Current Progress in Nitrogen Fixing Plants and Microbiome Research

Enhancing nitrogen use efficiency in agriculture by integrating agronomic practices and genetic advances

Nitrogen is a critical nutrient for plant growth and productivity, but inefficiencies in its use in agriculture present both economic and environmental challenges. Enhancing nitrogen use efficiency (NUE) is essential for promoting sustainable crop production and mitigating the negative impacts of nitrogen loss, such as water pollution and greenhouse gas emissions. This review discusses various strategies aimed at improving NUE, with a focus on agronomic practices, genetic advancements, and integrated management approaches. Traditional agronomic methods, including split nitrogen application and the use of controlled-release fertilizers, are explored alongside precision agriculture techniques, which enable real-time adjustments to nitrogen application based on crop and soil conditions. Advances in genetics and biotechnology, such as conventional breeding, genetic modification, and genome editing, have contributed to the development of crop varieties with improved nitrogen uptake and assimilation. Additionally, the role of beneficial microbes, including nitrogen-fixing bacteria and mycorrhizal fungi, is highlighted as a natural means of enhancing nitrogen availability and reducing reliance on synthetic fertilizers. The review further emphasizes sustainable practices such as legume-based crop rotations, continuous cover cropping, and organic fertilization, which contribute to soil nitrogen enrichment and overall soil health. By combining these agronomic, genetic, and microbial strategies, a holistic nitrogen management approach can be achieved, maximizing crop yields while minimizing environmental impacts. This integrated strategy supports the development of resilient and sustainable agricultural systems, promoting long-term soil fertility and productivity.

Investigating biological nitrogen fixation via single-cell transcriptomics

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

Nitrogen fixation rates and aerial root production among maize landraces

In Mexico, the center of maize origin (Zea mays ssp. mays), there are landraces from the highlands that develop extensive aerial root systems which secrete a carbohydrate-rich mucilage. This mucilage produces a favorable environment for nitrogenase activity by diazotrophs. This plant-microbial interaction enables the fixation of nitrogen (N) from the atmosphere, reducing the required N that otherwise must come from the soil and/or fertilizers. The objective of this research was to investigate the degree to which other landraces of maize and nutrient management affect aerial root growth and the ability of maize to perform and benefit from N2 fixation. In two replicated field experiments in Columbus, Ohio, USA in 2019 and 2020, we planted 21 maize landraces and three improved varieties with and without fertilizer to measure their growth, production of aerial roots, and rate of atmospheric N2 fixation using the 15N natural abundance method. Maize accessions varied in the growth rate and number of nodes with aerial roots. Up to 36% of plant N was derived from the atmosphere, with values varying by accession, the reference plant used, and the fertilizer level. Moreover, there was a positive relationship between early growth parameters and numbers of nodes with aerial roots, which, in turn, predicted the amount of N derived from the atmosphere. Thus, larger seedlings may experience enhanced root growth and thereby benefit more from N fixation. By phenotyping a diverse set of maize accessions with and without fertilizer, this study explores both environmental and quantitative genetic variation in the traits involved in N fixation capacity, clarifying that N fixation found in the Sierra Mixe landrace is more broadly distributed than previously thought. In sum, farmers stewarding genetic diversity in a crop center of origin have preserved traits essential for biological symbioses that contribute to maize's nutrient requirements. These traits may enable maize crops grown by Mexican farmers, and farmers globally, to benefit from N fixation from the atmosphere.

The hidden language of plant-beneficial microbes: chemo-signaling dynamics in plant microenvironments

Plants and microorganisms coexist within complex ecosystems, significantly influencing agricultural productivity. Depending on the interaction between the plant and microbes, this interaction can either help or harm plant health. Microbes interact with plants by secreting proteins that influence plant cells, producing bioactive compounds like antibiotics or toxins, and releasing molecules such as N-acyl homoserine lactones to coordinate their behaviour. They also produce phytohormones which help regulate growth and stress responses in plants. Plants also interact with the associated microorganisms by exuding substances such as carbon and nitrogen sources, quorum-sensing molecules, peptide signals, secondary metabolites such as flavonoids and strigolactones. A successful exchange of chemical signals is essential for maintaining these associations, with significant implications for plant growth and development. This review explores the intricate array of signaling molecules and complex mechanisms governing plant-microbe interactions, elucidating the pivotal role of chemo-communication pathways. By examining these molecular dialogues, the review aims to deepen our understanding of chemo-signaling molecules, paving the way for future applications of these networks in promoting agricultural sustainability.

Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition

While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.

Plant microbiome technology for sustainable agriculture

Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.

