Rhizobacteria Revolution: Amplifying Crop Resilience and Yield in a Changing Climate Through Plant Growth Promotion

The rapid progression of climate change poses significant challenges to global agriculture, necessitating innovative solutions to ensure food security for an expanding population. Plant growth-promoting rhizobacteria (PGPR) offer a promising avenue for sustainable agriculture by enhancing crop resilience and productivity under environmental constraints. These beneficial microbes regulate key physiological processes in plants, such as phytohormone synthesis and nutrient solubilization. This enhances root architecture, improves soil fertility, and enables crops to adapt to resource-limited conditions. Moreover, PGPR strengthen plant defenses against abiotic stressors such as salinity, drought, and nutrient deficiencies, as well as biotic threats like pathogens. Empirical evidence demonstrates that PGPR inoculation can significantly enhance crop yields across diverse agroecosystems by increasing nutrient use efficiency and stress tolerance. Despite their proven potential, the effective deployment of PGPR in farming systems requires addressing critical issues related to scalability, formulation, and integration with existing practices. This review underscores the role of PGPR in mitigating climate-induced agricultural challenges, highlighting the need for interdisciplinary collaborations and robust knowledge-sharing networks to drive the adoption of PGPR-based interventions. By leveraging these microbial allies, we can pave the way for climate-resilient farming systems and safeguard global food security amidst an uncertain future.

Transformative strategies for saline soil restoration: Harnessing halotolerant microorganisms and advanced technologies

Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotolerant microorganisms and their synergistic interactions with plants. Halotolerant microorganisms enhance plant resilience through diverse mechanisms under salinity, including exopolysaccharide production, sodium sequestration, and phytohormone regulation. It improves ionic balance, nutrient uptake, and root development, facilitated by osmoregulatory and genetic adaptations. In this discussion, we explored emerging technologies, including genome editing (e.g., CRISPR-Cas9), synthetic biology, and advanced omics-based tools such as metagenomics and metatranscriptomics. These cutting-edge approaches offer profound insights into microbial diversity and their functional adaptations to saline environments. By leveraging these technologies, it is possible to design targeted bioremediation strategies through the customization of microbial functionalities to address specific environmental challenges effectively. Advanced methodologies, such as microbial volatile organic compounds (mVOCs), nanotechnology, and stress-tolerant microbial consortia, significantly enhance plant stress tolerance and facilitate soil restoration. Moreover, integrating digital technologies, including machine learning and artificial intelligence (AI), optimizes bioremediation processes by providing precise, scalable, and adaptable solutions tailored to diverse agricultural ecosystems. The synergistic application of halotolerant microbe-mediated approaches with advanced biotechnological and digital innovations presents a transformative strategy for saline soil restoration. Future research should focus on harmonizing these technologies and methodologies to maximize plant-microbe interactions and establish resilient, sustainable agricultural systems.

Harnessing phosphate-solubilizing microorganisms for mitigation of nutritional and environmental stresses, and sustainable crop production

MAIN CONCLUSION

Phosphate-solubilizing microorganisms enhance nutrients availability, mitigate environmental stresses, and increase plant growth. The bioengineering of phosphate-solubilizing microbes and host plants may further improve their efficacy for increasing crop yield. Unsustainable agricultural practices are followed in current crop production systems worldwide for resolving food demand issues of ever-increasing human population. In addition, global food crop production is further affected due to continuous climatic change, erratic rains, and environmental stresses during the recent past causing threat to microbial as well as plant biodiversity. The application of plant beneficial microorganisms into agricultural practices has emerged recently as an innovative and sustainable approach to increase crop yield with limited resources and in vulnerable environment. These beneficial microbes improve crop productivity by enhancing nutrients' availability and mitigation of abiotic stresses along with suppression of plant diseases. However, there have been limited studies on the stress ameliorative role of phosphate-solubilizing microorganisms (PSMs), and there is still a need to elucidate the contribution of PSMs in improving plant health and crop productivity under harsh environmental conditions. This review summarizes the role of PSMs in improving phosphorus availability in soil through solubilization or mineralization of organic phosphate, and by assisting plants in amelioration of environmental stresses. Other beneficial activities of PSMs, such as release of phytohormones, production of ACC deaminase, strengthening of antioxidant system, and induction of systemic resistance, also contribute toward stress mitigation and plant growth promotion under stressful environments. Improvement in efficacy of PSMs and host plants using genetic engineering techniques has been discussed leading to increases in crop yields. However, further research is needed to develop sustainable climate-resilient approach by improving plant growth-promoting activities of PSMs even under environmental stresses to increase soil fertility and crop production in different agroecosystems.

Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome

Plants in grasslands navigate a complex landscape of interactions including competition for resources and defense against pathogens. Foliar fungi can suppress plant growth directly through pathogenic interactions, or indirectly via host growth-defense tradeoffs. The exclusion of foliar fungi allows the reallocation of resources from defense to growth and reproduction. In addition, plants also invest photosynthates in rhizodeposition, or root exudates, which play a significant role in shaping the rhizosphere microbial community. However, it remains unclear what impact the exclusion of foliar fungi has on the allocation of resources to rhizodeposition and the composition of the rhizosphere microbial community. Using a 6-year foliar fungicide study in plots planted with 16 species of native prairie plants, we asked whether foliar fungi influence the rhizosphere microbial composition of a common prairie grass (Andropogon gerardii) and a common legume (Lespedeza capatita). We found that foliar fungicide increased aboveground biomass and season-long plant production, but did not alter root biomass, seed production, or rhizosphere microbial diversity. The magnitude of change in aboveground season-long plant production was significantly associated with the magnitude of change in the rhizosphere microbial community in paired foliar fungicide-treated vs. control plots. These results suggest important coupling between foliar fungal infection and plant investment in rhizodeposition to modify the local soil microbial community.

