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Application of metal-resistant plant growth-promoting bacteria is an efficient method for enhancing crop yields by improving biomass accumulation and plant tolerance to heavy metals. The present study aimed to isolate and characterize these bacteria from rhizosphere soil and root exudates of plants grown on agricultural soils contaminated with heavy metals. Plant growth-promoting properties of isolated strains were assayed by evaluating their abilities to solubilize insoluble phosphate, produce indole-3-acetic acid (IAA), and fix nitrogen. Resistance to metals toxicity and metal removal potential of the selected strains were investigated by MIC and MBC values determination and atomic absorption spectroscopy (AAS), respectively. Pantoea agglomeransexhibited the maximum solubilization of insoluble phosphate and IAA production. In the case of Cd2+, the highest MIC value belonged to Enterobacter ludwigi. Pseudomonas taiwanensis, P. agglomerans, and E. ludwigi exhibited the greatest MIC value (8mM) in the case of Pb2+. P. agglomerans and E. ludwigi showed the highest MBC of Pb2+(>120mM) and the greatest MBC of Cd2+ (30mM) belonged to P. agglomerans. Also, E. ludwigi exhibited the highest metal removal percentage for Pb2+ as 31.81% and Cd2+ as 37.58%. As results showed, these four isolated strains can be used as novel and efficient agents for improving plant growth, especially in heavy metals polluted agricultural soils. [ABSTRACT FROM AUTHOR]

Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3'-phospho-5'-adenylyl sulfate, 5'-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Naeij et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Urease-producing bacteria are abundant in soils, which can precipitate calcium carbonate nanocrystals by enzymatic hydrolysis of urea in the presence of calcium ions. This process is known as microbially induced calcium carbonate precipitation (MICP), and it has received much attention in recent years as an eco-friendly technology. Therefore, the purpose of the present study was to isolate local extremophile bacterial strains capable of producing calcium carbonate. Among a total of 44 isolated urease-producing strains from sandy soils, one strain with a high level of urease activity (8.16 U/ml) and production of a large amount of calcium carbonate (410 mg/100 ml) was selected for further investigation. 16S rRNA gene sequencing showed that this strain had 99.66% sequence identity to Bhargavaea cecembensis. The SEM-EDX and XRD analyses indicated that irregular vaterite and aggregated nanocalcite were the dominant polymorphs produced by this strain. The size of these nanocalcite crystals ranged between 25 and 42 nm. The selected strain showed high levels of tolerance to different conditions of temperature, pH, and salinity. This strain grows at high temperatures up to 50 °C, alkaline pH (9-11), and high concentrations of NaCl (20-25% w/v). Flow cytometry analysis demonstrated 96% cell viability of the isolated strain after desiccation stress. Bhargavaea was first reported in 2009 as a new genus, and it belongs to the Firmicutes. So far, there has been no report on its MICP potential. The present study is the first one to report nanocrystal calcium carbonate precipitation in polyextremophile Bhargavaea cecembensis, which makes it a suitable candidate for bio-cementation under extreme circumstances., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The screen of Polyketide Synthase ( PKS ) and Nonribosomal Peptide Synthetase ( NRPS ) gene groups is a quick way to discover new therapeutic agents. However, errors in laboratory techniques cause a loss of touch with reality. This study aimed to evaluate the presence of PKS and NRPS gene groups in previously isolated strains by optimizing their specialized amplification by degenerate primers and indicating the evolutionary relationships with reference strains., Methods: PKS-I , II , and NRPS genes PCR amplification was performed using three degenerate primer sets for 22 actinomycete strains with antibacterial activity. Annealing temperature and the amount of template DNA and primers were optimized. PCR products of PKS-I, II , and NRPS from three strains were sequenced after TA cloning. Besides, strains with high antibacterial activity were identified by biochemical features and partial 16S rDNA sequencing and hypothetically classified by a phylogenetic tree., Results: High frequencies of PKS-I (86.4%), PKS-II (81.8%), and NRPS (95.4%) genes were found among the strains after optimization. Fourteen strains (64%) contained all of the genes, and 100% of strains had at least two genes. These numbers are pretty distinct in comparison with the previous researches. All of the sequenced strains were members of Streptomyces genus., Conclusion: Our research showed that degenerate PCR strongly depends on the variation of annealing temperature and primer concentration, resulting in an unexpected shift in PCR outputs. The sequencing results confirmed the optimized conditions for specialized PCR of PKS-I , PKS-II , and NRPS gene groups., Competing Interests: Conflict of Interest The authors declare that they have no conflict of interest., (Copyright© 2023 Avicenna Research Institute.)

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus -related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales ), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales , will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales . The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature., Competing Interests: The authors declare no conflicts of interest.