Microbes in Agriculture: Prospects and Constraints to Their Wider Adoption and Utilization in Nutrient-Poor Environments

Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant growth promotion include mycorrhizal fungi, associative diazotrophs, and the N2-fixing rhizobia belonging to the α, β and γ class of Proteobacteria. Mycorrhizal fungi generally contribute to increasing the surface area of soil-root interface for optimum nutrient uptake by plants. However, when transformed into bacteroids inside root nodules, rhizobia also convert N2 gas in air into ammonia for use by the bacteria and their host plant. Thus, nodulated legumes can meet a high proportion of their N requirements from N2 fixation. The percentage of legume N derived from atmospheric N2 fixation varies with crop species and genotype, with reported values ranging from 50-97%, 24-67%, 66-86% 27-92%, 50-92%, and 40-75% for soybean (Gycine max), groundnut (Arachis hypogea), mung bean (Vigna radiata), pigeon pea (Cajanus cajan), cowpea (Vigna unguiculata), and Kersting's groundnut (Macrotyloma geocarpum), respectively. This suggests that N2-fixing legumes require little or no N fertilizer for growth and grain yield when grown under field conditions. Even cereals and other species obtain a substantial proportion of their N nutrition from associative and endophytic N2-fixing bacteria. For example, about 12-33% of maize N requirement can be obtained from their association with Pseudomonas, Hebaspirillum, Azospirillum, and Brevundioronas, while cucumber can obtain 12.9-20.9% from its interaction with Paenebacillus beijingensis BJ-18. Exploiting the plant growth-promoting traits of soil microbes for increased crop productivity without any negative impact on the environment is the basis of green agriculture which is done through the use of biofertilizers. Either alone or in combination with other synergistic rhizobacteria, rhizobia and arbuscular mycorrhizal (AM) fungi have been widely used in agriculture, often increasing crop yields but with occasional failures due to the use of poor-quality inoculants, and wrong application techniques. This review explores the literature regarding the plant growth-promoting traits of soil microbes, and also highlights the bottle-necks in tapping this potential for sustainable agriculture.

Advances in Soybean Genetic Improvement

The soybean (Glycine max) is a globally important crop due to its high protein and oil content, which serves as a key resource for human and animal nutrition, as well as bioenergy production. This review assesses recent advancements in soybean genetic improvement by conducting an extensive literature analysis focusing on enhancing resistance to biotic and abiotic stresses, improving nutritional profiles, and optimizing yield. We also describe the progress in breeding techniques, including traditional approaches, marker-assisted selection, and biotechnological innovations such as genetic engineering and genome editing. The development of transgenic soybean cultivars through Agrobacterium-mediated transformation and biolistic methods aims to introduce traits such as herbicide resistance, pest tolerance, and improved oil composition. However, challenges remain, particularly with respect to genotype recalcitrance to transformation, plant regeneration, and regulatory hurdles. In addition, we examined how wild soybean germplasm and polyploidy contribute to expanding genetic diversity as well as the influence of epigenetic processes and microbiome on stress tolerance. These genetic innovations are crucial for addressing the increasing global demand for soybeans, while mitigating the effects of climate change and environmental stressors. The integration of molecular breeding strategies with sustainable agricultural practices offers a pathway for developing more resilient and productive soybean varieties, thereby contributing to global food security and agricultural sustainability.

Isolation and identification of plant growth-promoting rhizobacteria from Spinifex littoreus in Parangkusumo Coastal Sand Dunes, Indonesia

Utilizing coastal land for agriculture presents challenges such as low water content, high soil salinity, and low organic compound content. To support plant growth under these conditions, biofertilizers composed of plant growth promoting Rhizobacteria (PGPR), especially those inhabiting coastal areas, are needed. The Parangkusumo sand dunes on the southern coast of Java, Indonesia, is a unique coastal ecosystem characterized by arid conditions, high temperatures, and high soil salinity. To date, no studies have reported the isolation of PGPR from this ecosystem. This study is the first to isolate and identify PGPR associated with Spinifex littoreus, a dominant plant species in the Parangkusumo sand dunes, which are adapted to the harsh condition of Parangkusumo sand dunes. Ten rhizobacterial isolates were obtained, with five identified as members of the Bacillaceae family. All isolates demonstrated phosphate solubilization activity, while seven exhibited cellulolytic activity. One isolate, Priestia aryabhattai strain 2, notably showed phosphate solubilization and nitrogen fixation activities. The findings of this PGPR activity screening offer valuable insights for developing biofertilizers tailored for coastal agricultural applications.

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.

Exploring microbial diversity and function in companion planting systems of white clover and orchard grass

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Applicability of metabolomics to improve sustainable grapevine production

Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.

Isolation and Characterization Identification of Edophytic Nitrogen-Fixing Bacteria from Peanut Nodules

This work was carried out to isolate and perform molecular identification and selection of endophytic nitrogen-fixing bacteria (ENFB) to be utilized as biofertilizer. In this research, nodulous samples of peanuts were collected from inside dyke areas, namely, Phuoc Hung of An Phu, An Giang, Vietnam. Ten colonies were isolated from nutrient agar plates containing YMA's medium. All isolates were rod shaped, Gram negative, and no spore creation. Biochemical tests indicated that they were obligate aerobes, catalase, oxidase, urea hydrolysis, well motile ability, and no nitrate reduction. The salt tolerance observed that most survived at 0.5% and 2% salinity (except Enterobacter cloacae subsp. dissolvens strain LMG 2683), while at 4%, only 3 isolates (Bacillus aryabhattai strain CM44, Enterobacter asburiae strain IIWM-JS-07L, and Bacillus songklensis strain KCa6) and at 5% only, 2 isolates survived, namely, Enterobacter asburiae strain IIWM-JS-07L and Bacillus songklensis strain KCa6. The result showed that most of ten ENFB strains could adapt to the range of 25°C and 45°C (except Enterobacter cloacae subsp. dissolvens strain LMG 2683 and Enterobacter mori strain cjy13 at 25°C). Out of ten isolates, three were finally selected for the next studies, which potentially have N-fixing ability and are utilized as biofertilizer in agricultural cultivation.

Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review

Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants' stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities.

Core Bacterial Taxa Determine Formation of Forage Yield in Fertilized Soil

Understanding the roles of core bacterial taxa in forage production is crucial for developing sustainable fertilization practices that enhance the soil bacteria and forage yield. This study aims to investigate the impact of different fertilization regimes on soil bacterial community structure and function, with a particular focus on the role of core bacterial taxa in contributing to soil nutrient content and enhancing forage yield. Field experiments and high-throughput sequencing techniques were used to analyze the soil bacterial community structure and function under various fertilization regimes, including six treatments, control with no amendment (CK), double the standard rate of organic manure (T01), the standard rate of organic manure with nitrogen input equal to T04 (T02), half the standard rate of inorganic fertilizer plus half the standard rate of organic manure (T03), the standard rate of inorganic fertilizer reflecting local practice (T04), and double the standard rate of inorganic fertilizer (T05). The results demonstrated that organic manure treatments, particularly T01, significantly increased the forage yield and the diversity of core bacterial taxa. Core taxa from the Actinomycetota, Alphaproteobacteria, and Gammaproteobacteria classes were crucial in enhancing the soil nutrient content, directly correlating with forage yield. Fertilization significantly influenced functions relating to carbon and nitrogen cycling, with core taxa playing central roles. The diversity of core microbiota and soil nutrient levels were key determinants of forage yield variations across treatments. These findings underscore the critical role of core bacterial taxa in agroecosystem productivity and advocate for their consideration in fertilization strategies to optimize forage yield, supporting the shift towards sustainable agricultural practices.

Sustainable media feedstocks for cellular agriculture

The global food system is shifting towards cellular agriculture, a second domestication marked by cultivating microorganisms and tissues for sustainable food production. This involves tissue engineering, precision fermentation, and microbial biomass fermentation to establish food value chains independent of traditional agriculture. However, these techniques rely on growth media sourced from agricultural, chemical (fossil fuels), and mining supply chains, raising concerns about land use competition, emissions, and resource depletion. Fermentable sugars, nitrogen, and phosphates are key ingredients derived from starch crops, energy-intensive fossil fuel based processes, and finite phosphorus resources, respectively. This review explores sustainable alternatives to reduce land use and emissions associated with cellular agriculture media ingredients. Sustainable alternatives to first generation sugars (lignocellulosic substrates, sidestreams, and gaseous feedstocks), sustainable nitrogen sources (sidestreams, green ammonia, biological nitrogen fixation), and efficient use of phosphates are reviewed. Especially cellulosic sugars, gaseous chemoautotrophic feedstocks, green ammonia, and phosphate recycling are the most promising technologies but economic constraints hinder large-scale adoption, necessitating more efficient processes and cost reduction. Collaborative efforts are vital for a biotechnological future grounded in sustainable feedstocks, mitigating competition with agricultural land and emissions.

Polycyclic aromatic hydrocarbon: underpinning the contribution of specialist microbial species to contaminant mitigation in the soil

The persistence of PAHs poses a significant challenge for conventional remediation approaches, necessitating the exploration of alternative, sustainable strategies for their mitigation. This review underscores the vital role of specialized microbial species (nitrogen-fixing, phosphate-solubilizing, and biosurfactant-producing bacteria) in tackling the environmental impact of polycyclic aromatic hydrocarbons (PAHs). These resistant compounds demand innovative remediation strategies. The study explores microbial metabolic capabilities for converting complex PAHs into less harmful byproducts, ensuring sustainable mitigation. Synthesizing literature from 2016 to 2023, it covers PAH characteristics, sources, and associated risks. Degradation mechanisms by bacteria and fungi, key species, and enzymatic processes are examined. Nitrogen-fixing and phosphate-solubilizing bacteria contributions in symbiotic relationships with plants are highlighted. Biosurfactant-producing bacteria enhance PAH solubility, expanding microbial accessibility for degradation. Cutting-edge trends in omics technologies, synthetic biology, genetic engineering, and nano-remediation offer promising avenues. Recommendations emphasize genetic regulation, field-scale studies, sustainability assessments, interdisciplinary collaboration, and knowledge dissemination. These insights pave the way for innovative, sustainable PAH-contaminated environment restoration.

Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review

The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.

