Roles of microbes in supporting sustainable rice production using the system of rice intensification

MdPHR2 and MdARF6-4 synergistically regulate arbuscular mycorrhizal symbiosis and the transcription of MdPHT1;13, enhancing phosphorus uptake in apple rootstocks

Phosphorus in the soil is easily chelated into forms that are unavailable to plants, leading to phosphorus deficiency, which severely affects the growth, development, and fruit quality of apple trees. To address phosphorus deficiency, we used four different arbuscular mycorrhizal fungi (AMF) to investigate their effects on the growth and development of apple rootstocks and phosphorus uptake in the soil. We identified Glomus mosseae (Gm) fungi as the most effective AMF for promoting growth and found that under phosphorus-deficient conditions, inoculating with Gm fungi promoted the growth of the above-ground parts of the plants and phosphorus absorption, while it inhibited root growth. After inoculating with Gm fungi, we found phosphorus starvation response factors (PHRs) and auxin response factors (ARFs) were upregulated. Knockdown of MdPHR2 or MdARF6-4 resulted in decreased root arbuscular structures, total mycorrhizal colonization rate, and root phosphorus content, indicating that MdPHR2 and MdARF6-4 positively regulate the symbiosis of Gm fungi and phosphorus absorption. In contrast, overexpressing MdARF6-4 led to reduced root development but increased root phosphorus content under Gm fungi inoculation, suggesting that MdARF6-4 is involved in Gm-mediated phosphorus absorption and root development. Moreover, both MdPHR2 and MdARF6-4 directly bound to the promoter area of the downstream phosphorus transporter MdPHT1;13, and these two transcription factors interacted with each other in vivo and in vitro. In summary, our study demonstrates that the interaction between MdPHR2 and MdARF6-4 synergistically regulates the Gm symbiosis and the transcription of MdPHT1;13, thereby promoting phosphorus absorption in apple rootstocks.

Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience

The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.

Roles of Phyllosphere Microbes in Rice Health and Productivity

The phyllosphere, comprising the aerial portions of plants, is a vibrant ecosystem teeming with diverse microorganisms crucial for plant health and productivity. This review examines the functional roles of phyllosphere microorganisms in rice (Oryza sativa), focusing on their importance in nutrient uptake, disease resistance, and growth promotion. The molecular mechanisms underlying these interactions are explored along with their potential applications in enhancing sustainable rice production. The symbiotic relationships between rice plants and their associated microorganisms are highlighted, offering insights into improved agricultural practices. Furthermore, this review addresses the challenges and future developments in translating laboratory findings into practical applications. By synthesizing current research, this comprehensive analysis serves as a valuable resource for leveraging phyllosphere microbes in rice farming and related fields.

Multi-walled carbon nanotubes affect yield, antioxidant response, and rhizosphere microbial community of scented rice under combined cadmium-lead (Cd-Pb) stress

Rice production is threatened by heavy metal stress. The use of multi-walled carbon nanotubes (MWCNTs) in agriculture has been reported in previous studies. We aimed to quantify the impact of MWCNTs on the growth and physiological characteristics of scented rice under cadmium (Cd) and lead (Pb) stresses. Therefore, a pot experiment was conducted, two scented rice varieties Yuxiangyouzhan and Xiangyaxiangzhan were used as materials grown under different concentrations of MWCNTs (0, 100, and 300 mg kg-1 recorded as CK, CNPs100, and CNPs300, respectively). The yield, antioxidant response, and rhizosphere microbial community of scented rice were studied. The results showed that compared with the CK treatment, the CNPs100 and CNPs300 treatments increased leaf dry weight by 17.95%-56.22% at the heading stage, and the H2O2 content in leaves decreased significantly by 36.64%-42.27% at the maturity stage. Under CNPs100 treatment, the grain yield of two scented rice varieties increased significantly by 17.54% and 27.40%, respectively. The MWCNTs regulated the distribution of the Cd and Pb in different plant tissues. The content of Cd (0.11-0.20 mg kg-1) and Pb (0.01-0.04 mg kg-1) in grain were at a safety level (<0.2 mg kg-1). Moreover, MWCNTs increased soil microbial community abundance and altered community composition structure under Cd-Pb stress, which in turn improved agronomic traits and quality of scented rice. Overall, this study suggested that the application of MWCNTs regulates the growth, yield, physiological response, and soil microbial community, the genotypes response effect of scented rice to MWCNTs is needed further studied.

