Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments

Colonization dynamic and distribution of the endophytic fungus Microdochium bolleyi in plants measured by qPCR

Microdochium bolleyi is a fungal endophyte of cereals and grasses proposed as an ideal model organism for studying plant-endophyte interactions. A qPCR-based diagnostic assay was developed to detect M. bolleyi in wheat and Brachypodium distachyon tissues using the species-specific primers MbqITS derived from the ITS of the ribosomal gene. Specificity was tested against 20 fungal organisms associated with barley and wheat. Colonization dynamics, endophyte distribution in the plant, and potential of the seed transmission were analyzed in the wheat and model plant B. distachyon. The colonization of plants by endophyte starts from the germinating seed, where the seed coats are first strongly colonized, then the endophyte spreads to the adjacent parts, crown, roots near the crown, and basal parts of the stem. While in the lower distal parts of roots, the concentration of M. bolleyi DNA did not change significantly in successive samplings (30, 60, 90, 120, and 150 days after inoculation), there was a significant increase over time in the roots 1 cm under crown, crowns and stem bases. The endophyte reaches the higher parts of the base (2-4 cm above the crown) 90 days after sowing in wheat and 150 days in B. distachyon. The endophyte does not reach both host species' leaves, peduncles, and ears. Regarding the potential for seed transmission, endophyte was not detected in harvested grains of plants with heavily colonized roots. Plants grown from seeds derived from parental plants heavily colonized by endophyte did not exhibit any presence of the endophyte, so transmission by seeds was not confirmed. The course of colonization dynamics and distribution in the plant was similar for both hosts tested, with two differences: the base of the wheat stem was colonized earlier, but B. distachyon was occupied more intensively and abundantly than wheat. Thus, the designed species-specific primers could detect and quantify the endophyte in planta.

The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L

Introduction

With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered.

Methods

The soybean plants were exposed to cold stress (8-10°C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated.

Results and discussion

We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.

The phytomicrobiome: solving plant stress tolerance under climate change

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan

The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).

Impact of Enniatin and Deoxynivalenol Co-Occurrence on Plant, Microbial, Insect, Animal and Human Systems: Current Knowledge and Future Perspectives

Fusarium mycotoxins commonly contaminate agricultural products resulting in a serious threat to both animal and human health. The co-occurrence of different mycotoxins in the same cereal field is very common, so the risks as well as the functional and ecological effects of mycotoxins cannot always be predicted by focusing only on the effect of the single contaminants. Enniatins (ENNs) are among the most frequently detected emerging mycotoxins, while deoxynivalenol (DON) is probably the most common contaminant of cereal grains worldwide. The purpose of this review is to provide an overview of the simultaneous exposure to these mycotoxins, with emphasis on the combined effects in multiple organisms. Our literature analysis shows that just a few studies on ENN-DON toxicity are available, suggesting the complexity of mycotoxin interactions, which include synergistic, antagonistic, and additive effects. Both ENNs and DON modulate drug efflux transporters, therefore this specific ability deserves to be explored to better understand their complex biological role. Additionally, future studies should investigate the interaction mechanisms of mycotoxin co-occurrence on different model organisms, using concentrations closer to real exposures.

Synergic mitigation of saline-alkaline stress in wheat plant by silicon and Enterobacter sp. FN0603

Although microorganisms and silicon are well documented as factors that mitigate salt stress, their effect mitigating saline-alkaline stress in plants remains unknown. In this study, wheat plant seeds were treated with silicon, Enterobacter sp. FN0603 alone and in combination of both. Wheat seeds were soaked in silicon and bacterial solutions and sown in pots containing artificial saline-alkaline soils to compare the effects among all treatments. The results showed that the treatments with silicon and FN0603 alone significantly changed plant morphology, enhanced the rhizosphere soil nutrient content and enzyme activities, improved some important antioxidant enzyme activities (e.g., superoxide dismutase) and the contents of small molecules (e.g., proline) that affected osmotic conditions in the top second leaves. However, treatment with silicon and FN0603 in combination significantly further increased these stress tolerance indexes and eventually promoted the plant growth dramatically compared to the treatments with silicon or FN0603 alone (p < 0.01), indicating a synergic plant growth-promoting effect. High relative abundance of strain FN0603 was detected in the treated plants roots, and silicon further improved the colonization of FN0603 in stressed wheat roots. Strain FN0603 particularly when present in combination with silicon changed the root endophytic bacterial and fungal communities rather than the rhizosphere communities. Bipartite network analysis, variation partitioning analysis and structure equation model further showed that strain FN0603 indirectly shaped root endophytic bacterial and fungal communities and improved plant physiology, rhizosphere soil properties and plant growth through significantly and positively directing FN0603-specific biomarkers (p < 0.05). This synergetic effect of silicon and plant growth-promoting microorganism in the mitigation of saline-alkaline stress in plants via shaping root endophyte community may provide a promising approach for sustainable agriculture in saline-alkaline soils.

Rhizobacteria modify soil biological indices and induce tolerance to osmotic stress in tomato depending on the salinity level and bacteria species

Salinity is a major abiotic stress that impacts crop productivity globally. Plant growth-promoting rhizobacteria (PGPRs) exploit several mechanisms to not only decrease soil salinity but also improve the systemic tolerance of plants to osmotic stress. In this work, the effect of five PGPR strains was investigated on the growth and physiological responses of tomato plants, including stomatal closure, proline, and K⁺ and Na⁺ content under a range of salt stress, 0, 2.5, 5, 7.5, and 10 dS m^-1. The effect of PGPR strains and salinity levels on the soil biological characteristics was also investigated. Salt stress affected the plant growth and physiological factors and soil biological factors in a dose-dependent manner. The highest saline stress, 10 dS m^-1, reduced shoot and root dry weight and root volume up to 51.3, 41.5, and 51.8%, respectively. It also increased stomatal resistance and proline content 2.01- and 3.66-folds and decreased K⁺/Na⁺ ratio 4.16-folds, respectively. It also reduced basal respiration, substrate-induced respiration, and microbial biomass carbon up to 2.25-, 4.83-, and 6.7-folds and increased qCO2 3.18-folds, respectively. PGPR strains were able to modulate salt tolerance mechanisms, improve plant growth factors, and improve soil biological indicators. Bacillus megaterium P2 was the best strain in the balancing K⁺/Na⁺ uptake at least at 10 dS m^-1. However, the efficiency of strains was dependent on the magnitude of salt stress. Therefore, it is possible to introduce PGPR strains based on soil salt level or exploit rhizobacteria consortia to manage salt stress in different conditions.