Tomato yield, and water use efficiency as affected by nitrogen rate and irrigation regime in the central low lands of Ethiopia

Tomato yield can be increased by the application of optimum water and fertilizer. A field experiment was conducted in Efratana Gidim district, North Shewa, Amhara, Ethiopia, during 2019 and 2020. The objective was to determine the nitrogen (N) rate and irrigation regime for optimum tomato yield and water use efficiency (WUE). The experiment consisted of three-irrigation regimes (75% ETc (Evapotranspiration from the crop), 100% ETc, and 125% ETc) and four nitrogen (N) rates (control; i.e. without N application1, 46 kg N ha-1, 92 kg N ha-1, and 138 kg N ha-1). The treatments were laid out in a split-plot design with four replications. The Irrigation regime were assigned to the main plot, while the N rate were assigned to the subplot. Data on growth, yield, and yield-related traits of tomatoes, include; plant height, number of fruit clusters per plant, fruit length, fruit diameter, number of marketable fruits, number of un-marketable fruits, the total number of fruits, marketable fruit yield, un-marketable fruit yield, total yield were collected. The data were subjected to analysis of variance using R studio. The results indicated that the experimental site had low total N content, and the application of N fertilizer significantly improved tomato yield. Increasing irrigation depth also significantly increased tomato yield. The result indicated that the highest mean marketable fruit yield (35,903 kg ha-1) was obtained from the combined application of 125% ETc with 92 kg N ha-1, while the lowest (13,655 kg ha-1) marketable fruit yield was obtained from 75% ETc with 92 kg N ha-1. The analysis of variance showed that the highest (5.4 kg m-3) WUE recorded from 75% ETc with 46 kg N ha-1 increased WUE by 77% (2.4 kg m-3) compared with the lowest (2.3 kg m-3) WUE recorded from 125% ETc with 0 kg N ha-1. The partial budget analysis also indicated that the highest net benefit (266,272 ETB (Ethiopian Birr) ha-1) and an acceptable marginal rate of return (1240%) for the invested capital was recorded from the combined application of 125% ETc with 92 kg N ha-1. Therefore, the application of 125% ETc with 92 kg N ha-1 resulted in the highest net benefit.

Phytoremediation mechanism and role of plant growth promoting rhizobacteria in weed plants for eco-restoration of hazardous industrial waste polluted site: a review

Plants have numerous strategies for phytoremediation depending upon the characteristic of pollutants. Plant growth promoting rhizobacteria (PGPR) are essential to the process of phytoremediation and play a key part in it. The mechanism of PGPR for phytoremediation is mediated by two methods; under the direct method there is phytohormone production, nitrogen fixation, nutrient mineral solubilization, and siderophore production while the indirect method includes quorum quenching, antibiosis, production of lytic enzyme, biofilm formation, and hydrogen cyanide production. Due to their economic and environmental viability, most researchers have recently concentrated on the potential of weed plants for phytoremediation. Although weed plants are considered unwanted and noxious, they have a high growth rate and adaptability which opens a high scope for its role in phytoremediation of contaminated site. The interaction of plant with rhizobacteria starts from root exudates containing various organic acids and peptides which act as nutrients essential for colonization and siderophore production by the rhizospheric bacteria. The rhizobacteria, while colonizing, tend to promote plant growth and health either directly by providing phytohormones and minerals or indirectly by suppressing growth of possible phytopathogens. Recently, several weed plants have been reported for phytoextraction of heavy metals (Ni, Pb, Zn, Hg, Cd, Cu, As, Fe, and Cr) contaminants from various agro-based industries. These potential native weed plants have high prospect of eco-restoration of polluted site with complex organo-metallic waste for sustainable development.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Responses of soil enzymatic activities and microbial biomass phosphorus to improve nutrient accumulation abilities in leguminous species

Fertilizers application are widely used to get a higher yield in agricultural fields. Nutrient management can be improved by cultivating leguminous species in order to obtain a better understanding of the mechanisms that increase the amount of available phosphorus (P) and potassium (K) through fertilizer treatments. A pot experiment was conducted to identify the leguminous species (i.e., chickpea and pea) under various fertilizer treatments. Experimental design is as follows: T0 (control: no fertilizer was applied), T1: P applied at the level of (90 kg ha-1), T2: (K applied at the level of 90 kg ha-1), and T3: (PK applied both at 90 kg ha-1). All fertilizer treatments significantly (p < 0.05) improved the nutrient accumulation abilities and enzymes activities. The T3 treatment showed highest N uptake in chickpea was 37.0%, compared to T0. While T3 developed greater N uptake in pea by 151.4% than the control. However, T3 treatment also increased microbial biomass phosphorus in both species i.e., 95.7% and 81.5% in chickpeas and peas, respectively, compared to T0 treatment. In chickpeas, T1 treatment stimulated NAGase activities by 52.4%, and T2 developed URase activities by 50.1% higher than control. In contrast, T3 treatment enhanced both BGase and Phase enzyme activities, i.e., 55.8% and 33.9%, respectively, compared to the T0 treatment. Only the T3 treatment improved the activities of enzymes in the pea species (i.e., BGase was 149.7%, URase was 111.9%, Phase was 81.1%, and NAGase was 70.0%) compared to the control. Therefore, adding combined P and K fertilizer applications to the soil can increase the activity of enzymes in both legume species, and changes in microbial biomass P and soil nutrient availability make it easier for plants to uptake the nutrients.

Nitrogen sensing and regulatory networks: it's about time and space

A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.

Nitrogen-fixing organelle in a marine alga

Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."

