Plant beneficial microbiome a boon for improving multiple stress tolerance in plants.

Beneficial microbes or their products have been key drivers for improving adaptive and growth features in plants under biotic and abiotic stress conditions. However, the majority of these studies so far have been utilized against individual stressors. In comparison to individual stressors, the combination of many environmental stresses that plants experience has a greater detrimental effect on them and poses a threat to their existence. Therefore, there is a need to explore the beneficial microbiota against combined stressors or multiple stressors, as this will offer new possibilities for improving plant growth and multiple adaptive traits. However, recognition of the multifaceted core beneficial microbiota from plant microbiome under stress combinations will require a thorough understanding of the functional and mechanistic facets of plant microbiome interactions under different environmental conditions in addition to agronomic management practices. Also, the development of tailored beneficial multiple stress tolerant microbiota in sustainable agriculture necessitates new model systems and prioritizes agricultural microbiome research. In this review, we provided an update on the effect of combined stressors on plants and their microbiome structure. Next, we discussed the role of beneficial microbes in plant growth promotion and stress adaptation. We also discussed how plant-beneficial microbes can be utilized for mitigating multiple stresses in plants. Finally, we have highlighted some key points that warrant future investigation for exploring plant microbiome interactions under multiple stressors.

Differential responses in some quinoa genotypes of a consortium of beneficial endophytic bacteria against bacterial leaf spot disease.

Many effective plant-microbe interactions lead to biological changes that can stimulate plant growth and production. This study evaluated the effect of the interaction between quinoa (Chenopodium quinoa Willd.) and endophytic bacterial strains on differential responses under biotic stress. Four strains of endophytic bacteria were used to inoculate three quinoa genotypes. Endophytic bacteria, isolated from the endosphere of healthy genotypes of quinoa plants, were used to evaluate their biocontrol activity against Pseudomonas syringae on quinoa plants, which causes leaf spot disease, depending on some different parameters. Quinoa genotype plants were treated with four treatments: pathogenic bacteria only (T1), internal bacteria only (T2), pathogenic bacteria + endogenous bacteria (T3), and untreated as the control (T4). The results indicated that there was a significant difference between chlorophyll content index of infected plants without bioagent (untreated) compared to plants bio-inoculated with endophytic bacteria. The highest mean disease incidence was on the plants without bacterial inoculum (90, 80, and 100%) for quinoa genotypes G1, G2, and G3, respectively. The results showed that there were significant differences in the weight of grains/plant, as the value ranged from 8.1 to 13.3 g when treated with pathogens (T1) compared to the treatment with pathogens and endogenous bacteria (T3), which ranged from 11.7 to 18.6 g/plant. Decreases in total aromatic amino acids appeared due to the pathogen infection, by 6.3, 22.8, and 24.1% (compared to the control) in G1, G2, and G3, respectively. On the other hand, genotype G3 showed the highest response in the levels of total aromatic and total neutral amino acids. The endophytic strains promoted quinoa seedling growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acids, showing that complex interactions might be associated with enhancement of quinoa seedling performance by endophytic bacteria. The endophytic bacterial strains were able to reduce the severity of bacterial leaf spot disease by 30, 40, and 50% in quinoa genotypes G1, G2, and G3, respectively, recording significant differences compared to the negative control. The results indicated that, G1 genotype was superior in different performance indicators (pathogen tolerance index, yield injury %, superiority measure and relative performance) for grain weight/plant under pathogen infection condition when treated with endophyte bacteria. Based on this study, these bacterial strains can be used as a biotechnology tool in quinoa seedling production and biocontrol to diminish the severity of bacterial leaf spot disease.

Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives.

Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.

Improving environmental stress resilience in crops by genome editing: insights from extremophile plants.

In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.

Evaluation of Salicornia bigelovii Germplasm for Food Use in Egypt and the United Arab Emirates Based on Agronomic Traits and Nutritional Composition.