Evaluating the underlying physiological and molecular mechanisms in the system of rice intensification performance with Trichoderma-rice plant symbiosis as a model system

The system of rice intensification (SRI) is an extensively-researched and increasingly widely-utilized methodology for alleviating current constraints on rice production. Many studies have shown physiological and morphological improvements in rice plants induced by SRI management practices to be very similar to those that are associated with the presence of beneficial microbial endophytes in or around rice plants, especially their roots. With SRI methods, grain yields are increased by 25-100% compared to conventional methods, and the resulting plant phenotypes are better able to cope with biotic and abiotic stresses. SRI management practices have been shown to be associated with significant increases in the populations of certain microorganisms known to enhance soil health and plant growth, e.g., Azospirillum, Trichoderma, Glomus, and Pseudomonas. This article evaluates the effects of applying Trichoderma as a model microbe for assessing microbial growth-promotion, biological control activity, and modulation of gene expression under the conditions created by SRI practices. Information about the molecular changes and interactions associated with certain effects of SRI management suggests that these practices are enhancing rice plants' expression of their genetic potentials. More systematic studies that assess the effects of SRI methods respectively and collectively, compared with standard rice production methods, are needed to develop a more encompassing understanding of how SRI modifications of crops' growing environment elicit and contribute to more robust and more productive phenotypes of rice.

Chemical fertilizer reduction combined with bio-organic fertilizers increases cauliflower yield via regulation of soil biochemical properties and bacterial communities in Northwest China

The continuous application of chemical fertilizers in vegetable cropping has led to deterioration of the soil environment and reduced yield and quality. The objective of this study was to evaluate the effect of combining chemical and bio-organic fertilizers on cauliflower yield, soil biochemical properties, and the bacterial community. Six treatments were established: no fertilizer (CK, control), chemical fertilizers (CF, conventional dosage for this region), balanced fertilization (BF, 30% reduction of chemical fertilizers), and balanced fertilization plus 3,000, 6,000, or 12,000 kg.ha-1 bio-organic fertilizer (Lvneng Ruiqi Biotechnology Co., Ltd., Gansu, China) (BF + OF1, BF + OF2, BF + OF3, respectively). A two-season field experiment with cauliflower was conducted under the different fertilizer treatments in irrigation districts along the Yellow River, Northwest China. The results indicate that the yield, soil organic matter, total potassium content, and enzyme activity under the bio-organic treatments were generally higher than those under the CF treatment. Compared with the CF treatment, the BF treatment increased soil organic matter content, enzyme activity and soil bacterial relative abundance. Moreover, the bacterial alpha-diversity were higher than those of conventional fertilization. The predominant phyla, including Proteobacteria, Actinobacteria, Gemmatimonadetes, and Chloroflexi, were the main contributors to the microbiome shift, as demonstrated by their remarkable enrichment in the soil under BF + OF2 and BF + OF3 treatments. Furthermore, Pearson correlation analyses show significant correlations among the soil organic matter, available P and K, electrical conductivity, and relative abundance of potentially beneficial microbial groups, such as the genera Massilia, Bacillus, Lysobacter, and Nitrosospira. Overall, this study suggests that balanced fertilization and the application of bio-organic fertilizers are essential to ensure soil fertility and long-term sustainable green productivity.

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

Exploiting Potential of <i>Trichoderma harzianum</i> and <i>Glomus versiforme</i> in Mitigating <i>Cercospora</i> Leaf Spot Disease and Improving Cowpea Growth

BACKGROUND AND OBJECTIVE

Trichoderma species are of utmost importance in agro-biotechnological applications because, in their interactions with plant hosts, they out-compete most pathogenic microorganisms. This study aimed at exploiting the potential of Trichoderma harzianum together with Glomus versiforme and its mutants, in inhibiting cowpea leaf spot rot induced due to Cercospora canescens infestation and improving agronomic growth parameter in a screen house experiment.

MATERIALS AND METHODS

The experiment was designed using single and co-inoculation of the bioagents: in all, eleven treatments were applied, consisting of Glom_verwild, Glom_ver30, Glom_ver60, Glom_ver90, Trich_h, Glom_verwild+Trich_h, Glom_ver30+Trich_h, Glom_ver60+Trich_h, Glom_ver90+Trich_h, Pathogen alone and control. Cowpea growth yield parameters and disease severity were assessed after 7 weeks.

RESULTS

The deployed treatments improved agronomic growth parameters substantially (p<0.05) relative to control. Glom_ver 60+Trich_h treatment exerted the highest agronomic growth improvement yield. In addition, the best reduction in the incidence and severity of cowpea leaf spot disease was obtained using Glom_ver 60+Trich_h. A significantly higher germination rate in seeding, confirms both inhibitory and growth improvement potency of the bio inoculants treatment.

CONCLUSION

This study's findings confirmed the beneficial impacts of the treatment of seed and soil with dual T. harzianum and G. versiforme, in improving the immunity of cowpea to Cercospora canescens leaf spot infection and improve cowpea growth.

The endosphere microbial communities, a great promise in agriculture

Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner.