Search Results (70)

Data-driven approaches are increasingly required to optimize biofertilization strategies in forage systems. Machine learning (ML) provides an efficient tool for identifying functional drivers in complex plant–soil–microbe systems, offering important perspectives for precision data-driven agriculture. However, despite its potential, ML remains data-driven in studies involving diazotrophic inoculation using biochar as a pelletizing material, particularly in forage grasses. This study applied ML to predict the key drivers controlling Brachiaria brizantha performance and soil quality under biochar-pelletized diazotrophic bacteria (DB). Five isolates were inoculated with or without biochar, and plant traits and soil attributes, including pH, potassium, phosphorus, sodium, and urease activity were evaluated. These data were integrated into multivariate analyses and ML algorithms, including Linear Discriminant Analysis, Random Forest, and Support Vector Machine, to identify the functional drivers that best discriminate treatment performance and uncover mechanistic functional drivers. All isolates increased soil potassium content, with the highest values in the biochar amended treatments, and a 39% increase. Soil pH and urease activity were significantly modulated by isolate identity, while biomass allocation patterns differed among treatments. Overall, the results highlight that biochar pelletization can enhance the effectiveness of DB inoculants. ML revealed that dry foliar biomass, soil pH, and fresh root weight were the most predictive variables, highlighting consistent signatures explaining plant–soil responses to biochar-pelletized DB. These findings demonstrate that interpretable ML can disentangle complex plant–soil–microbe interactions, support precision biofertilization design, and serve as an efficient decision-support tool for sustainable pasture management. Beyond the present system, this study establishes a transferable and scalable analytical framework for precision biofertilization strategies in forage systems and other biochar-mediated agroecosystems, advancing predictive and data-driven approaches in sustainable agricultural engineering. Full article

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application. Full article

As a pulse crop, mung beans are associated with nitrogen-fixing bacteria, which can improve soil fertility, lower the need for nitrogen fertilizers, and increase yield and soil quality for subsequent harvests. This study aimed to identify effective rhizobial inoculants for mung beans (Vigna radiata L.) by evaluating selected strains for cowpea (Vigna unguiculata L.), soybean (Glycine max L.), and common bean (Phaseolus vulgaris L.) under controlled (axenic) conditions. Cowpea, soybean, and common bean strains were tested as mung beans inoculants under axenic conditions. Promising strains were then tested in the field to assess grain yield and to quantify nitrogen fixation using the ¹⁵N natural abundance method. The cowpea strain BR 3302 (Bradyrhizobium viridifuturi) increased mung bean yield by 18%, achieving results similar to a 240 kg N ha⁻¹ fertilizer application. The soybean strain BR 96 (B. elkanii) facilitated the highest nitrogen fixation (35.3 kg N ha⁻¹), significantly surpassing the contribution of indigenous diazotrophic bacteria (18.5 kg N ha⁻¹). Interestingly, BR 3302 appeared to primarily enhance nitrogen uptake from the soil (65% of plant N), indicating the presence of other potential plant growth-promoting mechanisms beyond nitrogen fixation. This research demonstrates that Bradyrhizobium strains can benefit mung beans through both enhanced nitrogen fixation and additional growth-promoting mechanisms, offering a sustainable approach to improve mung beans production. Full article

Improving nitrogen use efficiency (NUE) in maize is critical for reducing fertilizer inputs and mitigating environmental impacts. The rhizosphere microbiome—the plant’s “second genome”—plays a key role in nitrogen acquisition, assimilation, and signaling. This review synthesizes recent advances from multi-omics studies, functional validation, and field experiments, highlighting how maize roots recruit and coordinate microbial taxa, including diazotrophs, nitrifiers, organic nitrogen mineralizers, and growth-promoting bacteria, to enhance NUE under variable nitrogen availability. We integrate mechanistic insights into transporter-mediated nitrogen uptake, microbial regulation of root development and exudation, and host genetic determinants, such as ZmC2, ZmSBT3, and ZmNLP8, that influence microbiome assembly. Evidence from synthetic communities, isotope tracing, and host–microbiome association studies demonstrates that microbial contributions to plant nitrogen can be substantial and genetically modulated. Finally, we discuss microbiome-based interventions, including functional strain discovery, microbial fertilizers, biostimulants, and microbiome-assisted breeding, assessing their potential and limitations. We conclude by highlighting key challenges and proposing an integrative framework to guide microbiome-informed strategies for sustainable improvement of maize NUE. Full article

