The Dead Can Nurture: Novel Insights into the Function of Dead Organs Enclosing Embryos

Detailed analysis of agro-industrial byproducts/wastes to enable efficient sorting for various agro-industrial applications

Agriculture-based industries generate huge amounts of byproducts/wastes every year, which are not exploited or disposed efficiently posing an environmental problem with implications to human and animal health. Finding strategies to increase the recycling of agro-industrial byproducts/wastes (AIBWs) is a primary objective of the current study. A thorough examination of AIBWs in conjunction with experimental research is proposed to facilitate sorting for various agro-industrial applications and consequently increasing byproduct/waste utilization. Accordingly, two sustainable, locally available sources of AIBWs, namely, wheat bran (WB) and garlic straw and peels (GSP) were studied in detail including content and composition of proteins, phytohormones and nutritional elements, as well as the effect of AIBW extracts on plant and microbial growth. Hundreds of proteins were recovered from AIBW mainly from WBs, including chaperons, metabolite and protein modifying enzymes, and antimicrobial proteins. In-gel assays showed that WB and GSP possess high protease and nuclease activities. Conspicuously, phytohormone analysis of AIBWs revealed the presence of high levels of strigolactones, stimulants of seed germination of root parasitic weeds, as well as indole acetic acid (IAA) and abscisic acid (ABA). Garlic straw extract strongly inhibited germination of the weed Amaranthus palmeri but not of Abutilon theophrasti and all examined AIBWs significantly affected post-germination growth. Bacterial growth was strongly inhibited by garlic straw, but enhanced by WBs, which can be used at least partly as a bacterial growth medium. Thus, an in-depth examination of AIBW characteristics will enable appropriate sorting for diverse agro-industrial applications, which will increase their utilization and consequently their economic value.

What Worth the Garlic Peel

Plants have two types of reproduction: sexual, resulting in embryo production, and asexual, resulting in vegetative bodies commonly derived from stems and roots (e.g., bulb, tuber). Dead organs enclosing embryos (DOEEs, such as seed coat and pericarp) are emerging as central components of the dispersal unit acting to nurture the embryo and ensure its survival in the habitat. Here we wanted to investigate the properties of dead organs enclosing plant asexual reproductive bodies, focusing on the garlic (Allium sativum) bulb. We investigated the biochemical and biological properties of the outer peel enclosing the bulb and the inner peel enclosing the clove using various methodologies, including bioassays, proteomics, and metabolomics. The garlic peels differentially affected germination and post-germination growth, with the outer peel demonstrating a strong negative effect on seed germination of Sinapis alba and on post-germination growth of Brassica juncea. Proteome analysis showed that dead garlic peels possess 67 proteins, including chitinases and proteases, which retained their enzymatic activity. Among primary metabolites identified in garlic peels, the outer peel accumulated multiple sugars, including rhamnose, mannitol, sorbitol, and trehalose, as well as the modified amino acid 5-hydroxylysine, known as a major component of collagen, at a higher level compared to the clove and the inner peel. Growth of Escherichia coli and Staphylococcus aureus was promoted by garlic peel extracts but inhibited by clove extract. All extracts strongly inhibited spore germination of Fusarium oxysporum f.sp. melonis. Thus, the garlic peels not only provide physical protection to vegetative offspring but also appear to function as a refined arsenal of proteins and metabolites for enhancing growth and development, combating potential pathogens, and conferring tolerance to abiotic stresses.