Modulation of plant carbon and nitrogen metabolism by novel actinobacteria Rhodospirillum sp. to combat galaxolide toxicity in barley and maize plants

The phytotoxic effect of cosmetics such as galaxolide (HHCB) has been investigated, however, their metabolic basis of this impact is still obscure. Thus, we investigated the effect of HHCB on the biomass accumulation, photosynthesis, primary and secondary metabolites in two species from different functional groups i.e., barley (C3) and maize (C4). In addition, the metabolic bases of HHCB stress mitigating impact of the bioactive Rhodospirillum sp. JY3 were investigated. HHCB toxicity on plant growth and physiology was significantly reduced in PGPB treated plants. At metabolism level, sugars levels and metabolic enzymes (e.g., invertase, sucrose synthase, starch synthase) were increased. Consequentially, this provided a route for organic, amino and fatty acids biosynthesis. PGPB further mitigated the phytotoxic impact of HHCB upon the levels of organic acids (e.g., oxalic, citric, succinic, malic and isobutyric acids), amino acids, particularly proline, in addition to unsaturated fatty acids. Furthermore, plant growth-promoting bacteria (PGPB) treatment reduced HHCB toxicity through increasing antioxidant metabolites (e.g., polyamines and anthocyanin), their precursors (e.g., phenylalanine, naringenin, cinnamic and coumaric acids) and their related biosynthetic enzymes such as chalcone synthase and cinnamate-4-hydroxylase. Overall, this study, for the first time, significantly contributes to quenching the environmental hazards and maintaining agriculture sustainability using eco-friendly tools.

Recycled Phosphorus Bioamendments from Wastewater Impact Rhizomicrobiome and Benefit Crop Growth: Sustainability Implications at Water-Food Nexus

Phosphorus recovery through enhanced biological phosphorus removal (EBPR) processes from agricultural wastes holds promise in mitigating the impending global P shortage. However, the complex nutrient forms and the microbial augments, expected to exert a profound impact on crop rhizomicrobiome and thus crop health, remained unexplored. In this study, we investigated the impacts of EBPR biosolids on crops growth and rhizomicrobiome in comparison to chemical fertilizer and Vermont manure compost. Our findings revealed that EBPR biosolid augmentation promoted the best maize shoot growth traits with the least nutrient deficiency, evidencing its agricultural benefits. Biosolid augmentation significantly impacted the rhizomicrobiome with decreased biodiversity but higher activities with enriched taxa capable of utilizing various carbon sources. The novel single-cell Raman spectroscopy phenotyping technique uncovered the surprisingly high abundance (up to 30%) of polyphosphate-accumulating organisms (PAOs) in the rhizosphere and their distinctive variations in different biosolid amendments. Furthermore, the interactions between EBPR-derived PAOs such as Candidatus Accumulibacter phosphatis and soil native plant growth promoting rhizobacteria highlighted the previously overlooked status and yet-to-be-characterized functions of PAOs in P cycling. This study provides a novel perspective leveraging EBPR biosolids to facilitate plant growth with agronomic benefits, thereby contributing to more sustainable and ecologically responsible agricultural practices.

The Rhizospheric Alkali-Halotolerant Bacillus sp. KhSb-159 Enhanced Growth Parameters of the Mung Bean Crop

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in enhancing plant growth through various direct and indirect mechanisms. In this investigation, we isolated a potential PGPR, Bacillus sp. KhSb-159, from the rhizosphere of Sorghum bicolor L. located at Kharaghoda, Little Rann of Kutch (LRK), Gujarat (India). The isolated Bacillus sp. KhSb-159 displayed distinctive characteristics, forming circular, sticky, opaque, moderate-sized colonies with brown pigmentation. Interestingly, this strain exhibited growth at an alkaline pH of 9, even in the presence of 1 M NaCl (w/v). Further analysis revealed its capacity to produce indole acetic acid (IAA), ammonia, siderophores, and the ability to solubilize phosphate. In addition, KhSb-159 showed extracellular enzyme secretion, including amylase, protease, and cellulase. Bacillus sp. strain KhSb-159 demonstrated its potential to enhance the growth of mung bean crops which is a significant agricultural application. The treated seeds exhibited improvements in various growth parameters such as shoot length, root length, plant biomass, number of leaves, number of roots, fresh weight of shoot, dry weight of shoot, fresh weight of root, dry weight of root, fresh weight of leaves, and dry weight of leaves. Overall, Bacillus sp. strain KhSb-159 would be a good choice for bioformulation in sustainable agriculture due to its diverse range of abilities. This study has implications for the advancement of eco-friendly farming methods and offers insightful information about using rhizobacterial strains to maximize plant growth.

Microbial mediated silver nanoparticles enhance the potential of bioactive metabolites in the medicinal plant Linum usitatissimum

Medicinal plants contain phytochemicals that confer therapeutic potentials, allowing plants to perform various biologically significant functions. However, the therapeutic potential of these bioactive metabolites against multidrug-resistant bacteria is limited. Hence, the potential use of rhizopheric bacteria to isolate silver nanoparticles to enhance the potential of bioactive metabolites has been adopted by researchers. Therefore, this research aimed to biogenically produce silver nanoparticles using the rhizospheric soil of Aloe barbadensis miller and to evaluate its impact in regulating the potential of bioactive metabolites produced from the medicinal plant Linum usitatissimum. The powder extract of Linum usitatissimum was macerated under four different environmental conditions including cold maceration, warm maceration, fermented, and unfermented for extraction of metabolites. Macerated extracts were then evaluated for phytochemical detection of bioactive metabolites like alkaloids, steroids, phenols, and saponins. Biogenic AgNPs were primarily confirmed by visible color change from colorless to brown and were further characterized using UV-vis spectroscopy, giving two absorbance peaks at 440 nm and 445 nm. Functional groups attached to biogenic AgNPs were detected by Fourier transform infrared (FTIR) analysis. The crystalline nature of biogenic AgNPs was evaluated by X-ray diffraction (XRD) giving a diffraction peak at angles of around 36°, 46°, 67°, and 77°. The particle size and morphological appearance of biogenic AgNPs were confirmed by Scanning Electron Microscopy (SEM). The total phenolic content of biogenic AgNPs and bioactive metabolites was estimated by the Folin-Ciocalteu (F-C) assay. The antimicrobial efficacy of biogenic AgNPs and bioactive metabolites against MDR bacterial strains was accessed. This research shows that biogenic AgNPs can be used as a strong agent in enhancing the antimicrobial potential of bioactive metabolites against MDR bacteria and they can be investigated for further experimental findings.

Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland

This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.

The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization

Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.

Biotechnological advances in plant growth-promoting rhizobacteria for sustainable agriculture

The rhizosphere, the soil zone surrounding plant roots, serves as a reservoir for numerous beneficial microorganisms that enhance plant productivity and crop yield, with substantial potential for application as biofertilizers. These microbes play critical roles in ecological processes such as nutrient recycling, organic matter decomposition, and mineralization. Plant growth-promoting rhizobacteria (PGPR) represent a promising tool for sustainable agriculture, enabling green management of crop health and growth, being eco-friendly alternatives to replace chemical fertilizers and pesticides. In this sense, biotechnological advancements respecting genomics and gene editing have been crucial to develop microbiome engineering which is pivotal in developing microbial consortia to improve crop production. Genome mining, which involves comprehensive analysis of the entire genome sequence data of PGPR, is crucial for identifying genes encoding valuable bacterial enzymes and metabolites. The CRISPR-Cas system, a cutting-edge genome-editing technology, has shown significant promise in beneficial microbial species. Advances in genetic engineering, particularly CRISPR-Cas, have markedly enhanced grain output, plant biomass, resistance to pests, and the sensory and nutritional quality of crops. There has been a great advance about the use of PGPR in important crops; however, there is a need to go further studying synthetic microbial communities, microbiome engineering, and gene editing approaches in field trials. This review focuses on future research directions involving several factors and topics around the use of PGPR putting special emphasis on biotechnological advances.