Many cyanobacteria synthesize cyanophycin, a nitrogen-rich amino acid polymer with metabolic engineering and biomanufacturing potential. In non-diazotrophic cyanobacteria, cyanophycin serves as a source of nitrogen under nitrogen stress conditions. However, the role of these storage granules in diazotrophic cyanobacteria, which fix nitrogen on demand, is yet to be understood. The enzyme cyanophycin synthetase, encoded by cphA, synthesizes cyanophycin from the amino acids aspartate and arginine. We probed the consequences of the inability to synthesize cyanophycin on the physiology of a nitrogen-fixing unicellular cyanobacterium, Cyanothece sp. ATCC 51142, by generating a markerless cphA deletion strain (∆cphA) using CRISPR/Cpf1. Under continuous high light and N₂-fixing conditions, the ∆cphA strain exhibited a growth defect and phycobilisome degradation, implying nitrogen starvation. Interestingly, under low light conditions, the nitrogen starvation phenotype was not observed. This suggests a critical role for the nitrogen storage bodies in maintaining an optimal cellular carbon/nitrogen balance, especially when the cellular nitrogen fixing machinery cannot match high levels of carbon fixation. Thus, when photosynthetic efficiency is high, the cyanophycin storage granules act as a readily available nitrogen source that ensures optimal metabolism and growth. This study illustrates the essential role of cyanophycin when engineering unicellular nitrogen-fixing cyanobacteria for use as production chassis. Full article

Efficient biological nitrogen fixation (BNF) is crucial for sustainable soybean productivity. Current strategies involve the use of Bradyrhizobium diazoefficiens and co-inoculation with plant growth-promoting bacteria like Azospirillum brasilense. To further optimize BNF and plant performance, we investigated the effect of co-inoculation with A. brasilense and B. diazoefficiens combined with the strategic application of the micronutrients Molybdenum (Mo), Cobalt (Co), and Nickel (Ni) on soybean grown under greenhouse conditions. We evaluated plant growth, photosynthetic parameters, accumulation of N, nitrate reductase activity, and nifH gene expression at the R1 reproductive stage. Our main finding was that the co-inoculation combined with the simultaneous application of Mo, Co, and Ni significantly maximized vegetative growth, photochemical efficiency, and BNF. Specifically, this triple supplementation increased nifH gene expression (0.22) compared to the inoculated control (0.003), leading to a substantial enhancement of photosynthetic parameters, including photosystem II (PSII) efficiency and net carbon assimilation (A). For example, the total dry mass was 14.36 g in the Mo + Co + Ni + AZO + BRADY combination and 6.50 g in the non-inoculated and non-micronutrient-treated plants. The total N content was also higher in the plants treated with Mo + Co + Ni + AZO + BRADY (73.20 g kg⁻¹). Crucially, the data also demonstrated that excessive levels of Co impaired the symbiosis, underscoring the necessity of precise dose management. These results confirm the strong synergistic potential of combining microbial co-inoculation with targeted mineral nutrition as a high-impact, sustainable strategy for boosting soybean productivity. Full article