Influence of Fertilization Methods and Types on Wheat Rhizosphere Microbiome Community and Functions

To investigate the effects of fertilization methods and types on wheat rhizosphere microorganisms, macroelement (N, K) and microelement (Zn) fertilizers were applied on wheat by foliar spraying (FS) and root irrigation (RI) methods in a field experiment. The results indicated that fertilization methods and types can have significant impacts on the diversity and structure of rhizospheric microorganisms in wheat. The application method produced more significant effects than the fertilizer type. RI-N played a more important role in improving the wheat yield and quality and affected the changes in some nitrogen-fixing bacterial communities. Finally, eight strains of bacteria belonging to Pseudomonas azotoformans and P. cedrina showed positive effects on the growth of wheat seedlings. Overall, our study provides a better understanding of the dynamics of wheat rhizosphere microbial communities and their relation to fertilization, yield, and quality, showing that plant growth-promoting rhizobacteria with nitrogen fixing may be a potential approach for more sustainable agriculture production.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov

A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17  :  0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).

Variability in Leaf Color Induced by Chlorophyll Deficiency: Transcriptional Changes in Bamboo Leaves

The diversity of leaf characteristics, particularly leaf color, underscores a pivotal area of inquiry within plant science. The synthesis and functionality of chlorophyll, crucial for photosynthesis, largely dictate leaf coloration, with varying concentrations imparting different shades of green. Complex gene interactions regulate the synthesis and degradation of chlorophyll, and disruptions in these pathways can result in abnormal chlorophyll production, thereby affecting leaf pigmentation. This study focuses on Bambusa multiplex f. silverstripe, a natural variant distinguished by a spectrum of leaf colors, such as green, white, and green-white, attributed to genetic variations influencing gene expression. By examining the physiological and molecular mechanisms underlying chlorophyll anomalies and genetic factors in Silverstripe, this research sheds light on the intricate gene interactions and regulatory networks that contribute to leaf color diversity. The investigation includes the measurement of photosynthetic pigments and nutrient concentrations across different leaf color types, alongside transcriptomic analyses for identifying differentially expressed genes. The role of key genes in pathways such as ALA biosynthesis, chlorophyll synthesis, photosynthesis, and sugar metabolism is explored, offering critical insights for advancing research and plant breeding practices.

Elevated CO2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure

Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Isolation and evaluation of Qatari soil rhizobacteria for antagonistic potential against phytopathogens and growth promotion in tomato plants

Plant growth promoting rhizobacteria are a diverse group of microorganisms that enhance the growth of plants under various conditions. In this study, 55 isolates of endogenous rhizobacteria were collected from the rhizosphere of Avicennia marina, Suaeda vermiculata, Salsola soda, Anabasis setifera, Salicornia europaea, Arthrocnemum macrostachyum, Limonium axillare, Tetraena qatarensis, Aeluropus lagopoides, and Prosopis juliflora. The isolates were evaluated in-vitro for their antagonist potential against Fusarium oxysporum and Botrytis cinerea using the dual culture technique, where the maximum growth inhibition reached 49% and 57%, respectively. In-vivo evaluation was accomplished to determine the growth-promoting potential of the rhizobacteria under greenhouse conditions where the strain ANABR3 (Bacillus subtilis) showed the strongest growth-promoting effects. Further in-vivo testing regarding the effectiveness of rhizobacteria in the presence of the phytopathogen was also completed using the Hoagland medium. LEMR3 and SALIR5 (both identified as two strains of B. subtilis) supported the tomato seedlings to overcome the disease and significantly (p ≤ 0.05) increased above and belowground biomass compared to the control. Additionally, several characterizing tests were carried out on the selected strains, these strains were found to possess numerous features that promote plant growth directly and indirectly such as the production of IAA, HCN, hydrolytic enzymes, ACC deaminase, NH3, and some rhizobacteria were capable of phosphate solubilization. In conclusion, this study showed that local rhizobacterial isolates collected from arid lands possess valuable traits, making them promising bio-control agents and bio-fertilizers for agricultural purposes.

Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities

This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.

Soil microbes: a natural solution for mitigating the impact of climate change

Soil microbes are microscopic organisms that inhabit the soil and play a significant role in various ecological processes. They are essential for nutrient cycling, carbon sequestration, and maintaining soil health. Importantly, soil microbes have the potential to sequester carbon dioxide (CO2) from the atmosphere through processes like carbon fixation and storage in organic matter. Unlocking the potential of microbial-driven carbon storage holds the key to revolutionizing climate-smart agricultural practices, paving the way for sustainable productivity and environmental conservation. A fascinating tale of nature's unsung heroes is revealed by delving into the realm of soil microbes. The guardians of the Earth are these tiny creatures that live beneath our feet and discreetly work their magic to fend off the effects of climate change. These microbes are also essential for plant growth enhancement through their roles in nutrient uptake, nitrogen fixation, and synthesis of growth-promoting chemicals. By understanding and managing soil microbial communities, it is possible to improve soil health, soil water-holding capacity, and promote plant growth in agricultural and natural ecosystems. Added to it, these microbes play an important role in biodegradation, bioremediation of heavy metals, and phytoremediation, which in turn helps in treating the contaminated soils. Unfortunately, climate change events affect the diversity, composition, and metabolism of these microbes. Unlocking the microbial potential demands an interdisciplinary endeavor spanning microbiology, ecology, agronomy, and climate science. It is a call to arms for the scientific community to recognize soil microbes as invaluable partners in the fight against climate change. By implementing data-driven land management strategies and pioneering interventions, we possess the means to harness their capabilities, paving the way for climate mitigation, sustainable agriculture, and promote ecosystem resilience in the imminent future.