Enhancing the Resilience of Agroecosystems Through Improved Rhizosphere Processes: A Strategic Review

As farming practices evolve and climate conditions shift, achieving sustainable food production for a growing global population requires innovative strategies to optimize environmentally friendly practices and minimize ecological impacts. Agroecosystems, which integrate agricultural practices with the surrounding environment, play a vital role in maintaining ecological balance and ensuring food security. Rhizosphere management has emerged as a pivotal approach to enhancing crop yields, reducing reliance on synthetic fertilizers, and supporting sustainable agriculture. The rhizosphere, a dynamic zone surrounding plant roots, hosts intense microbial activity fueled by root exudates. These exudates, along with practices such as green manure application and intercropping, significantly influence the soil's microbial community structure. Beneficial plant-associated microbes, including Trichoderma spp., Penicillium spp., Aspergillus spp., and Bacillus spp., play a crucial role in improving nutrient cycling and promoting plant health, yet their interactions within the rhizosphere remain inadequately understood. This review explores how integrating beneficial microbes, green manures, and intercropping enhances rhizosphere processes to rebuild microbial communities, sequester carbon, and reduce greenhouse gas emissions. These practices not only contribute to maintaining soil health but also foster positive plant-microbe-rhizosphere interactions that benefit entire ecosystems. By implementing such strategies alongside sound policy measures, sustainable cropping systems can be developed to address predicted climate challenges. Strengthening agroecosystem resilience through improved rhizosphere processes is essential for ensuring food security and environmental sustainability in the future. In conclusion, using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.

Effects of two Bacillus velezensis strains isolated from different sources on the growth of Capsicum annum

Microbial inoculants offer an environmentally friendly approach to enhance plant growth and control disease. In this study, two Bacillus velezensis strains, HKSSLJEBR3 (R3) and Ya-1 were isolated from pepper plant roots and tropical rainforest soil, respectively. Both strains exhibited strong antifungal activity against Fusarium oxysporum f. sp. capsici, with inhibition rates of 48.54 ± 0.66% for R3 and 49.35 ± 1.44% for Ya-1. In greenhouse trials, R3 significantly boosted pepper growth, with a 22.12% increase in plant height, 46.44% more leaves, and 56.29% greater fresh weight. These enhancements were likely due to the strong affinity between R3 and pepper plants. Both strains also improved soil quality, with R3 increasing available potassium (AK) by 5.13% and soil organic matter (SOM) by 4.03%, while Ya-1 showed more significant increases. Metagenomic analysis revealed that both strains altered the rhizosphere microbiome, with R3 promoting Pseudomonas and suppressing Fusarium. These results suggest that the R3 strain has strong potential for enhancing pepper growth, improving soil health, and reshaping the rhizosphere microbiome.

Rhizosphere microbiome regulation: Unlocking the potential for plant growth

Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.

Effects of Rhizobacteria Strains on Plant Growth Promotion in Tomatoes (Solanum lycopersicum)

Numerous factors, such as soil fertility, climatic conditions, human activity, pests, and diseases, limit agricultural yields. Pesticides and fertilizers have become indispensable tools to satisfy the global food demand. However, its adverse environmental effects have led to the search for more sustainable and ethical techniques. Biofertilizers and biopesticides based on plant- growth-promoting rhizobacteria (PGPRs) are efficient and ecological treatments that promote plant growth and protection against pathogens and abiotic stresses. In this study, twelve rhizobacterial strains with plant-growth-promoting attributes were selected to evaluate their plant-growth-promoting effect on tomato plants (Solanum lycopersicum L. var Robin). Soil inoculation with these strains resulted in a significant increase in shoot length, up to 50% when compared with control plants. Regarding fresh biomass, rhizobacterial treatments significantly improved seedlings' fresh aerial weight with a maximum increase of 77%. Root biomass also demonstrated a substantial improvement, yielding 62.26% greater fresh root weight compared to the control. Finally, dry root weights exhibited the most remarkable enhancements, with values between 49 and 124%, when compared to the control plants. Concerning the nutritional status, the strains inoculation increased the macronutrients and micronutrients content in the aerial and root parts of the plants. All these findings suggest that rhizobacteria from different ecosystems and agriculture soils of the Canary Islands could be used as fertilizer inoculants to increase crop yield and promote more sustainable practices in modern agriculture.

Harnessing Pseudomonas spp. for sustainable plant crop protection

This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.

Molecular Communication of Microbial Plant Biostimulants in the Rhizosphere Under Abiotic Stress Conditions

Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant-microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture.

Deciphering differences in microbial community characteristics and main factors between healthy and root rot-infected Carya cathayensis rhizosphere soils

Introduction

Fusarium-induced root rot of Carya cathayensis (C. cathayensis) is a typical soil-borne disease that has severely damaged the Carya cathayensis industry in China. Understanding the interaction among soil microbial communities, soil characteristics, and pathogenic bacteria is very important for the ecological prevention and control of Carya cathayensis root rot.

Methods

We used Miseq Illumina high-throughput sequencing technology to study the microbial community in the rhizosphere soil of healthy and diseased C. cathayensis, quantified the abundance of bacteria, fungi, and pathogenic fungi, and combined these with soil chemistry and enzyme activity indicators to analyze the characteristics of healthy and diseased rhizosphere soils.

Results

We found that the pH, soil organic carbon(SOC), available nitrogen (AN), available phosphorus (AP), available potassium (AK),N-acetyl-β-D-glucosaminidase (NAG) β-glucosidase (BG), fungal gene copy number, bacterial community diversity and network complexity of the diseased soil were significantly lower (p < 0.05), while Fusarium graminearum copies number levels increased (p < 0.05). Additionally, the study found that healthy soils were enriched with beneficial bacteria such as Subgroup_7 (0.08%), MND1 (0.29%), SWB02 (0.08%), and Bradyrhizobium (0.09%), as well as potential pathogen-suppressing fungi such as Mortierella (0.13%), Preussia (0.03%), and Humicol (0.37%), were found to be associated with the growth and development of C. cathayensis.