Azospirillum is a well-studied genus of plant growth-promoting rhizobacteria (PGPR) and one of the most extensively researched diazotrophs. This genus can colonize rhizosphere soil and enhance plant growth and productivity by supplying essential nutrients to the host. Azospirillum–plant interactions involve multiple mechanisms, including nitrogen fixation, the production of phytohormones (auxins, cytokinins, indole acetic acid (IAA), and gibberellins), plant growth regulators, siderophore production, phosphate solubilization, and the synthesis of various bioactive molecules, such as flavonoids, hydrogen cyanide (HCN), and catalase. Thus, Azospirillum is involved in plant growth and development. The genus Azospirillum also enhances membrane activity by modifying the composition of membrane phospholipids and fatty acids, thereby ensuring membrane fluidity under water deficiency. It promotes the development of adventitious root systems, increases mineral and water uptake, mitigates environmental stressors (both biotic and abiotic), and exhibits antipathogenic activity. Biological nitrogen fixation (BNF) is the primary mechanism of Azospirillum, which is governed by structural nif genes present in all diazotrophic species. Globally, Azospirillum spp. are widely used as inoculants for commercial crop production. It is considered a non-pathogenic bacterium that can be utilized as a biofertilizer for a variety of crops, particularly cereals and grasses such as rice and wheat, which are economically significant for agriculture. Furthermore, Azospirillum spp. influence gene expression pathways in plants, enhancing their resistance to biotic and abiotic stressors. Advances in genomics and transcriptomics have provided new insights into plant-microbe interactions. This review explored the molecular mechanisms underlying the role of Azospirillum spp. in plant growth. Additionally, BNF phytohormone synthesis, root architecture modification for nutrient uptake and stress tolerance, and immobilization for enhanced crop production are also important. A deeper understanding of the molecular basis of Azospirillum in biofertilizer and biostimulant development, as well as genetically engineered and immobilized strains for improved phosphate solubilization and nitrogen fixation, will contribute to sustainable agricultural practices and help to meet global food security demands. Full article

Phyllosphere microbial communities influence the growth and productivity of plants, particularly in epiphytic plants, which are disconnected from nutrients available in the soil. We characterized the phyllosphere of 30 individuals of the epiphytic cycad, Zamia pseudoparasitica, collected from three forest sites during the rainy and dry seasons in the Republic of Panama. We used DNA metabarcoding to describe the total bacteria community with the 16S rRNA gene and the diazotrophic community with nifH gene. Common taxa included members of the Rhizobiales, Frankiales, Pseudonocardiales, Acetobacteriales, and the diazotrophic community was dominated by Cyanobacateria. We observed similar patterns of alpha diversity across sites and seasons, and no community differences were seen within sites between the rainy and dry seasons for either the 16S rRNA or nifH genes. However, pairwise comparisons showed some statistically significant differences in community composition between sites and seasons, but these explained only a small portion of the variation. Beta diversity partitioning indicated that communities were more phylogenetically closely related than expected by chance, indicative of strong environmental or host filtering shaping these phyllosphere communities. These results highlight the influence of host-driven selection and habitat stability in shaping phyllosphere microbiota, offering new insights into microbial assembly in tropical canopy ecosystems. Full article

Cyanobacteria-based bioinoculants represent a sustainable solution for enhancing soil fertility and crop productivity. This research assessed the biofertilizing potential of two indigenous nitrogen-fixing cyanobacteria strains (Nostoc punctiforme Har. and Anabaena cylindrica Lemmerm.) on tomato growth and yield. A greenhouse experiment was conducted to study their effects on soil properties, plant growth and physiology, and fruit yield/quality. The strains were applied individually, as a consortium, or combined with organic or mineral fertilizers at half the standard dose (50%). All bioinoculants improved soil fertility, plant growth, and fruit yield/quality compared to the control. The most significant improvement was observed in the consortium amended with 50% of conventional fertilizer (compost or NPK), compared with individual strains. Correlation analysis revealed strong positive associations between photosynthetic pigments, plant productivity, and fruit biochemical traits, indicating coordinated physiological responses under the applied treatments. The results demonstrated that the consortium of diazotrophic terrestrial cyanobacteria possesses tomato biofertilizer properties that can be efficiently used in crop production. These findings suggest that such formulations offer a cost-effective approach to tomato cultivation and present a sustainable alternative for integrated and optimized fertilizer management. Full article

