Rhizobium Impacts on Seed Productivity, Quality, and Protection of Pisum sativum upon Disease Stress Caused by Didymella pinodes: Phenotypic, Proteomic, and Metabolomic Traits

Understanding the root of the problem for tackling pea root rot disease

Pea (Pisum sativum), a crop historically significant in the field of genetics, is regaining momentum in sustainable agriculture due to its high protein content and environmental benefits. However, its cultivation faces significant challenges from root rot, a complex disease caused by multiple soil-borne pathogens prevalent across most pea growing regions. This disease leads to substantial yield losses, further complicated by the dynamic interactions among pathogens, soil conditions, weather, and agricultural practices. Recent advancements in molecular diagnostics provide promising tools for the early and precise detection of these pathogens, which is critical for implementing effective disease management strategies. In this review, we explore how the availability of latest pea genomic resources and emerging technologies, such as CRISPR and cell-specific transcriptomics, will enable a deeper understanding of the molecular basis underlying host-pathogen interactions. We emphasize the need for a comprehensive approach that integrates genetic resistance, advanced diagnostics, cultural practices and the role of the soil microbiome in root rot. By leveraging these strategies, it is possible to develop pea varieties that can withstand root rot, ensuring the crop's resilience and its continued importance in global agriculture.

Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.)

Proso millet is an important but under-researched and underutilized crop with the potential to become a future smart crop because of its climate-resilient features and high nutrient content. Assessing diversity and marker-trait associations are essential to support the genomics-assisted improvement of proso millet. This study aimed to assess the population structure and diversity of a proso millet diversity panel and identify marker-trait associations for agronomic and grain nutrient traits. In this study, genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping raw genotyping-by-sequencing (GBS) data onto the proso millet genome, resulting in 5621 quality-filtered SNPs in 160 diverse accessions. The modified Roger's Distance assessment indicated an average distance of 0.268 among accessions, with the race miliaceum exhibiting the highest diversity and ovatum the lowest. Proso millet germplasm diversity was structured according to geographic centers of origin and domestication. Genome-wide association mapping identified 40 marker-trait associations (MTAs), including 34 MTAs for agronomic traits and 6 for grain nutrients; 20 of these MTAs were located within genes. Favourable alleles and phenotypic values were estimated for all MTAs. This study provides valuable insights into the population structure and diversity of proso millet, identified marker-trait associations, and reported favourable alleles and their phenotypic values for supporting genomics-assisted improvement efforts in proso millet.

Post Natal Microbial and Metabolite Transmission: The Path from Mother to Infant

The entero-mammary pathway is a specialized route that selectively translocates bacteria to the newborn's gut, playing a crucial role in neonatal development. Previous studies report shared bacterial and archaeal taxa between human milk and neonatal intestine. However, the functional implications for neonatal development are not fully understood due to limited evidence. This study aimed to identify and characterize the microbiota and metabolome of human milk, mother, and infant stool samples using high-throughput DNA sequencing and FT-ICR MS methodology at delivery and 4 months post-partum. Twenty-one mothers and twenty-five infants were included in this study. Our results on bacterial composition suggest vertical transmission of bacteria through breastfeeding, with major changes occurring during the first 4 months of life. Metabolite chemical characterization sheds light on the growing complexity of the metabolites. Further data integration and network analysis disclosed the interactions between different bacteria and metabolites in the biological system as well as possible unknown pathways. Our findings suggest a shared bacteriome in breastfed mother-neonate pairs, influenced by maternal lifestyle and delivery conditions, serving as probiotic agents in infants for their healthy development. Also, the presence of food biomarkers in infants suggests their origin from breast milk, implying selective vertical transmission of these features.

Widely Targeted Metabolomics Provides New Insights into Nutritional Profiling and Reveals the Flavonoid Pathway of Pea (Pisum sativum L.)

To learn more about the nutritional composition and health benefits for human consumers of peas, we used a widely targeted metabolomics-based approach to reveal the metabolite components from three main varieties, and a total of 1095 metabolites were identified. A comparison of 487 differentially accumulated metabolites shared among three varieties of fresh and dried peas found most of the amino acids and derivatives were downregulated and most of the lipids and flavonoids were upregulated in dried peas. Furthermore, comparing the main nutrient profiles exclusively showed that there were few differences in free fatty acids, sugars, vitamins, and alkaloids between dried and fresh peas. Peas are especially enriched with B-group vitamins. Through detailed identification and classification, the flavonoid pathway of peas was revealed; a variety of glycosylated derivatives from kaempferol, quercetin, and luteolin were confirmed to be abundant in peas. It was also found that isoflavones are richer in peas than in many other plants, and putatively the isoflavone synthesis pathway originates from liquiritigenin and naringenin. Our study not only offers guidance for understanding the nutritional components of peas, but also provides the basis for healthy diet analysis of the edible value and health benefits of peas.

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

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

Optimized methods for random and targeted mutagenesis in field pea (Pisum sativum L.)

Field pea is an important pulse crop for its dense nutritional profile and contribution to sustainable agricultural practices. Recently, it has received extensive attention as a potential leading source of plant-based proteins. However, the adoption of peas as a mainstream source of proteins is affected by a relatively moderate protein content, anti-nutritional factors and high levels of off-flavor components that reduce protein quality. Availability of genetic variation for desirable seed quality traits is the foundation for the sustainable development of pea varieties with improved protein content and quality. Mutagenesis has been an important tool in gene functional characterization studies and creating genetic variability for crop breeding. Large-scale mutagenesis of a crop using physical and chemical agents requires diligent selection of the mutagen and optimization of its dose to increase the frequency of mutations. In this study, we present detailed optimized protocols for physical and chemical mutagenesis of pea using gamma irradiation and ethyl methanesulfonate (EMS), respectively. Gamma radiation and EMS titration kill curves were established to identify optimal doses of the two mutagenic agents. Based on germination, survival rate and growth phenotypes, a gamma radiation dose of 225 Gy and EMS concentration of 5 mm were selected as optimal dosages for mutagenesis in field pea. The presented protocol has been modified from previously established mutagenesis protocols in other crop plants. Our results indicate that the optimal mutagen dosage is genotype dependent. CRISPR/Cas-based gene editing provides a precise and rapid method for targeted genetic manipulation in plants. With the recent success of gene editing in pea using CRISPR/Cas, this innovative technology is expected to become an integral component of the gene discovery and crop improvement toolkit in pea. Here, we describe an optimized methods for targeted mutagenesis of pea protoplasts, including mesophyll protoplast extraction, PEG-mediated transformation and gene editing of a LOX gene using CRISPR/Cas system. The general strategies and methods of mutagenesis described here provide an essential resource for mutation breeding and functional genomics studies in pea. These methods also provide a foundation for similar studies in other crops.

Metabolome Profiling: A Breeding Prediction Tool for Legume Performance under Biotic Stress Conditions

Legume crops such as common bean, pea, alfalfa, cowpea, peanut, soybean and others contribute significantly to the diet of both humans and animals. They are also important in the improvement of cropping systems that employ rotation and fix atmospheric nitrogen. Biotic stresses hinder the production of leguminous crops, significantly limiting their yield potential. There is a need to understand the molecular and biochemical mechanisms involved in the response of these crops to biotic stressors. Simultaneous expressions of a number of genes responsible for specific traits of interest in legumes under biotic stress conditions have been reported, often with the functions of the identified genes unknown. Metabolomics can, therefore, be a complementary tool to understand the pathways involved in biotic stress response in legumes. Reports on legume metabolomic studies in response to biotic stress have paved the way in understanding stress-signalling pathways. This review provides a progress update on metabolomic studies of legumes in response to different biotic stresses. Metabolome annotation and data analysis platforms are discussed together with future prospects. The integration of metabolomics with other “omics” tools in breeding programmes can aid greatly in ensuring food security through the production of stress tolerant cultivars.