Discussion

In summary, this research comprehensively reveals the differences in environmental and biological factors between healthy and diseased soils, as well as their correlations. It provides a theoretical basis for optimal soil environmental regulation and the construction of healthy microbial communities. This foundation facilitates the development of multifaceted strategies for the prevention and control of C. cathayensis root rot.

Coordinated influence of Funneliformis mosseae and different plant growth-promoting bacteria on growth, root functional traits, and nutrient acquisition by maize

Rhizospheric interactions among plant roots, arbuscular mycorrhizal fungi, and plant growth-promoting bacteria (PGPB) can enhance plant health by promoting nutrient acquisition and stimulating the plant immune system. This pot experiment, conducted in autoclaved soil, explored the synergistic impacts of the arbuscular mycorrhizal fungus Funneliformis mosseae with four individual bacterial strains, viz.: Cronobacter sp. Rz-7, Serratia sp. 5-D, Pseudomonas sp. ER-20 and Stenotrophomonas sp. RI-4 A on maize growth, root functional traits, root exudates, root colonization, and nutrient uptake. The comprehensive biochemical characterization of these bacterial strains includes assessments of mineral nutrient solubilization, plant hormone production, and drought tolerance. The results showed that all single and interactive treatments of the mycorrhizal fungus and bacterial strains improved maize growth, as compared with the control (no fungus or PGPB). Among single treatments, the application of the mycorrhizal fungus was more effective than the bacterial strains in stimulating maize growth. Within the bacterial treatments, Serratia sp. 5-D and Pseudomonas sp. ER-20 were more effective in enhancing maize growth than Cronobacter sp. Rz-7 and Stenotrophomonas sp. RI-4 A. All bacterial strains were compatible with Funneliformis mosseae to improve root colonization and maize growth. However, the interaction of mycorrhiza and Serratia sp. 5-D (M + 5-D) was the most prominent for maize growth improvement comparatively to all other treatments. We observed that bacterial strains directly enhanced maize growth while indirectly promoting biomass accumulation by facilitating increased mycorrhizal colonization, indicating that these bacteria acted as mycorrhizal helper bacteria.

Tipping the plant-microbe competition for nitrogen in agricultural soils

Nitrogen (N) is the most limiting nutrient in agroecosystems, and its indiscriminate application is at the center of the environmental challenges facing agriculture. To solve this dilemma, crops' nitrogen use efficiency (NUE) needs to increase - in other words, more of the applied nitrogen needs to reach humans. Microbes are the key to cracking this problem. Microbes use nitrogen as an energy source, an electron acceptor, or incorporate it in their biomass. These activities change the form and availability of nitrogen for crops' uptake, impacting its NUE, yields and produce quality. Plants (and microbes) have, however, evolved many mechanisms to compete for soil nitrogen. Understanding and harnessing these competitive mechanisms would enable us to tip the nitrogen balance to the advantage of crops. We will review these competitive mechanisms and highlight some approaches that were applied to reduce microbial competition for N in an agricultural context.

Drought stress mitigation through bioengineering of microbes and crop varieties for sustainable agriculture and food security

Climate change and agriculture are intrinsically connected and sudden changes in climatic conditions adversely impact global food production and security. The climate change-linked abiotic stressors like drought and high temperatures are resulting in crop failure. The most severe abiotic stress drought significantly affect the stomatal closure, production of reactive oxygen species, transpiration, photosynthesis or other physiological processes and plant morphology, and adversely affect plant growth and crop yield. Therefore, there is an exigent need for cost effective and eco-friendly modern technologies to induce drought tolerance in crop plants leading to climate-adapted sustainable agricultural practices for sustained food production. Among many options being pursued in this regard, the use of plant growth promoting microbes (PGPMs) is the most sustainable approach to promote drought stress resilience in crop plants leading to better plant growth and crop productivity. These PGPMs confer drought resistance via various direct or indirect mechanisms including production of antioxidants, enzymes, exopolysaccharides, modulation of phytohormones level, osmotic adjustment by inducing the accumulation of sugars, along with increases in nutrients, water uptake and photosynthetic pigments. However, several technological and ecological challenges limit their use in agriculture and sometimes treatment with plant beneficial microbes fails to produce desired results under field conditions. Thus, development of synthetic microbial communities or host mediated microbiome engineering or development of transgenic plants with the capacity to express desired traits may promote plant survival and growth under drought stress conditions. The present review critically assesses research evidence on the plant growth and stress resilience promoting potentials of PGPMs and their genes as an approach to develop drought resilient plants leading to increased crop productivity. Effective collaboration among scientific communities, policymakers and regulatory agencies is needed to create strong frameworks that both promote and regulate the utilization of synthetic microbial communities and transgenic plants in agriculture.

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Rhizosphere microbiomes derived from vermicompost alter gene expression and regulatory pathways in tomato (Solanum lycopersicum, L.)

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17 weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies.

Sustainable agriculture: leveraging microorganisms for a circular economy

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.

Phytoremediation of Arsenic (As) in rice plants, mediated by Bacillus subtilis strain IU31 through antioxidant responses and phytohormones synthesis

Bacteria-assisted phytoremediation uses bacteria to promote plant health and improve its ability to remediate toxic heavy metals like Arsenic (As). Here, we isolated rhizobacteria and identified them as Bacillus subtilis strain IU31 using 16S rDNA sequencing. IU31 showed phosphate solubilization potential on Pikovskaya agar medium and produced siderophores, which were detected on Chromium Azurol-S (CAS) agar medium. Indole-3-acetic acid (IAA) and gibberellins (GAs), namely GA1, GA3, GA4, GA7, GA9, GA12, GA15, and GA24, were quantified by GC/MS-SIM analysis. The expression levels of genes involved in GA and IAA biosynthesis, such as cyp112, cyp114, trpA, and trpB, were assessed using semi-quantitative RT-PCR. Plant bioassays showed that As at a 15 mg/kg concentration reduced plant growth, chlorophyll content, and biomass. However, IU31 inoculation significantly improved plant growth dynamics, enhancing As accumulation by up to 50% compared with uninoculated plants. IU31 inoculation induced the bioconcentration factor (BCF) and bioaccumulation factor (BAF) of As in plants compared to uninoculated plants, but the translocation factor (TF) of As was unaffected by IU31 inoculation. IU31 inoculation effectively restored glutathione-S-transferase (GST) and catalase (CAT) enzyme activities, as well as glutathione (GSH) and hydrogen peroxide concentrations to nearly normal levels, which were significantly elevated in plants exposed to As stress. These results show that IU31 improves plant health and growth by producing IAA and GAs, which might contribute to the uptake and detoxification of As.

