal associations follow the 3rd strategy, but also present traits of internalization. As most ancient type, arbuscular mycorrhiza (AM) formed by a monophyletic fungal group with reduced species richness did constantly support the mineral nutrition of terrestrial plants and enabled their ecological radiation and actual biodiversity level. In contrast ectomycorrhiza (EM) evolved later and independently within different taxa of fungi able to degrade complex organic plant residues, and the diversity levels of EM fungal and tree partners are balanced. Despite their different origins and diversity levels, AM and EM fungi display similar patterns of diversity dynamics in ecosystems. At each time or succession interval, a few dominant and many rare fungi are recruited by plants roots from a wide reservoir of propagules. However, the dominant fungal partners are frequently replaced in relation to changes in the vegetation or ecological conditions. While the initial establishment of AM and EM fungal communities corresponds to a neutral recruitment, their further succession is rather driven by niche differentiation dynamics.