Understanding the dominant populations and biological functions of endophytic nitrogen-fixing bacteria in apple plants is of great significance for the healthy growth management and sustainable development of apple cultivation. In this study, we investigated the community diversity and potential plant growth-promoting abilities of endophytic nitrogen-fixing bacteria in different tissues of apple trees by combining high-throughput sequencing of the nifH gene with traditional isolation and cultivation techniques. Sequencing results revealed that the endophytic bacteria were affiliated with 10 phyla, 14 classes, 30 orders, 42 families, and 72 genera. Rhizobium was the dominant genus in the roots and twigs, while Desulfovibrio dominated the leaf tissues. The diversity and richness of endophytic bacteria in the roots were significantly higher than those in the leaves. Using four types of nitrogen-free media, a total of 138 presumptive endophytic nitrogen-fixing bacterial strains were isolated from roots, leaves, and twigs. These isolates belonged to 32 taxonomic groups spanning 5 phyla, 8 classes, 11 orders, 13 families, and 18 genera. The nifH gene was successfully amplified from the representative strains of all 32 groups using specific primers. Nitrogenase activity among the isolates ranged from 26.86 to 982.28 nmol/(h·mL). Some strains also exhibited the ability to secrete indole-3-acetic acid (IAA), solubilize phosphate and potassium, and produce siderophores. Six individual strains and three microbial consortia were tested for their plant growth-promoting effects on apple tissue culture seedlings. All treatments showed growth-promoting effects to varying degrees, with the RD01+RC16 consortium showing the most significant results: plant height, number of leaves, and chlorophyll content were 2.4, 3.3, and 4.2 times higher than those of the control, respectively. These findings demonstrate the rich diversity of endophytic nitrogen-fixing bacteria in apple plants and their promising potential for application in promoting host plant growth. Full article

Two novel marine hydrogen- and sulfur-oxidizing bacteria, designated HSL1-7^T and HSL3-1^T, were isolated from mangrove sediments from Fujian Province, China. Strain HSL1-7^T exhibited Gram-negative, rod-shaped to slightly curved morphology with polar flagellum-driven motility, whereas strain HSL3-1^T was Gram-negative, rod-shaped and non-motile. Strain HSL1-7^T and HSL3-1^T were obligate chemolithoautotrophs, capable of using molecular hydrogen and thiosulfate as an energy source, and molecular oxygen and elemental sulfur as the electron acceptors for growth. Cellular fatty acid profiles revealed similar predominant components (C_16:1ω7c, C_16:0, C_18:1ω7c, and C_14:0) in both strains. Strains HSL1-7^T and HSL3-1^T were strongly diazotrophic, as demonstrated by ¹⁵N₂ fixation when a fixed nitrogen source was absent from the growth medium. The DNA G+C contents of strains HSL1-7^T and HSL3-1^T were determined to be 36.1% and 57.3%, respectively. Based on the 16S rRNA gene sequences, strains HSL1-7^T and HSL3-1^T exhibited the highest sequence similarities with Sulfurimonas marina B2^T (98.5% and 94.45%, respectively). Notably, the 16S rRNA gene sequence similarity between strains HSL1-7^T and HSL3-1^T was 93.19%, indicating that they represent distinct species within the genus Sulfurimonas. Comparative genomic analyses revealed the presence of diverse metabolic profiles in strains HSL1-7^T and HSL3-1^T, including carbon fixation, hydrogen oxidation, sulfur oxidation, and nitrogen fixation. The combined phenotypic, chemotaxonomic, and phylogenetic evidence, including average nucleotide identity and in silico DNA-DNA hybridization values, shows that strains HSL1-7^T and HSL3-1^T represent two novel species of the genus Sulfurimonas for which the names Sulfurimonas microaerophilic sp. nov. and Sulfurimonas diazotrophicus sp. nov. are proposed, with the type strains HSL1-7^T (=MCCC 1A18899^T = KCTC 25640^T) and HSL3-1^T (=MCCC 1A18844^T), respectively. Full article