An emerging role of heterotrimeric G-proteins in nodulation and nitrogen sensing

MAIN CONCLUSION

A comprehensive understanding of nitrogen signaling cascades involving heterotrimeric G-proteins and their putative receptors can assist in the production of nitrogen-efficient plants. Plants are immobile in nature, so they must endure abiotic stresses including nutrient stress. Plant development and agricultural productivity are frequently constrained by the restricted availability of nitrogen in the soil. Non-legume plants acquire nitrogen from the soil through root membrane-bound transporters. In depleted soil nitrogen conditions, legumes are naturally conditioned to fix atmospheric nitrogen with the aid of nodulation elicited by nitrogen-fixing bacteria. Moreover, apart from the symbiotic nitrogen fixation process, nitrogen uptake from the soil can also be a significant secondary source to satisfy the nitrogen requirements of legumes. Heterotrimeric G-proteins function as molecular switches to help plant cells relay diverse stimuli emanating from external stress conditions. They are comprised of Gα, Gβ and Gγ subunits, which cooperate with several downstream effectors to regulate multiple plant signaling events. In the present review, we concentrate on signaling mechanisms that regulate plant nitrogen nutrition. Our review highlights the potential of heterotrimeric G-proteins, together with their putative receptors, to assist the legume root nodule symbiosis (RNS) cascade, particularly during calcium spiking and nodulation. Additionally, the functions of heterotrimeric G-proteins in nitrogen acquisition by plant roots as well as in improving nitrogen use efficiency (NUE) have also been discussed. Future research oriented towards heterotrimeric G-proteins through genome editing tools can be a game changer in the enhancement of the nitrogen fixation process. This will foster the precise manipulation and production of plants to ensure global food security in an era of climate change by enhancing crop productivity and minimizing reliance on external inputs.

The role of plant growth promoting rhizobacteria in strengthening plant resistance to fluoride toxicity: a review

A wide variety of bacteria are present in soil but in rhizospheric area, the majority of microbes helps plant in defending diseases and facilitate nutrient uptake. These microorganisms are supported by plants and they are known as plant growth-promoting rhizobacteria (PGPR). The PGPRs have the potential to replace chemical fertilizers in a way that is more advantageous for the environment. Fluoride (F) is one of the highly escalating, naturally present contaminants that can be hazardous for PGPRs because of its antibacterial capacity. The interactions of F with different bacterial species in groundwater systems are still not well understood. However, the interaction of PGPR with plants in the rhizosphere region reduces the detrimental effects of pollutants and increases plants' ability to endure abiotic stress. Many studies reveal that PGPRs have developed F defense mechanisms, which include efflux pumps, Intracellular sequestration, enzyme modifications, enhanced DNA repair mechanism, detoxification enzymes, ion transporter/antiporters, F riboswitches, and genetic mutations. These resistance characteristics are frequently discovered by isolating PGPRs from high F-contaminated areas or by exposing cells to fluoride in laboratory conditions. Numerous studies have identified F-resistant microorganisms that possess additional F transporters and duplicates of the well-known targets of F. Plants are prone to F accumulation despite the soil's low F content, which may negatively affect their growth and development. PGPRs can be used as efficient F bioremediators for the soil environment. Environmental biotechnology focuses on creating genetically modified rhizobacteria that can degrade F contaminants over time. The present review focuses on a thorough systemic analysis of contemporary biotechnological techniques, such as gene editing and manipulation methods, for improving plant-microbe interactions for F remediation and suggests the importance of PGPRs in improving soil health and reducing the detrimental effects of F toxicity. The most recent developments in the realm of microbial assistance in the treatment of F-contaminated environments are also highlighted.

Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant

A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).

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

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

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions

Microbiomes interact dynamically with their environment to perform exploitable functions such as production of valuable metabolites and degradation of toxic metabolites for a wide range of applications in human health, agriculture, and environmental cleanup. Developing computational models to predict the key bacterial species and environmental factors to build and optimize such functions are crucial to accelerate microbial community engineering. However, there is an unknown web of interactions that determine the highly complex and dynamic behavior of these systems, which precludes the development of models based on known mechanisms. By contrast, entirely data-driven machine learning models can produce physically unrealistic predictions and often require significant amounts of experimental data to learn system behavior. We develop a physically-constrained recurrent neural network that preserves model flexibility but is constrained to produce physically consistent predictions and show that it can outperform existing machine learning methods in the prediction of certain experimentally measured species abundance and metabolite concentrations. Further, we present a closed-loop, Bayesian experimental design algorithm to guide data collection by selecting experimental conditions that simultaneously maximize information gain and target microbial community functions. Using a bioreactor case study, we demonstrate how the proposed framework can be used to efficiently navigate a large design space to identify optimal operating conditions. The proposed methodology offers a flexible machine learning approach specifically tailored to optimize microbiome target functions through the sequential design of informative experiments that seek to explore and exploit community functions.