Salicylic Acid in Plant Symbioses: Beyond Plant Pathogen Interactions

Plants form beneficial symbioses with a wide variety of microorganisms. Among these, endophytes, arbuscular mycorrhizal fungi (AMF), and nitrogen-fixing rhizobia are some of the most studied and well understood symbiotic interactions. These symbiotic microorganisms promote plant nutrition and growth. In exchange, they receive the carbon and metabolites necessary for their development and multiplication. In addition to their role in plant growth and development, these microorganisms enhance host plant tolerance to a wide range of environmental stress. Multiple studies have shown that these microorganisms modulate the phytohormone metabolism in the host plant. Among the phytohormones involved in the plant defense response against biotic environment, salicylic acid (SA) plays an important role in activating plant defense. However, in addition to being a major actor in plant defense signaling against pathogens, SA has also been shown to be involved in plant-microbe symbiotic interactions. In this review, we summarize the impact of SA on the symbiotic interactions. In addition, we give an overview of the impact of the endophytes, AMF, and rhizobacteria on SA-mediated defense response against pathogens.

Rhizobia and endophytic bacteria isolated from rainforest fragments within an iron ore mining site of the Eastern Brazilian Amazon

The aim of the present study was to isolate and evaluate the diversity of rhizobial and endophytic bacterial strains from undisturbed native rainforests within an iron ore mining site of the Serra Norte de Carajás in the Eastern Brazilian Amazon region to assess their biotechnological utility in reclamation of areas. Experiments were conducted to capture strains from samples of the soil of these forests at the sites Arenito II, Noroeste II, and Sul IV using Macroptilium atropurpureum and Mimosa acutistipula var. ferrea as trap host plants. Only M. atropurpureum nodulated, and the different bacterial strains were isolated from its nodules. There was no difference in the number of nodules among the areas, but the Arenito II bacterial community was the most efficient, indicated by the aboveground biomass production and suitable shoot mass/root mass ratio. Fifty-two (52) bacterial isolates were obtained, distributed in five groups, including nodulating and endophytic bacteria: 32 from Arenito II, 12 from Noroeste II, and 8 from Sul IV. The nodulating Bradyrhizobium genus was common to the three areas, whereas Paraburkholderia was found only in Arenito II. The nodD1 gene was amplified in all the strains of both nodulating genera. Strains of the nodulating genus Methylobacterium were also isolated from the three areas; however, they did not nodulate the host of origin, and their nodD1 gene was not amplified. Endophytic strains were also isolated from the genera Paenibacillus, Pantoea, and Leifsonia in Arenito II, Leifsonia in Noroeste I, and Paenibacillus in Sul IV. The greater nodulation and rhizobial and endophytic bacterial diversity observed in Arenito II were probably due to the more suitable edaphic properties of the area. The isolated strains were incorporated in the collection of the Department of Soil Science of UFLA and will be investigated in relation to their symbiotic characteristics with native host plants, as well as their ability to perform other biological processes.

Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications

In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.

Physiological and Biochemical Characterization of the GABA Shunt Pathway in Pea (Pisum sativum L.) Seedlings under Drought Stress

The physiological and biochemical role of the γ-aminobutyric acid (GABA) shunt pathway in green pea seedlings (Pisum sativum L.) was studied in response to soil water holding capacity levels: 80%, 60%, 40%, 20%, and 10% grown under continuous light at 25 °C for 7 days and 14 days, separately. Characterization of seeds germination pattern, seedlings growth (plant height, fresh and dry weight, and chlorophyll contents), GABA shunt metabolite (GABA, glutamate, and alanine) levels, total protein and carbohydrate levels, and oxidative damage (MDA level) were examined. Data showed a significant effect of drought stress on seed germination, plant growth, GABA shunt metabolites level, total protein and carbohydrate contents, and MDA level. A significant decline in seed germination percentage was recorded at a 20% drought level, which indicated that 20% of soil water holding capacity is the threshold value of water availability for normal germination after 14 days. Seedling fresh weight, dry weight, and plant height were significantly reduced with a positive correlation as water availability was decreased. There was a significant decrease with a positive correlation in Chl a and Chl b contents in response to 7 days and 14 days of drought. GABA shunt metabolites were significantly increased with a negative correlation as water availability decreased. Pea seedlings showed a significant increase in protein content as drought stress was increased. Total carbohydrate levels increased significantly when the amount of water availability decreased. MDA content increased slightly but significantly after 7 days and sharply after 14 days under all water stress levels. The maximum increase in MDA content was observed at 20% and 10% water levels. Overall, the significant increases in GABA, protein and carbohydrate contents were to cope with the physiological impact of drought stress on Pisum sativum L. seedlings by maintaining cellular osmotic adjustment, protecting plants from oxidative stress, balancing carbon and nitrogen (C:N) metabolism, and maintaining cell metabolic homeostasis and cell turgor. The results presented in this study indicated that severe (less than 40% water content of the holding capacity) and long-term drought stress should be avoided during the germination stage to ensure proper seedling growth and metabolism in Pisum sativum L.

Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems

Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.

Phloem Sap Proteins Are Part of a Core Stress Responsive Proteome Involved in Drought Stress Adjustment

During moderate drought stress, plants can adjust by changes in the protein profiles of the different organs. Plants transport and modulate extracellular stimuli local and systemically through commonly induced inter- and intracellular reactions. However, most proteins are frequently considered, cell and organelle specific. Hence, while signaling molecules and peptides can travel systemically throughout the whole plant, it is not clear, whether protein isoforms may exist ubiquitously across organs, and what function those may have during drought regulation. By applying shotgun proteomics, we extracted a core proteome of 92 identical protein isoforms, shared ubiquitously amongst several Medicago truncatula tissues, including roots, phloem sap, petioles, and leaves. We investigated their relative distribution across the different tissues and their response to moderate drought stress. In addition, we functionally compared this plant core stress responsive proteome with the organ-specific proteomes. Our study revealed plant ubiquitous protein isoforms, mainly related to redox homeostasis and signaling and involved in protein interaction networks across the whole plant. Furthermore, about 90% of these identified core protein isoforms were significantly involved in drought stress response, indicating a crucial role of the core stress responsive proteome (CSRP) in the plant organ cross-communication, important for a long-distance stress-responsive network. Besides, the data allowed for a comprehensive characterization of the phloem proteome, revealing new insights into its function. For instance, CSRP protein levels involved in stress and redox are relatively more abundant in the phloem compared to the other tissues already under control conditions. This suggests a major role of the phloem in stress protection and antioxidant activity enabling the plants metabolic maintenance and rapid response upon moderate stress. We anticipate our study to be a starting point for future investigations of the role of the core plant proteome. Under an evolutionary perspective, CSRP would enable communication of different cells with each other and the environment being crucial for coordinated stress response of multicellular organisms.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Proteomics Reveals the Mechanism Underlying the Inhibition of Phytophthora sojae by Propyl Gallate

Phytophthora sojae is a serious soil-borne pathogen, and the major control measures undertaken include the induction of soybean-resistance genes, fungicides, and scientific and reasonable planting management. Owing to the safety and resistance of fungicides, it is of great importance to screen new control alternatives. In a preliminary study, we observed that propyl gallate (PG) exerts a considerable inhibitory effect on P. sojae and can effectively prevent and cure soybean diseases, although the underlying mechanism remains unclear. To explore the inhibitory mechanism of PG on P. sojae, we analyzed the differences in the protein profile of P. sojae before and after treatment with PG using tandem mass tag (TMT) proteomics. Proteomic analysis revealed that the number of differentially expressed proteins (DEPs) was 285, of which 75 were upregulated and 210 were downregulated, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways primarily comprised glycolysis, tricarboxylic acid cycle, fatty acid metabolism, secondary metabolite generation, and other pathways. Among the DEPs involved in PG inhibition of P. sojae are two closely related uncharacterized proteins encoded by PHYSODRAFT_522340 and PHYSODRAFT_344464, denoted PsFACL and PsCPT herein. The CRISPR/Cas9 knockout technique revealed that PsFACL and PsCPT were involved in the growth rate and pathogenicity. In addition, the results of gas chromatography-mass spectrometry (GC-MS) showed that there were differences in fatty acid levels between wild-type (WT) and CRISPR/Cas9 knockout transformants. Knocking out PsFACL and PsCPT resulted in the restriction of the synthesis and β-oxidation of long-chain fatty acids, respectively. These suggest that PsFACL and PsCPT were also involved in the regulation of the fatty acid metabolism. Our results aid in understanding the mechanism underlying the inhibition of P. sojae growth by PG.

Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions

Current agricultural and food systems encourage research and development on major crops, neglecting regionally important minor crops. Small millets include a group of small- seeded cereal crops of the grass family Poaceae. This includes finger millet, foxtail millet, proso millet, barnyard millet, kodo millet, little millet, teff, fonio, job’s tears, guinea millet, and browntop millet. Small millets are an excellent choice to supplement major staple foods for crop and dietary diversity because of their diverse adaptation on marginal lands, less water requirement, lesser susceptibility to stresses, and nutritional superiority compared to major cereal staples. Growing interest among consumers about healthy diets together with climate-resilient features of small millets underline the necessity of directing more research and development towards these crops. Except for finger millet and foxtail millet, and to some extent proso millet and teff, other small millets have received minimal research attention in terms of development of genetic and genomic resources and breeding for yield enhancement. Considerable breeding efforts were made in finger millet and foxtail millet in India and China, respectively, proso millet in the United States of America, and teff in Ethiopia. So far, five genomes, namely foxtail millet, finger millet, proso millet, teff, and Japanese barnyard millet, have been sequenced, and genome of foxtail millet is the smallest (423-510 Mb) while the largest one is finger millet (1.5 Gb). Recent advances in phenotyping and genomics technologies, together with available germplasm diversity, could be utilized in small millets improvement. This review provides a comprehensive insight into the importance of small millets, the global status of their germplasm, diversity, promising germplasm resources, and breeding approaches (conventional and genomic approaches) to accelerate climate-resilient and nutrient-dense small millets for sustainable agriculture, environment, and healthy food systems.

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach

Pulses are one of the most important categories of food plants, and Pea (Pisum sativum L.) as a member of pulses is considered a key crop for food and feed and sustainable agriculture. Integrative multi-omics and microsymbiont impact studies on the plant's immune system are important steps toward more productive and tolerant food plants and thus will help to find solutions against food poverty. Didymella pinodes is a main fungal pathogen of pea plants. Arbuscular mycorrhizal fungi (AMF) promote plant growth and alleviate various stresses. However, it remained unclear as to how the AMF effect on seed metabolism and how this influences resistance against the pathogen. This study assesses the AMF impacts on yield components and seed quality upon D. pinodes infection on two different P. sativum cultivars, susceptible versus tolerant, grown in pots through phenotypic and seed molecular analyses. We found that AMF symbiosis affects the majority of all tested yield components as well as a reduction of disease severity in both cultivars. Seeds of mycorrhizal pea plants showed strong responses of secondary metabolites with nutritional, medicinal, and pharmaceutical attributes, also involved in pathogen response. This is further supported by proteomic data, functionally determining those primary and secondary metabolic pathways, involved in pathogen response and induced upon AMF-colonization. The data also revealed cultivar specific effects of AMF symbiosis that increase understanding of genotype related differences. Additionally, a suite of proteins and secondary metabolites are presented, induced in seeds of P. sativum upon AMF-colonization and pathogen attack, and possibly involved in induced systemic resistance against D. pinodes, useful for modern breeding strategies implementing microsymbionts toward increased pathogen resistance.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.

Metabolic alterations in pea leaves during arbuscular mycorrhiza development

Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.

Subcellular Phenotyping: Using Proteomics to Quantitatively Link Subcellular Leaf Protein and Organelle Distribution Analyses of Pisum sativum Cultivars

Plant phenotyping to date typically comprises morphological and physiological profiling in a high-throughput manner. A powerful method that allows for subcellular characterization of organelle stoichiometric/functional characteristics is still missing. Organelle abundance and crosstalk in cell dynamics and signaling plays an important role for understanding crop growth and stress adaptations. However, microscopy cannot be considered a high-throughput technology. The aim of the present study was to develop an approach that enables the estimation of organelle functional stoichiometry and to determine differential subcellular dynamics within and across cultivars in a high-throughput manner. A combination of subcellular non-aqueous fractionation and liquid chromatography mass spectrometry was applied to assign membrane-marker proteins to cell compartmental abundances and functions of Pisum sativum leaves. Based on specific subcellular affiliation, proteotypic marker peptides of the chloroplast, mitochondria and vacuole membranes were selected and synthesized as heavy isotope labeled standards. The rapid and unbiased Mass Western approach for accurate stoichiometry and targeted absolute protein quantification allowed for a proportional organelle abundances measure linked to their functional properties. A 3D Confocal Laser Scanning Microscopy approach was developed to evaluate the Mass Western. Two P. sativum cultivars of varying morphology and physiology were compared. The Mass Western assay enabled a cultivar specific discrimination of the chloroplast to mitochondria to vacuole relations.

The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei

Increasing evidence has manifested that the gut bacterial microbiota of shrimps is closely related to the environmental factors, host developmental stage and health status like that of humans and animals does. These studies have provided an important guidance for improving shrimp culture benefits. In practice, aside from bacteria, eukaryotic microorganisms dominated by fungal microbiota (mycobiota), also play a key role in host growth, metabolism and homeostasis. However, little so far is known about the mycobiota in the digestive tract of shrimp. In this study, we used high-throughput sequencing of internal transcribed spacer 1 region to characterize the hepatopancreas and intestinal mycobiota of Pacific white shrimp and their connections with disease incidence and seasonal variation. The results showed that the hepatopancreas and intestinal mycobiota of Litopenaeus vannamei are dominated by the phyla Ascomycota and Basidiomycota, and the genera Alternaria, Tuber, Hortaea, Sarocladium, and Stagonospora. The fungal microbiota significantly varies under the influence of disease and seasonal variation. Sick shrimps had a higher level of potential pathogenic fungus, Candida in the intestine. Healthy shrimps had a higher abundance of the genera Didymella and Filobasidium in the gut, and Pyrenochaetopsis in the hepatopancreas. Of note, most of the fungi carried by Pacific white shrimps were pathogens to humans. This study has revealed the intestinal and hepatopancreas mycobiota of L. vannamei and the effects of diseases and seasonal variation to the mycobiota. Our study provides important guidance for Pacific white shrimp farming and sheds further insight on the fungal microbiota.

Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi

Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.

Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management

How to sustainably feed a growing global population is a question still without an answer. Particularly farmers, to increase production, tend to apply more fertilizers and pesticides, a trend especially predominant in developing countries. Another challenge is that industrialization and other human activities produce pollutants, which accumulate in soils or aquatic environments, contaminating them. Not only is human well-being at risk, but also environmental health. Currently, recycling, land-filling, incineration and pyrolysis are being used to reduce the concentration of toxic pollutants from contaminated sites, but too have adverse effects on the environment, producing even more resistant and highly toxic intermediate compounds. Moreover, these methods are expensive, and are difficult to execute for soil, water, and air decontamination. Alternatively, green technologies are currently being developed to degrade toxic pollutants. This review provides an overview of current research on microbial inoculation as a way to either replace or reduce the use of agrochemicals and clean environments heavily affected by pollution. Microorganism-based inoculants that enhance nutrient uptake, promote crop growth, or protect plants from pests and diseases can replace agrochemicals in food production. Several examples of how biofertilizers and biopesticides enhance crop production are discussed. Plant roots can be colonized by a variety of favorable species and genera that promote plant growth. Microbial interventions can also be used to clean contaminated sites from accumulated pesticides, heavy metals, polyaromatic hydrocarbons, and other industrial effluents. The potential of and key processes used by microorganisms for sustainable development and environmental management are discussed in this review, followed by their future prospects.

Crop metabolomics: from diagnostics to assisted breeding

BACKGROUND

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

AIM OF REVIEW

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Translational metabolomics applied to crop breeding programs.