Climate change significantly aggravates the quality of soil and water, especially in desert regions such as the United Arab Emirates (UAE) and Egypt concluding in an alarming increase in salinity in the reservoirs of the natural resources. Saline farming rises as a promising solution, utilizing low-quality water and land resources to grow salt-tolerant varieties of conventional crops and halophytes. Samphire (Salicornia spp.) is among the most popular multi-purpose halophytes that are locally consumed in several countries around the world as a vegetable. Six Salicornia bigelovii genotypes (ICBA-2, ICBA-3, ICBA-4, ICBA-8, ICBA-9, ICBA-10) were evaluated for their agronomic performance and nutritional composition in Dubai in UAE and, for the first time, at the Red Sea Governorate in Egypt in the 2019-2020 season using saline groundwater for irrigation (ECw = 26 and 6.6 dS/m, respectively). ICBA-10 performed well in both locations with high green biomass and seed yield (10.9 kgm-2 and 116.3 gm-2, respectively, in UAE; 7.7 kgm-2 and 82.9 gm-2, respectively, in Egypt). ICBA-10 was, overall, also good in ion accumulation, total amino acids and unsaturated fatty acids content in both locations for shoots and seeds. Our results indicated that a lack of a drainage system and leaching fraction, the silt loam texture and the drip irrigation system might have contributed in the gradual accumulation of salts in the soil at Mubarak Valley at the end of the experiment at a higher level than ICBA. Apart from the agronomic parameters, higher salinity levels also affected ion accumulation, the amino acids and the fatty acids content for both shoots and seeds, whereas the proximate composition was affected to a lesser extent. Our findings on the high unsaturated fatty acids content under higher salinity corroborate the nutritional value of S. bigelovii oil. Due to its euhalophyte nature, S. bigelovii is a valuable source of minerals, amino acids and antioxidants that render it the most promising salt-loving plant for food use.

The diversity of quinoa morphological traits and seed metabolic composition.

Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.

Plant Growth-Promoting Rhizobacteria Alleviate High Salinity Impact on the Halophyte Suaeda fruticosa by Modulating Antioxidant Defense and Soil Biological Activity.

Plant growth-promoting rhizobacteria (PGPR) are considered as bio-ameliorators that confer better salt resistance to host plants while improving soil biological activity. Despite their importance, data about the likely synergisms between PGPR and halophytes in their native environments are scarce. The objective of this study was to assess the effect of PGPR (Glutamicibacter sp. and Pseudomonas sp.) inoculation on biomass, nutrient uptake, and antioxidant enzymes of Suaeda fruticosa, an obligate halophyte native in salt marshes and arid areas in Tunisia. Besides, the activity of rhizospheric soil enzyme activities upon plant inoculation was determined. Plants were grown in pots filled with soil and irrigated with 600 mM NaCl for 1 month. Inoculation (either with Pseudomonas sp. or Glutamicibacter sp.) resulted in significantly higher shoot dry weight and less accumulation of Na+ and Cl- in shoots of salt-treated plants. Glutamicibacter sp. inoculation significantly reduced malondialdehyde (MDA) concentration, while increasing the activity of antioxidant enzymes (superoxide dismutase; catalase; ascorbate peroxidase; and glutathione reductase) by up to 100%. This provides strong arguments in favor of a boosting effect of this strain on S. fruticosa challenged with high salinity. Pseudomonas sp. inoculation increased shoot K+ and Ca2+ content and lowered shoot MDA concentration. Regarding the soil biological activity, Pseudomonas sp. significantly enhanced the activities of three rhizospheric soil enzymes (urease, ß-glucosidase, and dehydrogenase) as compared to their respective non-inoculated saline treatment. Hence, Pseudomonas sp. could have a great potential to be used as bio-inoculants in order to improve plant growth and soil nutrient uptake under salt stress. Indole-3-acetic acid concentration in the soil increased in both bacterial treatments under saline conditions, especially with Glutamicibacter sp. (up to +214%). As a whole, Glutamicibacter sp. and Pseudomonas sp. strains are promising candidates as part of biological solutions aiming at the phytoremediation and reclamation of saline-degraded areas.

Harnessing plant microbiome for mitigating arsenic toxicity in sustainable agriculture.

Heavy metal toxicity has become an impediment to agricultural productivity, which presents major human health concerns in terms of food safety. Among them, arsenic (As) a non-essential heavy metal has gained worldwide attention because of its noxious effects on agriculture and public health. The increasing rate of global warming and anthropogenic activities have promptly exacerbated As levels in the agricultural soil, thereby causing adverse effects to crop genetic and phenotypic traits and rendering them vulnerable to other stresses. Conventional breeding and transgenic approaches have been widely adapted for producing heavy metal resilient crops; however, they are time-consuming and labor-intensive. Hence, finding new mitigation strategies for As toxicity would be a game-changer for sustainable agriculture. One such promising approach is harnessing plant microbiome in the era of 'omics' which is gaining prominence in recent years. The use of plant microbiome and their cocktails to combat As metal toxicity has gained widespread attention, because of their ability to metabolize toxic elements and offer an array of perquisites to host plants such as increased nutrient availability, stress resilience, soil fertility, and yield. A comprehensive understanding of below-ground plant-microbiome interactions and their underlying molecular mechanisms in exhibiting resilience towards As toxicity will help in identifying elite microbial communities for As mitigation. In this review, we have discussed the effect of As, their accumulation, transportation, signaling, and detoxification in plants. We have also discussed the role of the plant microbiome in mitigating As toxicity which has become an intriguing research frontier in phytoremediation. This review also provides insights on the advancements in constructing the beneficial synthetic microbial communities (SynComs) using microbiome engineering that will facilitate the development of the most advanced As remedial tool kit in sustainable agriculture.

Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves.

Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley's response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.

Evaluating the contribution of osmotic and oxidative stress components on barley growth under salt stress.

Salt stress is considered one of the most devastating environmental stresses, affecting barley growth and leading to significant yield loss. Hence, there is considerable interest in investigating the most effective traits that determine barley growth under salt stress. The objective of this study was to elucidate the contribution of osmotic and oxidative stress components in leaves and roots growth under salt stress. Two distinct barley (Hordeum vulgare) salt-stress tolerant genotypes, Barrage Malleg (BM, tolerant) and Saouef (Sf, sensitive), were subjected to 200 mM NaCl at early vegetative stages. Stressed and control leaves and roots tissue were assessed for several growth traits, including fresh and dry weight and plant length, as well as the content of osmoprotectants proline and soluble sugars. In addition, malondialdehyde content and activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX), as well as their corresponding gene expression patterns, were investigated. The results showed better performance of BM over Sf for leaf dry weight (LDW), root dry weight (RDW) and root length (RL). The salt-tolerant genotype (BM) had better osmoprotection against salt stress compared with the salt-sensitive genotype (Sf), with a higher accumulation of proline and soluble sugars in leaves and roots and a stronger antioxidant system as evidenced by higher activities of SOD, CAT and APX and more abundant Cu/Zn-SOD transcripts, especially in roots. Stepwise regression analysis indicated that under salt stress the most predominant trait of barley growth was Cu/Zn-SOD gene expression level, suggesting that alleviating oxidative stress and providing cell homeostasis is the first priority.

Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci.

Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.

Contrasting effects of municipal compost on alfalfa growth in clay and in sandy soils: N, P, K, content and heavy metal toxicity.

The limits for loading soils with Tunisian urban compost for cultivating Medicago sativa were determined in a 6-month experiment in a greenhouse. Mature municipal solid waste compost (MSWC) from Tunis city was applied to clay and sandy soils from cultivated fields at rates equivalent to 40, 80, 120tha(-1). In the absence of MSWC, the shoot biomass (dry weight) cumulated over four cuts was 2-2.5 lower in sandy soil than in clay soil. It was 20-25% augmented upon MSWC addition in clay soil, independently of MSWC dose. The opposite trend was observed in sandy soil, the shoot yields being diminished by MSWC in a dose dependent manner. In MSWC-amended clay soil but not in sandy soil, Cd, Cu, Zn, and Pb concentrations in shoots remained below or close to the tolerated values according to EEC norms. The MSWC might be used as conditioner for clay soil, but not for sandy soil.

Genotypic variability within Tunisian grapevine varieties (Vitis vinifera L.) facing bicarbonate-induced iron deficiency.

Morpho-physiological responses to bicarbonate-induced Fe deficiency were investigated in five Vitis vinifera L. Tunisian varieties (Khamri, Blanc3, Arich Dressé, Beldi, and Balta4). One-month-old woody cuttings were cultivated for 85days on a free calcareous soil irrigated with tap water containing increasing bicarbonate levels (0, 4, 8, 12, and 16mM NaHCO(3)). After this screening, a second experiment compared root biochemical responses of two contrasting genotypes (tolerant-sensitive) dealing with bicarbonate-induced iron deprivation (20microM Fe+/-10mM HCO(3)(-)) for 75days. Using morpho-physiological criteria, grapevine tolerance to HCO(3)(-)-induced Fe shortage appeared to be genotype-dependent: Balta4 and Beldi varieties showed the highest leaf-chlorosis score (especially at the extreme HCO(3)(-) levels), in contrast to Khamri variety. Growth parameters (shoot height, total leaf area, leaf number, and biomass production) as well as juvenile leaf chlorophyll content were also differently affected depending on both genotype and bicarbonate dose. At 16mM HCO(3)(-), Khamri was the less sensitive variety, contrasting with Balta4. On the other hand, chlorophyll content correlated positively with HCl-extractible Fe content of the juvenile leaves, suggesting that the grapevine response to iron deficiency may partly depend on to the plant ability to adequately supply young leaves with this element. Root biochemical responses revealed a relatively higher root acidification capacity in Khamri (tolerant) under Fe-deficiency while no significant changes occurred in Balta4 (sensitive). In addition, Fe(III)-reductase and phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) activities were strongly stimulated by Fe-deficiency in Khamri, while remaining constant in Balta4. These findings suggest that biochemical parameters may constitute reliable criteria for the selection of tolerant grapevine genotypes to iron chlorosis.

Effect of salt on physiological responses of barley to iron deficiency.

Iron chlorosis is very common on alkaline soils such as calcareous ones, since iron availability is limited by high pH. Under these conditions of iron deficiency, graminaceous plant species induce special mechanisms for iron acquisition, involving enhanced release of iron chelators called phytosiderophores. On the other hand, it is known that most of salt soils have alkaline pH. So, plants growing on this kind of soils are often subjected simultaneously to salinity and iron deficiency. This work aimed at (i) studying the physiological responses of barley (Hordeum vulgare L.) to iron deficiency, and (ii) evaluating the effect of salt on the iron nutrition and the phytosiderophore release. For this purpose, seedlings of Hordeum vulgare L. were cultivated under controlled conditions, either in a complete nutrient solution with or without NaCl, or in an iron free nutrient solution containing or not NaCl. The plant morphological aspect, chlorophyll content of young leaves, iron status, biomass production, and phytosiderophore release by roots were assessed. Plants subjected to Fe deficiency exhibited a severe chlorosis, accompanied by a significant biomass reduction. These plants developed more lateral roots than the control with a highly stimulated phytosiderophore release. However, the latter was greatly diminished when iron deficiency was associated to salinity. A depressive effect of salt on iron acquisition in plants subjected only to salt stress which was also observed and further confirmed by the important decrease of efficiency in iron acquisition. These results suggest that salinity may reduce capacity of plants to acquire iron from alkaline soils by inhibiting phytosiderophore release.

Differential tolerance to iron deficiency of chickpea varieties and Fe resupply effects.

The consequences of direct iron deficiency and iron resupply were evaluated during development stages of two Tunisian chickpea varieties (INRAT88 and Chetoui) cultivated in continuously aerated solution with or without 20 muM Fe. The chlorosis score was estimated during culture. Growth parameters, chlorophyll concentration, acidification capacity and Fe concentration were measured every three days during the 21-day treatment. After three weeks of treatment, the chlorosis index was 3-fold higher in Chetoui than in INRAT88, and a considerable decrease of chlorophyll concentration was observed in Chetoui plants since the 6th day of -Fe deprivation. Iron deficiency significantly inhibited whole-plant biomass deposition in both varieties. However, the growth reduction appeared earlier, and was more pronounced in Chetoui than in INRAT88. The whole-plant Fe content decreased dramatically under deficient conditions, and we note an Fe enrichment in shoots at the expense of roots. The sensitivity of Chetoui as compared to INRAT88 was confirmed by the behaviour of resupplied (-Fe/+Fe) plants. In fact, the addition of iron to deficient plants had no significant effect in Chetoui, whereas it led to a total recovery in INRAT88. The capacity of INRAT88 to maintain plant growth and to preserve adequate chlorophyll synthesis under limited iron conditions is related to its better Fe-use efficiency, in addition to its capacity to rapidly recover from this stress.

Differences in responses to iron deficiency between two legumes: lentil (Lens culinaris) and chickpea (Cicer arietinum).

Two legumes, lentil and chickpea, were cultivated in nutrient solutions: Fe lacking or containing 30 microM Fe. After 12 days of Fe starvation, lentil showed a severe yellowing of young leaves, a large decrease in chlorophyll concentration, and a significant decline of plant biomass. Chickpea showed a better response than did lentil, primarily due to a stronger acidification capacity. In addition, no chlorosis symptoms were observed in chickpea until the end of treatment. There was no significant difference in potassium uptake between the two species, but an enrichment of the young leaves at the expense of the old ones was noted in chickpea, and at a lesser extent, in lentil, when they were exposed to Fe deficiency. Moreover, this constraint led to a significant decrease of iron content in the two legumes. However, chickpea displayed higher accumulation levels of HCl-extractible iron in young and old leaves than did lentil. This protection of young leaves against K(+) and Fe(2+) impoverishment confers to these organs the capacity to preserve their chlorophyll status and their photosynthetic integrity. Furthermore, the better performance of chickpea under conditions of low Fe availability could be partially related to its seed iron reserves, higher than those of lentil.