Fe-Based Nanomaterials and Plant Growth Promoting Rhizobacteria Synergistically Degrade Polychlorinated Biphenyls by Producing Extracellular Reactive Oxygen Species

Plant growth promoting rhizobacteria (PGPR) produce extracellular reactive oxygen species (ROS) to protect plants from external stresses. Fe-based nanomaterials can potentially interact with PGPR and synergistically degrade organic pollutants, yet they have received no study. Here, we studied how the interaction between a typical PGPR (Pseudomonas chlororaphis, JD37) and Fe-based nanomaterials facilitated the degradation of 2,4,4'-trichlorobiphenyl (PCB28), by comparing the zerovalent iron of 20 nm (nZVI20), 100 nm (nZVI100), and 5 μm; iron oxide nanomaterials (α-Fe2O3, γ-Fe2O3, and Fe3O4) of ca. 20 nm; and ferrous and ferric salts. Although all Fe materials (0.1 g L-1) alone could not degrade aqueous PCB28 (0.1 mg L-1) under dark or aerobic conditions, nZVI20, nZVI100, α-Fe2O3, and Fe2+ promoted PCB28 degradation by JD37, with the half-life of PCB28 shortened from 16.5 h by JD37 alone to 8.1 h with nZVI100 cotreatment. Mechanistically, the nanomaterials stimulated JD37 to secrete phenazine-1-carboxylic acid and accelerated the NADH/NAD+ conversion, promoting O2*- generation; JD37 increased Fe(II) dissolution from the nanomaterials, facilitating *OH generation; and the ROS gradually degraded PCB28 into benzoic acid through dihydroxy substitution, oxidation to quinone, and Michael addition. These findings provide a new strategy of nanoenabled biodegradation of organic pollutants by applying Fe-based nanomaterials and PGPR.

A study of microbial diversity in a biofertilizer consortium

Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.

Marker trait association for biological nitrogen fixation traits in an interspecific cross of chickpea (Cicer arietinum × Cicer reticulatum)

A set of 165 Recombinant inbred lines (RILs) derived from an interspecific cross of chickpea was used to identify QTLs for key biological nitrogen fixation (BNF) traits. The phenotyping of BNF and related traits was done at two different agroclimatic zones viz., Central plain zone (Ludhiana) and Sub-Mountainous undulating zone (Gurdaspur) for 2 consecutive rabi seasons (2018-2020). Wild parent C. reticulatum ILWC292 showed significantly high performance in terms of biological nitrogen fixation (BNF) traits over the cultivated C. arietinum GPF-2. The triple interaction of genotypes × locations × years was significant (p 0.05) for all BNF traits in parental lines. Highly significant positive correlation was obtained between grain yield and key growth and symbiotic parameters at both the sites. Phenotypic analysis revealed nodule dry weight and leghaemoglobin content as key traits for BNF efficiency and contrasting DNA bulks were constituted on the basis of these traits. Out of 535 SSR markers, 139 exhibited polymorphism between the parental lines on polyacrylamide gel electrophoresis. A total of 30 SSR markers showed polymorphism between the higher and lower bulks for nodule dry weight and leghaemoglobin content. Out of these, 20 SSRs did not show any segregation distortion in RIL population as determined by chi square analysis (p < 0.05) and were used for quantitative trait loci (QTL) analysis. Using QTL cartographer, markers- CAGM02697, CAGM09835, CAGM09777, CAGM09227, CAGM09021, CAGM08679 were found linked with QTLs for BNF. These markers can be validated further for identification of genes for BNF traits and marker assisted selection in chickpea. To the best of our knowledge this is the first report on identification of genomic regions associated with key BNF traits in chickpea across different agro-climatic zones.

Supplementary information

The online version contains supplementary material available at 10.1007/s12298-023-01335-3.

Presence of microbiome decreases fitness and modifies phenotype in the aquatic plant Lemna minor

Plants live in close association with microbial organisms that inhabit the environment in which they grow. Much recent work has aimed to characterize these plant-microbiome interactions, identifying those associations that increase growth. Although most work has focused on terrestrial plants, Lemna minor, a floating aquatic angiosperm, is increasingly used as a model in host-microbe interactions and many bacterial associations have been shown to play an important role in supporting plant fitness. However, the ubiquity and stability of these interactions as well as their dependence on specific abiotic environmental conditions remain unclear. Here, we assess the impact of a full L. minor microbiome on plant fitness and phenotype by assaying plants from eight natural sites, with and without their microbiomes, over a range of abiotic environmental conditions. We find that the microbiome systematically suppressed plant fitness, although the magnitude of this effect varied among plant genotypes and depended on the abiotic environment. Presence of the microbiome also resulted in phenotypic changes, with plants forming smaller colonies and producing smaller fronds and shorter roots. Differences in phenotype among plant genotypes were reduced when the microbiome was removed, as were genotype by environment interactions, suggesting that the microbiome plays a role in mediating the plant phenotypic response to the environment.