Shift in the soil rhizobacterial community for enhanced solubilization and bioavailability of phosphorus in the rhizosphere of Allium hookeri Thwaites, through bioaugmentation of phosphate-solubilizing bacteria

Allium hookeri is an indigenous perennial herb known for its therapeutic properties. It's grown in the eastern Himalayas and East Asia, where it is used as a flavoring agent in local cuisines. This research aims to enhance soil phosphorus mobilization and promote A. hookeri growth using a consortium of phosphate-solubilizing bacteria (PSB). The synergistic effect of a bacterial consortium containing multiple PSBs (Arthrobacter luteolus and several Klebsiella spp.) combined with tricalcium phosphate (TCP), was investigated to enhance the growth of A. hookeri plants, and its influence on modulating the rhizosphere microbiome was also assessed. The greenhouse experiment revealed that the bacterial consortium with tricalcium phosphate (BTCP) treatment enhanced the dry shoot weight by 70%. Proteobacteria dominated the rhizosphere's microbiome in all treatments. BTCP treatment enhanced the relative abundance of several beneficial genera such Bacillus, Mesorhizobium, Pseudomonas, Ensifer, Hyphomicrobium, Planctomyces, and Bradyrhizobium. The augmentation of bacterial consortium increased P in shoots (4.36 ± 0.63 mg/g) and in roots (2.34 ± 0.27 mg/g), which was more than 500% higher as compared to the uninoculated control. Canonical correspondence analysis (CCA) indicated significant correlations (p ≤ 0.05) between phosphorus content in the shoot, fresh weight, and dry weight, with higher relative abundances of Bacteroidetes, Cyanobacteria, and Fibrobacteres. Functional genes related to siderophore biosynthesis, ABC transporters, phosphatenate, and phosphinate metabolism exhibited positive modulation, indicating higher relative abundances associated with the BTCP treatment. The findings demonstrate the crucial contribution of the bacterial consortium in promoting plant development, improving soil nutrient levels, and influencing the rhizospheric microbiota, implying its significance in sustainable agriculture.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04026-2.

Rhizoengineering with biofilm producing rhizobacteria ameliorates oxidative stress and enhances bioactive compounds in tomato under nitrogen-deficient field conditions

Nitrogen (N) deficiency limits crop productivity. In this study, rhizoengineering with biofilm producing rhizobacteria (BPR) contributing to productivity, physiology, and bioactive contents in tomato was examined under N-deficient field conditions. Here, different BPR including Leclercia adecarboxylata ESK12, Enterobacter ludwigii ESK17, Glutamicibacter arilaitensis ESM4, E. cloacae ESM12, Bacillus subtilis ESM14, Pseudomonas putida ESM17 and Exiguobacterium acetylicum ESM24 were used for the rhizoengineering of tomato plants. Rhizoengineered plants showed significant increase in growth attributes (15.73%-150.13 %) compared to the control plants. However, production of hydrogen peroxide (21.49-59.38 %), electrolyte leakage (19.5-38.07 %) and malondialdehyde accumulation (36.27-46.31 %) were increased remarkably more in the control plants than the rhizoengineered plants, thus N deficiency induced the oxidative stress. Compared to the control, photosynthetic rate, leaf temperature, stomatal conductance, intrinsic and instantaneous water use efficiency, relative water content, proline and catalase activity were incredibly enhanced in the rhizoengineered plants, suggesting both non-enzymatic and enzymatic antioxidant systems might protect tomato plants from oxidative stress under N-deficient field conditions. Yield (10.24-66.21 %), lycopene (4.8-7.94 times), flavonoids (52.32-110.46 %), phenolics (9.79-23.5 %), antioxidant activity (34.09-86.36 %) and certain minerals were significantly increased in the tomatoes from rhizoengineered plants. The principal component analysis (PCA) revealed that tomato plants treated with BPR induced distinct profiles compared to the control. Among all the applied BPR strains, ESM4 and ESM14 performed better in terms of biomass production, while ESK12 and ESK17 showed better results for reducing oxidative stress and increasing bioactive compounds in tomato, respectively. Thus, rhizoengineering with BPR can be utilized to mitigate the oxidative damage and increase the productivity and bioactive compounds in tomato under N-deficient field conditions.

Diverting organic waste from landfills via insect biomanufacturing using engineered black soldier flies (Hermetia illucens)

A major roadblock towards the realisation of a circular economy are the lack of high-value products that can be generated from waste. Black soldier flies (BSF; Hermetia illucens) are gaining traction for their ability to rapidly consume large quantities of organic wastes. However, these are primarily used to produce a small variety of products, such as animal feed ingredients and fertiliser. Using synthetic biology, BSF could be developed into a novel sustainable biomanufacturing platform to valorise a broader variety of organic waste feedstocks into enhanced animal feeds, a large variety of high-value biomolecules including industrial enzymes and lipids, and improved fertiliser.

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

Augmentation of physiology and productivity, and reduction of lead accumulation in lettuce grown in lead contaminated soil by rhizobacteria-assisted rhizoengineeing

Microbial-assisted rhizoengineering is a promising biotechnology for improving crop productivity. In this study, lettuce roots were bacterized with two lead (Pb) tolerant rhizobacteria including Pseudomonas azotoformans ESR4 and P. poae ESR6, and a consortium consisted of ESR4 and ESR6 to increase productivity, physiology and antioxidants, and reduce Pb accumulation grown in Pb-contaminated soil i.e., 80 (Pb in native soil), 400 and 800 mg kg-1 Pb. In vitro studies showed that these strains and the consortium produced biofilms, synthesized indole-3-acetic acid and NH3, and solubilized phosphate challenging to 0, 100, 200 and 400 mg L-1 of Pb. In static conditions and 400 mg L-1 Pb, ESR4, ESR6 and the consortium adsorbed 317.0, 339.5 and 357.4 mg L-1 Pb, respectively, while 384.7, 380.7 and 373.2 mg L-1 Pb, respectively, in shaking conditions. Fourier transform infrared spectroscopy results revealed that several functional groups [Pb-S, M - O, O-M-O (M = metal ions), S-S, PO, CO, -NH, -NH2, C-C-O, and C-H] were involved in Pb adsorption. ESR4, ESR6 and the consortium-assisted rhizoengineering (i) increased leaf numbers and biomass production, (ii) reduced H2O2 production, malondialdehyde, electrolyte leakages, and transpiration rate, (iii) augmented photosynthetic pigments, photosynthetic rate, water use efficiency, total antioxidant capacity, total flavonoid content, total phenolic content, and minerals like Ca2+ and Mg2+ in comparison to non-rhizoengineering plants grown in Pb-contaminated soil. Principal component analysis revealed that higher pigment production and photosynthetic rate, improved water use efficiency and increased uptake of Ca2+ were interlinked to increased productivity by bacterial rhizoengineering of lettuce grown in different levels of Pb exposures. Surprisingly, Pb accumulation in lettuce roots and shoots was remarkably decreased by rhizoengineering than in non-rhizoengineering. Thus, these bacterial strains and this consortium could be utilized to improve productivity and reduce Pb accumulation in lettuce.