Single and Combined Salinity and Heat Stresses Impact Yield and Dead Pericarp Priming Activity

In the face of climate change and the predicted increase in the frequency and severity of abiotic stresses (e.g., hot spell, salinity), we sought to investigate the effect of salinity (S), short episodes of high temperature (HS) and combination of salinity and high temperature (SHS), at the reproductive phase, on yield with a special focus on the properties of dead pericarps of Brassica juncea. Three interval exposures to HS resulted in massive seed abortion, and seeds from salt-treated plants germinated poorly. Germination rate and final germination of B. juncea seeds were slightly reduced in the presence of salt and SHS pericarp extracts. All pericarp extracts completely inhibited seed germination of tomato and Arabidopsis, but removal of pericarp extracts almost fully restored seed germination. Heat and salinity profoundly affected the accumulation of phytohormones in dead pericarps. Combined stresses highly reduced IAA and ABA levels compared with salt, and enhanced the accumulation of GA1, but abolished the positive effect of salt on the accumulation of GA4, JA and SA. Interestingly, pericarp extracts displayed priming activity and significantly affected seedling performance in a manner dependent on the species and on the origin of the pericarp. While control pericarps improved and reduced the seedlings’ performance of autologous and heterologous species, respectively, pericarps from salt-treated plants were harmless or improved heterologous seedling performance. Thus, the strategy employed by the germinating seed for securing resources is set up, at least partly, by the mother plant in conjunction with the maternal environment whose components are stored in the dead maternal organs enclosing the embryo.

Differential Response to Single and Combined Salt and Heat Stresses: Impact on Accumulation of Proteins and Metabolites in Dead Pericarps of Brassica juncea

Dead organs enclosing embryos, such as seed coats and pericarps, are emerging as important maternally-derived components of the dispersal unit that affect seed performance and fate. In the face of climate change and increased incidents of heatwaves, we sought to investigate the effect of salinity (S), short episodes of high temperature (HS), and combination of S + HS (SHS), at the reproductive phase, on the properties of dead pericarps of Brassica juncea. Proteome and metabolome analyses revealed multiple proteins and metabolites stored in dead pericarps whose levels and composition were altered under single and combined stress conditions. The protein profile of SHS showed a higher correlation with salt than with HS indicating the dominant effect of salt over heat stress. On the other hand, the analysis of metabolites showed that the profile of SHS has better correlation with HS than with salt. The integration of metabolic and proteomic data showed that changes in TCA cycle intermediates and certain amino acids (e.g., proline) under salt treatments (S and SHS) are highly correlated with changes in proteins involved in their biosynthetic pathways. Thus, accumulation of proteins and metabolites in dead pericarps is differently affected by single and combination of salt and heat stresses. Salinity appears to dominate plant response to combined stresses at the protein level, while heat appears to be the major factor affecting metabolite accumulation in dead pericarps.

Functional packaging of seeds

The encapsulation of seeds in hard coats and fruit walls (pericarp layers) fulfils protective and dispersal functions in many plant families. In angiosperms, packaging structures possess a remarkable range of different morphologies and functionalities, as illustrated by thermo and hygro-responsive seed pods and appendages, as well as mechanically strong and water-impermeable shells. Key to these different functionalities are characteristic structural arrangements and chemical modifications of the underlying sclerenchymatous tissues. Although many ecological aspects of hard seed encapsulation have been well documented, a detailed understanding of the relationship between tissue structure and function only recently started to emerge, especially in the context of environmentally driven fruit opening and seed dispersal (responsive encapsulations) and the outstanding durability of some seed coats and indehiscent fruits (static encapsulations). In this review, we focus on the tissue properties of these two systems, with particular consideration of water interactions, mechanical resistance, and force generation. Common principles, as well as unique adaptations, are discussed in different plant species. Understanding how plants integrate a broad range of functions and properties for seed protection during storage and dispersal plays a central role for seed conservation, population dynamics, and plant-based material developments.

Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks

MAIN CONCLUSION

We report a soybean gene co-expression network built with data from 1284 RNA-Seq experiments, which was used to identify important regulators, modules and to elucidate the fates of gene duplicates. Soybean (Glycine max (L.) Merr.) is one of the most important crops worldwide, constituting a major source of protein and edible oil. Gene co-expression networks (GCN) have been extensively used to study transcriptional regulation and evolution of genes and genomes. Here, we report a soybean GCN using 1284 publicly available RNA-Seq samples from 15 distinct tissues. We found modules that are differentially regulated in specific tissues, comprising processes such as photosynthesis, gluconeogenesis, lignin metabolism, and response to biotic stress. We identified transcription factors among intramodular hubs, which probably integrate different pathways and shape the transcriptional landscape in different conditions. The top hubs for each module tend to encode proteins with critical roles, such as succinate dehydrogenase and RNA polymerase subunits. Importantly, gene essentiality was strongly correlated with degree centrality and essential hubs were enriched in genes involved in nucleic acids metabolism and regulation of cell replication. Using a guilt-by-association approach, we predicted functions for 93 of 106 hubs without functional description in soybean. Most of the duplicated genes had different transcriptional profiles, supporting their functional divergence, although paralogs originating from whole-genome duplications (WGD) are more often preserved in the same module than those from other mechanisms. Together, our results highlight the importance of GCN analysis in unraveling key functional aspects of the soybean genome, in particular those associated with hub genes and WGD events.

Dead but Not Dead End: Multifunctional Role of Dead Organs Enclosing Embryos in Seed Biology

Dry fruits consist of two types, dehiscent and indehiscent, whereby the fruit is splitting open or remains closed at maturity, respectively. The seed, the dispersal unit (DU) of dehiscent fruits, is composed of three major parts, the embryo and the food reserve, encapsulated by the maternally-derived organ, the seed coat. Indehiscent fruit constitutes the DU in which the embryo is covered by two protective layers (PLs), the seed coat and the fruit coat. In grasses, the caryopsis, a one-seeded fruit, can be further enclosed by the floral bracts to generate two types of DUs, florets and spikelets. All protective layers enclosing the embryo undergo programmed cell death (PCD) at maturation and are thought to provide mainly a physical shield for embryo protection and a means for dispersal. In this review article, I wish to highlight the elaborate function of these dead organs enclosing the embryo as unique storage structures for beneficial substances and discuss their potential role in seed biology and ecology.

Extreme drought alters progeny dispersal unit properties of winter wild oat (Avena sterilis L.)

The dead husk is a vital component of the dispersal unit whose biochemical properties can be modified following exposure to drought. This might affect seed performance and fate, soil properties and consequently plant biodiversity. We investigated the effects of extreme drought on the dispersal unit (DU) properties of winter wild oat (Avena sterilis L.) in the Mediterranean ecosystems focusing on a commonly ignored component of the DU, namely the dead floral bracts (husk). DUs were collected from a climate change experimental research station in the Judean Hills, Israel, simulating extreme drought and from two additional sites differing in the rainfall amounts. Our results showed that drought conditions significantly affected A. sterilis reproductive traits displaying reduced DUs and caryopses weights. The husk contributes profoundly to seed performance showing that germination from the intact DUs or the intact florets 1 was higher, faster and more homogenous compared to naked caryopses; no effect of drought on germination properties was observed. The husk stored hundreds of proteins that retain enzymatic activity and multiple metabolites including phytohormones. Changes in rainfall amounts affected the composition and levels of proteins and other metabolites accumulated in the husk, with a notable effect on abscisic acid (ABA). The husk of both control and drought plants released upon hydration substances that selectively inhibited other species seed germination as well as substances that promoted microbial growth. Our data showed that the dead husk represents a functional component of the DU that have been evolved to nurture the embryo and to ensure its success in its unique habitat. Furthermore, drought conditions can modify husk biochemical properties, which in turn might affect seed performance and fate, soil microbiota and soil fertility and consequently plant species diversity.

Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L

The dead organs enclosing embryos (DOEEs) emerge as central components of the dispersal unit (DU) capable for long-term storage of active proteins and other substances that affect seed performance and fate. We studied the effect of maternal environment (salt and salt+heat) on progeny DU (dry indehiscent fruit) focusing on pericarp properties of Anastatica hierochuntica. Stressed plants displayed increased seed abortion and low level and rate of germination. Hydrated pericarps released antimicrobial factors and allelopathic substances that inhibit germination of heterologous species. Proteome analysis of dead pericarps revealed hundreds of proteins, among them nucleases, chitinases and proteins involved in reactive oxygen species detoxification and cell wall modification. Salt treatment altered the composition and level of proteins stored in the pericarp. We observed changes in protein profile released from seeds of salt-treated plants with a notable increase in a small anti-fungal protein, defensin. The levels of phytohormones including IAA, ABA and salicylic acid were reduced in dead pericarps of stressed plants. The data presented here highlighted the predominant effects of maternal environment on progeny DUs of the desert plant A. hierochuntica, particularly on pericarp properties, which in turn might affect seed performance and fate, soil fertility and consequently plant biodiversity.

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

Seed dormancy and timing of its release is an important developmental transition determining the survival of individuals, populations, and species in variable environments. Medicago truncatula was used as a model to study physical seed dormancy at the ecological and genetics level. The effect of alternating temperatures, as one of the causes releasing physical seed dormancy, was tested in 178 M. truncatula accessions over three years. Several coefficients of dormancy release were related to environmental variables. Dormancy varied greatly (4-100%) across accessions as well as year of experiment. We observed overall higher physical dormancy release under more alternating temperatures (35/15 °C) in comparison with less alternating ones (25/15 °C). Accessions from more arid climates released dormancy under higher experimental temperature alternations more than accessions originating from less arid environments. The plasticity of physical dormancy can probably distribute the germination through the year and act as a bet-hedging strategy in arid environments. On the other hand, a slight increase in physical dormancy was observed in accessions from environments with higher among-season temperature variation. Genome-wide association analysis identified 136 candidate genes related to secondary metabolite synthesis, hormone regulation, and modification of the cell wall. The activity of these genes might mediate seed coat permeability and, ultimately, imbibition and germination.

Dissection of flag leaf metabolic shifts and their relationship with those occurring simultaneously in developing seed by application of non-targeted metabolomics

Rice flag leaves are major source organs providing more than half of the nutrition needed for rice seed development. The dynamic metabolic changes in rice flag leaves and the detailed metabolic relationship between source and sink organs in rice, however, remain largely unknown. In this study, the metabolic changes of flag leaves in two japonica and two indica rice cultivars were investigated using non-targeted metabolomics approach. Principal component analysis (PCA) revealed that flag leaf metabolomes varied significantly depending on both species and developmental stage. Only a few of the metabolites in flag leaves displayed the same change pattern across the four tested cultivars along the process of seed development. Further association analysis found that levels of 45 metabolites in seeds that are associated with human nutrition and health correlated significantly with their levels in flag leaves. Comparison of metabolomics of flag leaves and seeds revealed that some flavonoids were specific or much higher in flag leaves while some lipid metabolites such as phospholipids were much higher in seeds. This reflected not only the function of the tissue specific metabolism but also the different physiological properties and metabolic adaptive features of these two tissues.

The role of seed appendage in improving the adaptation of a species in definite seasons: a case study of Atriplex centralasiatica

BACKGROUND

As a common accompanying dispersal structure, specialized seed appendages play a critical role in the successful germination and dispersal of many plants, and are regarded as an adaptation character for plants survival in diverse environments. However, little is known about how the appendages modulate the linkage between germination and environmental factors. Here, we tested the responses of germination to seasonal environmental signals (temperature and humidity) via seed appendages using Atriplex centralasiatica, which is widely distributed in salt marshlands with dry-cold winter in northern China. Three types of heteromorphic diaspores that differ in morphology of persistent bracteole and dormancy levels are produced in an individual plant of A. centralasiatica.

RESULTS

Except for the nondormant diaspore (type A, with a brown seed enclosed in a persistent bracteole), bracteoles regulated inner seed dormancy of the other two dormant diaspore types, i.e., type B (flat diaspore with a black inner seed) and type C (globular diaspore with a black inner seed). For types B and C, germination of bracteole-free seeds was higher than that of intact diaspores, and was limited severely when incubated in the bracteole-soaking solution. Dormancy was released at a low temperature (< 10 °C) and suitable humidity (5-15%) condition. Oppositely, high temperature and unfit humidity induced secondary dormancy via inhibitors released by bracteoles. Type C with deeper dormancy needed more stringent conditions for dormancy release and was easier for dormancy inducement than type B. The germination windows were broadened and the time needed for dormancy release decreased after the bracteole flushing for the two dormant types in the field condition.

CONCLUSIONS

Bracteoles determine the germination adaptation by bridging seeds and environmental signals and promising seedlings establishment only in proper seasons, which may also restrict species geographical distribution and shift species distributing ranges under the global climate change scenarios.

Continuum Modeling of Discrete Plant Communities: Why Does It Work and Why Is It Advantageous?

Understanding ecosystem response to drier climates calls for modeling the dynamics of dryland plant populations, which are crucial determinants of ecosystem function, as they constitute the basal level of whole food webs. Two modeling approaches are widely used in population dynamics, individual (agent)-based models and continuum partial-differential-equation (PDE) models. The latter are advantageous in lending themselves to powerful methodologies of mathematical analysis, but the question of whether they are suitable to describe small discrete plant populations, as is often found in dryland ecosystems, has remained largely unaddressed. In this paper, we first draw attention to two aspects of plants that distinguish them from most other organisms—high phenotypic plasticity and dispersal of stress-tolerant seeds—and argue in favor of PDE modeling, where the state variables that describe population sizes are not discrete number densities, but rather continuous biomass densities. We then discuss a few examples that demonstrate the utility of PDE models in providing deep insights into landscape-scale behaviors, such as the onset of pattern forming instabilities, multiplicity of stable ecosystem states, regular and irregular, and the possible roles of front instabilities in reversing desertification. We briefly mention a few additional examples, and conclude by outlining the nature of the information we should and should not expect to gain from PDE model studies.

Roles of Hardened Husks and Membranes Surrounding Brachypodium hybridum Grains on Germination and Seedling Growth

Several studies have assessed the function and significance of the presence of dead, hardened husks on germination and seedling growth in several grass species and reached to inconsistent results. Here, we assess the roles of husks (dead lemma and palea) and an inner membrane surrounding the grains on germination behaviour and seedling growth of Brachypodium hybridum, one of three species of the genetic model B. distachyon complex, in an arid mountain of Arabia. The interactive effects between temperature and the incubation light were assessed on germination of husked and dehusked-demembraned grains. Germination and seedling growth were assessed for different combinations of grain treatments (soaked and non-soaked husked, dehusked-membraned and dehusked-demembraned). Dehusked-demembraned grains were also germinated in different dormancy regulating compounds (DRCs) and light qualities (light, dark and different red: far red [R: FR] ratios). The results indicated an insignificant difference between husked and dehusked-membraned grains on final germination and the germination rate index (GRI), with the former producing significantly bigger seedlings. Removal of the inner-membrane resulted in a significant reduction in all traits. Soaking grains in water resulted in significant enhancements in germination and seedling growth of only husked grains. Husked-membraned and demembraned grains germinated more significantly and faster at lower rather than higher temperatures. None of different concentrations of several DRCs succeeded in enhancing final germination of dehusked-demembraned grains. Red-rich light significantly enhanced germination of dehusked-membraned grains in comparison to other light qualities. It could be concluded that the role of husks is to mainly enhance seedling growth, while the major role of the membrane is to increase final germination. The ability of red-rich light in enhancing the germination of dehusked-membraned but not dehusked-demembraned grains suggest a role for the inner membrane in regulating dormancy through differential filtering of light properties.