The development of microbial-based biostimulants to enhance the growth of crops and support a healthy and sustainable soil requires the isolation and large-scale industrial culture of effective microorganisms. In this study, work was undertaken to isolate and characterize free-living nitrogen-fixing bacteria capable of acting as biostimulants alone or by incorporation into and/or supplementation with a current commercial crop biostimulant for farmers. Free-living bacteria were isolated from soil, sugar cane mulch, and plant roots following preliminary culture in a nitrogen-free media that targeted specific groups of known diazotrophs. Following the identification of each isolate by 16S rDNA sequence analysis, isolates selected for further study were identified as most closely related to Priestia megaterium, Sphingobium yanoikuyae, and Burkholderia paludis. Each isolate was investigated for its capacity to promote plant growth in nitrogen-free media. Wheat seedlings were inoculated with the isolates separately, together as a consortium, or in combination with the commercial biostimulant, Great Land Plus^®. Compared to no-treatment control plants, the fresh weights were higher in both the shoots (183.2 mg vs. 330.6 mg; p < 0.05) and roots (320.4 mg vs. 731.3 mg; p < 0.05) of wheat seedlings inoculated with P. megaterium. The fresh weights were also higher in the shoots (267.8 mg; p < 0.05) and roots (610.3 mg; p = 0.05) of wheat seedlings inoculated with S. yanoikuyae. In contrast, the fresh weight of the shoot and root systems of plants inoculated with B. paludis were significantly lower (p < 0.05) than that of the no-treatment control plants. Moreover, when Great Land Plus^® was supplemented with a consortium of P. megaterium and S. yanoikuyae, or a consortium of P. megaterium, S. yanoikuyae, and B. paludis no promotion of plant growth was observed. Full article

Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely on the use of semisolid agar or broth to limit oxygen exposure. Without physical separation, only the most competitive strains are obtained. The distance between strains provided by plating on solid media in reduced oxygen environments has been found to increase the diversity of culturable potential diazotrophic bacteria. To obtain diverse nitrogen-fixing isolates from natural grasslands, we plated soil suspensions from 27 samples onto solid nitrogen-free agar and incubated them under atmospheric and oxygen-reducing conditions. Putative nitrogen fixers were confirmed by subculturing in liquid nitrogen-free media and PCR amplification of the nifH genes. Streaking of the 432 isolates on nitrogen-rich R2A revealed many cocultures. In most cases, only one community member then grew on NFA, indicating the coexistence of nonfixers in coculture with fixers when growing under nitrogen-limited conditions. To exclude isolates able to scavenge residual nitrogen, such as that from vitamins, we used a stringent nitrogen-free medium containing only 6.42 μmol/L total nitrogen and recultured them in a nitrogen-depleted atmosphere. Surprisingly, PCR amplification of nifH using various primer pairs yielded amplicons from only 17% of the 442 isolates. The majority of the nifH PCR-negative isolates were Bacillus and Streptomyces. It is unclear whether these isolates have highly effective uptake systems or nitrogen reduction systems that are not closely aligned with known nitrogenase families. We advise caution in determining the nitrogen fixation ability of plants from growth on nitrogen-free media, even where the total nitrogen is very limited. Full article

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. Full article

Organic farming encourages soil management practices that can improve soil health and fertility by increasing soil organic matter inputs and system sustainability. This study evaluated the effect of three years of continuous organic farming and intercropping orchard treatments on soil microbial diversity, microbial enumeration, respiration, soil fertility and fruit yields. Organic management resulted in higher soil organic matter content, Olsen P, and water holding capacity, but did not affect soil pH, electrical conductivity (EC), K, or Na levels. Growth parameters measured on all fruit trees were not significantly different among treatments. The enumeration of bacteria was significantly higher in organic plots when compared to conventionally managed plots. Soil respiration and substrate-induced respiration were significantly higher in the organic diverse plots in comparison to both conventional systems. The genomic analysis of prokaryotes (16S rRNA) and eukaryotes/fungi (ITS) revealed a significantly higher number of taxa, Shannon H index, and Equitability index in the organic systems for both prokaryotes and eukaryotes, in comparison to conventional farming, all of which are indicators of system sustainability. The relative abundance of Operational Taxonomic Units (OTUs) previously reported as diazotrophs, denitrifiers, or involved in the sulfur cycle, as well as Arbuscular Mychorrizae Fungi (AMF)/glomeromycotan, were highest in the organically managed soils than in the conventional plots. A multivariate correlation network clustering revealed that the microbial communities within the organic and conventional soils had strong dissimilarities regarding soil microbial niches. Our work provides evidence that organic management can be used for increasing soil microbial diversity and soil health, leading to higher levels of sustainability in fruit orchard systems. Full article