Streptomyces N2A, an endophytic actinobacteria that promotes soybean growth and increases yield and seed quality under field conditions

Sustainable agriculture based on the use of soil-beneficial microbes such as plant growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCA) is gaining great consideration to reduce the use of agrochemicals for crop production. With this aim, in this study, a total of 78 actinobacteria were isolated from the rhizosphere and endosphere of soybean roots. Based on in vitro compatibility with Bradyrhizobium japonicum, the ability to produce phytohormones, siderophores, exo-enzymes, antifungal compounds and phosphate solubilization (PGPR traits), two endophytic strains, named N2A and N9, were selected to evaluate their effects on plant growth and development at greenhouse and field conditions. Greenhouse trials showed significantly promoted seedling emergence compared to control and the conventional fungicide treatment. Analysis of growth and development associated parameters at reproductive stages and maturity at greenhouse, but also and most importantly, in field experiments showed significant improvements. Plant biomass, node number, pod number, and consequently yield, were higher in plants previously treated with N2A and co-inoculated with B. japonicum compared to the conventional seed treatment. Furthermore, a significant increase in health status and vigor was observed for seeds harvested from the N2A-treated plants in relation to seeds obtained from the conventional treatment. Thus, we demonstrated that Streptomyces sp. N2A can replace traditional chemical fungicides to protect the seed during germination, allowing good implantation, but also, stimulating the growth and development of soybean crop increasing yield and seed quality at field conditions. Altogether, this supports the potential use of Streptomyces N2A as a PGPR for soybean crop production more efficiently and sustainably.

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

Inoculation of Native Arbuscular Mycorrhizae and Bacillus subtilis Can Improve Growth in Vegetable Crops

Arbuscular mycorrhizal fungi (AMF) and some rhizobacteria are known as plant growth-promoting microorganism (PGPM) as they play significant roles in improving soil fertility structure, plant nutrition, growth, and health. However, little is known about the PGPM potential of AMF and rhizobacteria native to the Rift Valley and highland regions of Ethiopia. Hence, this study aimed to investigate the PGPM effect of single and co-inoculation of AMF and the Bacillus subtilis ALCR46 strain, on tomato (Lycopersicum esculentum L.), onion (Allium cepa L.), and squash (Cucurbita pepo L.) plants. The experimental setup was a randomized complete block design with three replications of the following treatments: (i) inoculation with a consortium of AMF, (ii) co-inoculation with a consortium of AMF and the Bacillus subtilis, (iii) inoculation with Rhizophagus clarus, (iv) co-inoculation with R. clarus and B. subtilis, (v) inoculation with B. subtilis, (vi) plants without inoculation (negative control), and (vii) plants treated with chemical fertilizer (positive control). Plants were maintained in a greenhouse for 60 days, and after harvest, plant growth parameters, percentage of AMF root colonization, and spore number were analyzed. The result shows that the growth of crops significantly increased by co-inoculation with the consortium of AMF and B. subtilis. AMF spore density and root colonization rate were also increased in co-inoculated plants. Highest root colonization, spore number, and mycorrhizal dependency were observed in A. cepa. Our results suggest that there is a synergistic effect between the AMF and B. subtilis ALCR46, and between AMF inoculants. However, the application of present findings under field conditions is required to be confirmed by further studies.

Synthetic consortia of four strains promote Schisandra chinensis growth by regulating soil microbial community and improving soil fertility

MAIN CONCLUSION

Synthetic consortia performed better in promoting Schisandra chinensis growth than individual strains, and this result provides valuable information for the development of synthetic microbial fertilizers. Schisandra chinensis is an herbal medicine that can treat numerous diseases. However, the excessive reliance on chemical fertilizers during the plantation of S. chinensis has severely restricted the development of the S. chinensis planting industry. Plant growth-promoting rhizobacteria (PGPR) can promote the growth of a wide range of crops, and synthetic consortia of them are frequently superior to those of a single strain. In this study, we compared the effects of four PGPR and their synthetic consortia on S. chinensis growth. The pot experiment showed that compared with the control, synthetic consortia significantly increased the plant height, biomass, and total chlorophyll contents of S. chinensis, and their combined effects were better than those of individual strains. In addition, they improved the rhizosphere soil fertility (e.g., TC and TN contents) and enzyme activities (e.g., soil urease activity) and affected the composition and structure of soil microbial community significantly, including promoting the enrichment of beneficial microorganisms (e.g., Actinobacteria and Verrucomicrobiota) and increasing the relative abundance of Proteobacteria, a dominant bacterial phylum. They also enhanced the synergistic effect between the soil microorganisms. The correlation analysis between soil physicochemical properties and microbiome revealed that soil microorganisms participated in regulating soil fertility and promoting S. chinensis growth. This study may provide a theoretical basis for the development of synthetic microbial fertilizers for S. chinensis.

Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops

Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices.

Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants

Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.

