Microbial biofertilizers offer a sustainable alternative to reduce inorganic fertilizer inputs in intensive vegetable production. While rhizobia are traditionally associated with legumes, their co-inoculation with native rhizobacteria for non-leguminous crops like tomatoes remains under-explored. This study aimed to isolate native rhizobacteria compatible with Bradyrhizobium diazoefficiens NE1-65 and evaluate their combined effect on the tomato plant (var. max F1) under reduced inorganic fertilizer rates. From the initial eighteen isolates screened on nitrogen-free media, and solubilization assays of phosphorus and potassium, three isolates (RM-8, RM-17, RM-18) were found compatible with B. diazoefficiens NE1-65. Isolate RM-17 (tentatively identified as Aureimonas sp. based on 16S rRNA gene sequence) was selected for its high K-solubilizing capacity (KSI = 8.60). Then, a 90-day growth trial compared various fertilizer application rates (0, 25, 50, 75, and 100%) with and without the bacterial consortia. The 75% fertilizer rate plus the consortia significantly outperformed the 100% fertilizer rate alone. Specifically, it increased plant height (11.57%), fruit diameter (9.23%), fruit number (53.90%), and fruit weight (16.15%). These findings demonstrate that the RM-17 and B. diazoefficiens NE1-65 consortia can partially substitute inorganic fertilizers while significantly enhancing tomato growth and yield, highlighting its potential application for sustainable tomato production systems.

Ultramafic soils, particularly those affected by mining, often contain toxic nickel (Ni) levels that hinder plant growth and ecosystem recovery. This study assessed engineered biochar–nanocomposite amendments to improve vetiver (Chrysopogon zizanioides) growth, biomass, and Ni phytoextraction in Ni-rich ultramafic soils from Santa Cruz, Zambales, the Philippines. Seven samples were tested: T₁—control (no application); T₂—biochar; T₃—nanocomposite; T₄—biochar + nano-silica; T₅—biochar + nano-calcium; T₆—biochar + nano-chitosan; and T₇—biochar + nanocomposite. Biochar combined with nano-silica (T4) significantly enhanced vetiver growth, producing the highest root, shoot, and total biomass (469.97 g plant⁻¹), indicating improved plant tolerance under Ni stress. The highest shoot Ni concentration (24.52 mg kg⁻¹) and translocation factor (0.56) were observed in the biochar + nano-chitosan treatment (T6), suggesting increased Ni bioavailability and uptake. However, translocation factor values remained below unity across all treatments, indicating limited Ni transfer from roots to shoots and a dominant phytostabilization behavior. Overall, nano-silica-engineered + biochar primarily enhanced biomass production, while nano-chitosan influenced Ni uptake dynamics, highlighting the potential of engineered biochar–nanomaterial amendments for sustainable rehabilitation of Ni-contaminated ultramafic soils.

This study investigates the impact of selected soil parameters and integrated fertilizer formulations on the productivity of three legume crops—mung bean, soybean, and cowpea—in order to identify the optimal strategies to maximize yields through reduced nitrogen and bio-augmentation. A five-year experiment composed of 2-year pot trials (2019–2020) and 3-year field trials (2022–2024) was conducted to assess the changes in soil parameters (N, P, K, OM, pH) and yield response of crops with varying amounts (1, 2, 4 kg) of Bradyrhizobium-based biofertilizer combined with a 25–50% reduction in mineral N fertilizer. The biofertilizer was composed of locally isolated strains, which were genetically identified in our previous reports as B. elkanii NE1-6, NE2-1, B. diazoefficiens NE1-65, Bradyrhizobium sp. NE1-19, NE1-34, and NE2-3. The results indicated that the amount of K strongly influenced yield increase for soybean (r = 0.85, p < 0.05) and mung bean (r = 0.67, p < 0.05), while the amount of N had the greatest influence on cowpea (r = 0.60, p < 0.05). Soybean yield was maximized with a 50% reduction in N fertilizer (20 kg N) combined with 2–4 kg biofertilizer, while cowpea and mung bean achieved increased yields at 25% reduced N fertilizer combined with 2–4 kg biofertilizer. This study confirms the viability of integrating Bradyrhizobium-based biofertilizer with a 25–50% reduction in mineral N fertilizer without yield loss by harnessing the efficient N-fixation ability of the strains in the consortium.

Bradyrhizobium exhibits exceptional genetic versatility, functional adaptability, and evolutionary resilience, serving as a critical stabilizing agent in tropical ecosystems. However, its full potential remains underexplored, largely because soil health assessments have historically relied on temperate region and studies often analyze traits in isolation rather than tracking genomic responses to combined environmental stresses. This review applies the niche breadth triangle framework to synthesize the genomic structure, evolutionary history, and multi stress tolerance of tropical Bradyrhizobium lineages. We traced the evolutionary trajectory of the strains, detailing how ancestral lineages fist adapted to to acidic, metal rich soils before acquiring mobile symbiosis islands and specialized secretion systems that broaden their host range. In addition, we highlight that tropical lineages harbor an expansive accessory genome of ~39% variable accessory genes, showcasing a significantly more promising adaptive potential than temperate Bradyrhizobium species. Key protective mechanisms reviewed include modified heat shock promoters, robust extracellular matrices, and photosynthetic metabolism, which preserve nitrogenase activity during drought, high temperatures, and flooding. High strain diversity ensures functional redundancy and niche complementarity, maintaining consistent N-fixation under pressure. Consequently, this work demonstrates how local management practices and stress resistant strains can improve rhizosphere conditions that simultaneously building climate resilient agricultural systems.

The diversity of indigenous bradyrhizobia from soils collected at 11 locations in the Philippines was investigated using PSB-SY2 local soybean cultivar as the host plant. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment for 16S rRNA, 16S-23S rRNA internal transcribed spacer (ITS) region and rpo B housekeeping gene was performed primarily to detect the genetic variation among the 424 isolates collected. Then, sequence analysis of 16S rRNA, ITS region and rpo B gene was performed for the representative isolates. Majority of the isolates were classified under Bradyrhizobium elkanii, B. diazoefficiens, B. japonicum, Bradyrhizobium sp., and few isolates were related to B. yuanmingense . Genetic variations observed through PCR-RFLP and sequence analyses of the ITS region and rpo B gene generally occurred in B. elkanii , suggesting an occurrence of gene transfer. Shannon’s diversity index showed varied results with a lowest score of 0.00 and highest at 0.98 indicating a very diverse population of bradyrhizobia across the country. Among all the factors considered in this work, soil management such as period of flooding and some soil properties provided major influence on the distribution and diversity of soybean bradyrhizobia in the country. Thus, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils. Importance: Agriculture production in the Philippines has been and is currently heavily dependent on chemical inputs with mainly rice or corn mono-cropping that it rendered the soil acidic and unproductive. Legume research in the country are mainly focused on plant varietal improvements and very few are aimed at understanding the ecological niche of rhizobia present in the soil. Since soybean has mutual relationship with rhizobia, this legume is a good fallow crop or a rotation crop after rice and corn to help build up the nitrogen stock in the soil. The significance of this research is the better understanding of the ecological niche of indigenous soybean bradyrhizobia, particularly in a tropical archipelago like the Philippines. This work was conceptualized with the utmost goal to increase soybean yield by harnessing and evaluating the indigenous rhizobia in the soil to make production more sustainable and human-friendly.