Transcriptomic and Metabolomic Analyses Reveal the Roles of Flavonoids and Auxin on Peanut Nodulation

Rhizobia form symbiotic relationships with legumes, fixing atmospheric nitrogen into a plant-accessible form within their root nodules. Nitrogen fixation is vital for sustainable soil improvements in agriculture. Peanut (Arachis hypogaea) is a leguminous crop whose nodulation mechanism requires further elucidation. In this study, comprehensive transcriptomic and metabolomic analyses were conducted to assess the differences between a non-nodulating peanut variety and a nodulating peanut variety. Total RNA was extracted from peanut roots, then first-strand and second-strand cDNA were synthesized and purified. After sequencing adaptors were added to the fragments, the cDNA libraries were sequenced. Our transcriptomic analysis identified 3362 differentially expressed genes (DEGs) between the two varieties. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DEGs were mainly involved in metabolic pathways, hormone signal transduction, secondary metabolic biosynthesis, phenylpropanoid biosynthesis, or ABC transport. Further analyses indicated that the biosynthesis of flavonoids, such as isoflavones, flavonols, and flavonoids, was important for peanut nodulation. A lack of flavonoid transport into the rhizosphere (soil) could prevent rhizobial chemotaxis and the activation of their nodulation genes. The downregulation of AUXIN-RESPONSE FACTOR (ARF) genes and lower auxin content could reduce rhizobia's invasion of peanut roots, ultimately reducing nodule formation. Auxin is the major hormone that influences the cell-cycle initiation and progression required for nodule initiation and accumulates during different stages of nodule development. These findings lay the foundation for subsequent research into the nitrogen-fixation efficiency of peanut nodules.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Phyllosphere symbiont promotes plant growth through ACC deaminase production

Plant growth promoting bacteria can confer resistance to various types of stress and increase agricultural yields. The mechanisms they employ are diverse. One of the most important genes associated with the increase in plant biomass and stress resistance is acdS, which encodes a 1-aminocyclopropane-1-carboxylate- or ACC-deaminase. The non-proteinogenic amino acid ACC is the precursor and means of long-distance transport of ethylene, a plant hormone associated with growth arrest. Expression of acdS reduces stress induced ethylene levels and the enzyme is abundant in rhizosphere colonizers. Whether ACC hydrolysis plays a role in the phyllosphere, both as assembly cue and in growth promotion, remains unclear. Here we show that Paraburkholderia dioscoreae Msb3, a yam phyllosphere symbiont, colonizes the tomato phyllosphere and promotes plant growth by action of its ACC deaminase. We found that acdS is required for improved plant growth but not for efficient leaf colonization. Strain Msb3 readily proliferates on the leaf surface of tomato, only occasionally spreading to the leaf endosphere through stomata. The strain can also colonize the soil or medium around the roots but only spreads into the root if the plant is wounded. Our results indicate that the degradation of ACC is not just an important trait of plant growth promoting rhizobacteria but also one of leaf dwelling phyllosphere bacteria. Manipulation of the leaf microbiota by means of spray inoculation may be more easily achieved than that of the soil. Therefore, the application of ACC deaminase containing bacteria to the phyllosphere may be a promising strategy to increasing plant stress resistance, pathogen control, and harvest yields.

Production of compost from logging residues

The implementation of forest management generates logging residue which can be used in several ways. One of the option is to use of logging residue in the composting process. Therefore, this study determined the possibility of producing compost based on logging residue and the produced fertilizer used to fertilize forest nurseries. Pine chips and sewage sludge were used for carrying out the study. The compost, as well as the leachate produced during composting, were characterized by high NPK content. The leachate collected at the end of the experiment was characterized by nitrogen content of approximately 6500 mg‧dm^-3, phosphorus of approximately 450 mg‧dm^-3, and potassium of approximately 500-700 mg‧dm^-3. In contrast, the compost produced contained approximately 0.57 g‧kg^-1 nitrogen, approximately 0.39 g‧kg^-1 phosphorus, and approximately 0.24 g‧kg^-1 potassium. The disadvantage in terms of the usefulness of the resulting fertilizer in forest nurseries is its pH, which exceeded 9.0.

Responses in Nodulated Bean (Phaseolus vulgaris L.) Plants Grown at Elevated Atmospheric CO2

The increase in the concentration of CO₂ in the atmosphere is currently causing metabolomic and physiological changes in living beings and especially in plants. Future climate change may affect crop productivity by limiting the uptake of soil resources such as nitrogen (N) and water. The contribution of legume-rhizobia symbioses to N₂ fixation increases the available biological N reserve. Elevated CO₂ (eCO₂) has been shown to enhance the amount of fixed N₂ primarily by increasing biomass. Greater leaf biomass under eCO₂ levels increases N demand, which can stimulate and increase N₂ fixation. For this reason, bean plants (Phaseolus vulgaris L.) were used in this work to investigate how, in a CO₂-enriched atmosphere, inoculation with rhizobia (Rhizobium leguminosarum) affects different growth parameters and metabolites of carbon and nitrogen metabolism, as well as enzymatic activities of nitrogen metabolism and the oxidative state of the plant, with a view to future scenarios, where the concentration of CO₂ in the atmosphere will increase. The results showed that bean symbiosis with R. leguminosarum improved N₂ fixation, while also decreasing the plant's oxidative stress, and provided the plant with a greater defense system against eCO₂ conditions. In conclusion, the nodulation with rhizobia potentially replaced the chemical fertilization of bean plants (P. vulgaris L.), resulting in more environmentally friendly agricultural practices. However, further optimization of symbiotic activities is needed to improve the efficiency and to also develop strategies to improve the response of legume yields to eCO_2, particularly due to the climate change scenario in which there is predicted to be a large increase in the atmospheric CO₂ concentration.