Soil phosphorus transformation and plant uptake driven by phosphate-solubilizing microorganisms

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

Serratia spp. as plant growth-promoting bacteria alleviating salinity, drought, and nutrient imbalance stresses

In agricultural environments, plants are often exposed to abiotic stresses including temperature extremes, salt stress, drought, and heavy metal soil contamination, which leads to significant economic losses worldwide. Especially salt stress and drought pose serious challenges since they induce ionic toxicity, osmotic stress, and oxidative stress in plants. A potential solution can be the application of bacteria of the Serratia spp. known to promote plant growth under normal conditions Thus the mini-review aims to summarize the current knowledge on plant growth promotion by Serratia spp. (under the conditions of salinity stress, drought, and nutrient deficit) and highlight areas for development in the field. So far, it has been proven that Serratia spp. strains exhibit a variety of traits contributing to enhanced plant growth and stress tolerance, such as phytohormone production, ACC deaminase activity, nitrogen fixation, P and Zn solubilization, antioxidant properties improvement, and modulation of gene expression. Nevertheless, further research on Serratia spp. is needed, especially on two subjects: elucidating its mechanisms of action on plants at the molecular level and the effects of Serratia spp. on the indigenous soil and plant microbiota and, particularly, the rhizosphere. In both cases, it is advisable to use omics techniques to gain in-depth insights into the issues. Additionally, some strains of Serratia spp. may be phytopathogens, therefore studies to rule out this possibility are recommended prior to field trials. It is believed that by improving said knowledge the potential of Serratia spp. to stimulate plant growth will increase and strains from the genus will serve as an eco-friendly biofertilizer in sustainable agriculture more often.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Use of Trichoderma in the Production of Forest Seedlings

Forest production has great relevance in the Brazilian economy, characterized by several production sectors, including the production of seedlings. With the focus on maximizing the capacity of survival, development, and adaptation of seedlings, Trichoderma is highlighted as a potentially useful genus of microorganisms for promoting growth and higher product quality. In this sense, this review aims to describe the main mechanisms of fungi action in forest seedlings' production. The different species of the genus Trichoderma have specific mechanisms of action, and the current scenario points to more advances in the number of species. The interaction process mediated by different mechanisms of action begins in the communication with plants, from the colonization process. After the interaction, chemical dialogues allow the plant to develop better because, from colonization, the forest seedlings can maximize height and increase shoot and root development. Fungi promote solubilization and availability of nutrients to seedlings, which show numerous benefits to the development. The use of beneficial microorganisms, such as fungi of the genus Trichoderma, has become a sustainable strategy to enhance seedling development, reducing the use of agrochemicals and industrial fertilizers.

Optical Coherence Tomography as a Non-Invasive Tool for Plant Material Characterization in Agriculture: A Review

Characterizing plant material is crucial in terms of early disease detection, pest control, physiological assessments, and growth monitoring, which are essential parameters to increase production in agriculture and prevent unnecessary economic losses. The conventional methods employed to assess the aforementioned parameters have several limitations, such as invasive inspection, complexity, high time consumption, and costly features. In recent years, optical coherence tomography (OCT), which is an ultra-high resolution, non-invasive, and real-time unique image-based approach has been widely utilized as a significant and potential tool for assessing plant materials in numerous aspects. The obtained OCT cross-sections and volumetrics, as well as the amplitude signals of plant materials, have the capability to reveal vital information in both axial and lateral directions owing to the high resolution of the imaging system. This review discusses recent technological trends and advanced applications of OCT, which have been potentially adapted for numerous agricultural applications, such as non-invasive disease screening, optical signals-based growth speed detection, the structural analysis of plant materials, and microbiological discoveries. Therefore, this review offers a comprehensive exploration of recent advanced OCT technological approaches for agricultural applications, which provides insights into their potential to incorporate OCT technology into numerous industries.

Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors

The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.

Combined Soil Microorganism Amendments and Foliar Micronutrient Nanofertilization Increased the Production of Allium cepa L. through Aquaporin Gene Regulation

The aim of this study was to investigate the impact of changes in aquaporin expression on the growth of onion (Allium cepa L.) plants when subjected to dual applications of microorganism-based soil amendments and foliar nanoencapsulated mineral nutrients. Multiple physiological parameters related to water, gas exchange, and nutrient content in leaf, root, and bulb tissues were determined. Additionally, the gene expression of aquaporins, specifically PIP1, PIP2 (aquaporin subfamily plasma membrane intrinsic protein), and TIP2 (aquaporin subfamily tonoplast intrinsic protein), was analyzed. The findings revealed that the foliar application of nutrients in a nanoencapsulated form significantly enhanced nutrient penetration, mobilization, and overall plant growth to a greater extent than free-form fertilizers. Amendments with microorganisms alone did not promote growth but influenced the production of secondary metabolites in the bulbs. The combination of microorganisms and nanoencapsulated mineral nutrients demonstrated synergistic effects, increasing dry matter, mineral content, and aquaporin gene expression. This suggests that aquaporins play a pivotal role in the transport of nutrients from leaves to storage organs, resulting in the overexpression of PIP2 aquaporins in bulbs, improved water uptake, and enhanced cell growth. Therefore, the combined treatment with microorganisms and nanoencapsulated mineral nutrients may be an optimal approach for enhancing onion productivity by regulating aquaporins under field conditions.

Synergistic benefits of Funneliformis mosseae and Bacillus paramycoides: Enhancing soil health and soybean tolerance to root rot disease

To explore the response of soil metabolite composition to soybean disease, the effect of the combined inoculation of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting bacteria on soybean root rot caused by Fusarium oxysporum was studied. A factorial completely randomized design with three factors (AMF, Bacillus. paramycoides, and rot disease stress) was conducted, and eight treatments, including normal groups and stress groups, were performed using pot experiments. GC‒MS and enzymatic assays were used to evaluate the soil factors and soybean growth indicators. The results showed that there were significant differences in the composition of metabolites among the different treatment groups, and 23 metabolites were significantly related to soybean biomass. The combined inoculation of Funneliformis mosseae and Bacillus paramycoides resulted in a significant reduction in harmful soil metabolites associated with root rot disease, such as ethylbenzene and styrene. This reduction in metabolites contributed to improving soil health, as evidenced by enhanced soybean defence enzyme activities and microbial activity, and β-1,3-glucanase, chitinase and phenylalanine ammonia-lyase activities were improved to alleviate plant rhizosphere stress. Furthermore, soybean plants inoculated with the synergistic treatments exhibited reduced root rot disease severity and improved growth indicators compared to control plants. Plant height, root dry weight (RDW), and shoot and root fresh weight (SRFW) were improved by 4.18-53.79%, and the AM fungal colonization rate was also improved under stress. The synergistic application of Funneliformis mosseae and Bacillus paramycoides can effectively enhance soil health by inhibiting the production of harmful soil metabolites and improving soybean tolerance to root rot disease. This approach holds promise for the sustainable management of soil-borne diseases in soybean cultivation.

Plant growth-promoting rhizobacteria: a potential bio-asset for restoration of degraded soil and crop productivity with sustainable emerging techniques

The rapid expansion of degraded soil puts pressure on agricultural crop yield while also increasing the likelihood of food scarcity in the near future at the global level. The degraded soil does not suit plants growth owing to the alteration in biogeochemical cycles of nutrients, soil microbial diversity, soil organic matter, and increasing concentration of heavy metals and organic chemicals. Therefore, it is imperative that a solution should be found for such emerging issues in order to establish a sustainable future. In this context, the importance of plant growth-promoting rhizobacteria (PGPR) for their ability to reduce plant stress has been recognized. A direct and indirect mechanism in plant growth promotion is facilitated by PGPR via phytostimulation, biofertilizers, and biocontrol activities. However, plant stress mediated by deteriorated soil at the field level is not entirely addressed by the implementation of PGPR at the field level. Thus, emerging methods such as CRISPR and nanotechnological approaches along with PGPR could manage degraded soil effectively. In the pursuit of the critical gaps in this respect, the present review discusses the recent advancement in PGPR action when used along with nanomaterials and CRISPR, impacting plant growth under degraded soil, thereby opening a new horizon for researchers in this field to mitigate the challenges of degraded soil.

Dynamics of organic acid exudation and rhizobacteria in maize rhizosphere respond to N-CDs

To sustainably feed the growing global population, it is essential to increase crop yields on limited land while reducing the use of fertilizers and agrochemicals. The rhizosphere regulation shows significant potential to address this challenge. Here, foliar applied doping of nitrogen in carbon dots (N-CDs) entered maize leaves, and were transported to the stems and roots. The internalized N-CDs significantly increased the biomass (26.4-93.8%) and photosynthesis (17.0-20.3 %) of maize seedling during the three-week application of N-CDs, providing the substrate for tricarboxylic acid cycle (TCA) in shoots and roots. Correspondingly, more organic acids involved in TCA cycle, such as citric acid (14.0-fold), succinic acid (4.4-fold) and malic acid (3.4-fold), were synthesized and then secreted into rhizosphere after exposed to N-CDs for one day. As the exposure time increased, greater secretion of above organic acids by the roots was induced. However, no significant change was observed in the relative abundance of rhizobacteria after foliar application with N-CDs for one day. After one week, the relative abundances of Azotobacter, Bacillus, Lysobacter, Mucilaginibacter, and Sphingomonas increased by 0.8-3.8 folds. The relative abundance of more beneficial rhizobacteria (Sphingomonas, Lysobacter, Rhizobium, Azotobacter, Pseudomonas, Mucilaginibacter and Bacillus) enriched by 0.3-6.0 folds after two weeks, and Sphingomonas, Flavisolibacter and Bacillus improved by 0.6-3.2 folds after three weeks. These dynamic changes suggested that N-CDs initiate the synthesis and secretion of organic acids and then recruited beneficial rhizobacteria. The hierarchical partitioning analysis further indicated that N-CDs-induced secretion of organic acids from the roots was the main drivers of rhizobacteria community dynamics. The differential microbes altered by N-CDs were mainly involved in nitrogen (N) and phosphorus (P) cycles, which are beneficial for N and P uptake, and maize growth. These results provide insights into understanding the rhizosphere regulation of nanomaterials to improve plant productivity and nutrient-use efficiency.

Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction

BACKGROUND

Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.

RESULTS

We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.

CONCLUSION

Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

Integrated physiological and omics analyses reveal the mechanism of beneficial fungal Trichoderma sp. alleviating cadmium toxicity in tobacco (Nicotiana tabacum L.)

Cadmium (Cd) is a highly toxic heavy metal and readily accumulates in tobacco, which imperils public health via Cd exposure from smoking. Beneficial microbes have a pivotal role in promoting plant growth, especially under environmental stresses such as heavy metal stresses. In this study, we introduced a novel fungal strain Trichoderma nigricans T32781, and investigated its capacity to alleviate Cd-induced stress in tobacco plants through comprehensive physiological and omics analyses. Our findings revealed that T32781 inoculation in soil leads to a substantial reduction in Cd-induced growth inhibition. This was evidenced by increased plant height, enhanced biomass accumulation, and improved photosynthesis, as indicated by higher values of key photosynthetic parameters, including the maximum quantum yield of photosystem Ⅱ (Fv/Fm), stomatal conductance (Gs), photosynthetic rate (Pn) and transpiration rate (Tr). Furthermore, element analysis demonstrated that T. nigricans T32781 inoculation resulted in a remarkable reduction of Cd uptake by 62.2% and a 37.8% decrease in available soil Cd compared to Cd-stressed plants without inoculation. The protective role of T32781 extended to mitigating Cd-induced oxidative stress by improving antioxidant enzyme activities of superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX). Metabolic profiling of tobacco roots identified 43 key metabolites, with notable contributions from compounds like nicotinic acid, succinic acid, and fumaric acid in reducing Cd toxicity in T32781-inoculated plants. Additionally, rhizosphere microbiome analysis highlighted the promotion of beneficial microbes, including Gemmatimonas and Sphingomonas, by T32781 inoculation, which potentially contributed to the restoration of plant growth under Cd exposure. In summary, our study demonstrated that T. nigricans T32781 effectively alleviated Cd stress in tobacco plants by reducing Cd uptake, alleviating Cd-induced oxidative stress, influencing plant metabolite and modulating the microbial composition in the rhizosphere. These findings offer a novel perspective and a promising candidate strain for enhancing Cd tolerance and prohibiting its accumulation in plants to reduce health risks associated with exposure to Cd-contaminated plants.

Application of Bacillus spp. Phosphate-Solubilizing Bacteria Improves Common Bean Production Compared to Conventional Fertilization

The use of phosphate-solubilizing bacteria (PSB) can be a sustainable strategy to increase phosphorus availability and promote satisfactory crop yields. The objective of this study was to evaluate whether inoculation with PSB in common bean increases (i) growth, (ii) nutrition, (iii) yield, and (iv) grain quality, and (v) reduces the chemical phosphorus application dose to obtain maximum yields. The experiment was conducted in an Oxisol using a randomized block design in a 4 × 4 factorial scheme, with four replicates, using the cultivar IAC 2051. The first factor was four doses of P2O5 (0, 20, 40 and 60 kg ha-1), and the second factor was four doses of PSB (0, 100, 200 and 300 mL ha-1). For leaf area and leaf chlorophyll content, the association of PSB inoculation with a P2O5 dose of 40 kg ha-1 promoted the best conditions for the common bean. P2O5 application increased yield by 79 kg ha-1 for each 10 kg ha-1 added. PSB inoculation at a dose of 192 mL ha-1 promoted P export of 15.3 kg ha-1, and the PSB dose of 159 mL ha-1 increased yield by 389 kg ha-1 (12%) compared to the control. Grain quality remained within the standards required by the consumer market, being little affected by the treatments. Improvements in common bean growth and nutritional and physiological status promoted by P2O5 application and PSB were essential in increasing yield, so these are sustainable production strategies.