Natural pyrite-enhanced co-culture system for simultaneous nitrate and ammonium removal under low C/N conditions: Mechanistic insights and real wastewater application.

Cold-active β-galactosidase has significant application value in the enzymatic synthesis of galacto-oligosaccharides (GOS); however, its low transglycosylation efficiency and poor selectivity toward high-degree polymerization (DP) products remain major challenges. In this study, a cold-active β-galactosidase (K3-β-gal) from marine Bacillus sp. K-3 was cloned and expressed. Four mutants (R252M, F261W, Y281R, and F355K) were constructed via semi-rational design, among which R252M exhibited markedly enhanced transglycosylation activity. Compared with the wild-type enzyme, R252M showed no change in optimum temperature (20°C) or optimum pH (6.0), and retained good stability under low-temperature and weakly acidic conditions. The total GOS yield increased from 21.68% to 38.12% (a 75.83% improvement), and the DP4/DP3 ratio increased from 0.95 to 2.6, while the hydrolytic activity (kcat/km) decreased by approximately 44%, indicating a shift in the catalytic equilibrium from hydrolysis toward transglycosylation. Molecular dynamics simulations revealed that R252M remodels the hydrogen-bond network in the active pocket, enhances protein rigidity, and reduces dynamic perturbations around the active site, which may contribute to substrate binding and transglycosylation efficiency.", This mutant holds promising potential for the green synthesis of high-DP GOS.

Sequential soil application of bacterial siderophores and biosurfactants enhances Cu, Ni, Pb, and Zn accumulation and physiological performance in Brassica juncea L. Czern.

Rhizosphere keystone taxa critically drive microbial community stability and soil biogeochemical cycles. However, the manipulation of such taxa remains a challenge. This study simulated plant-mediated modulation of keystone taxa via simplified synthetic root exudates to track their compositional shifts. The combination of luteolin, myristic acid, and glucose enhanced rhizosphere phosphatase activity, significantly enriched Domibacillus indicus D99, and converted it into a keystone taxon. This precise regulation was driven by transcriptional upregulation of C metabolism and an unusual fatty acid assimilation pathway. Additionally, metabolites produced by D. indicus D99 (such as bergapten and lactate) were preferentially utilized by phosphate-mineralizing bacteria, Bacillus sp. C67 and Domibacillus sp. C94. These partner bacteria exhibited less substrate overlap and pronounced resource partitioning, forming an efficient synergistic relationship with D. indicus D99 that amplified rhizosphere phosphatase activity and plant growth. This study highlights opportunities to utilize the ecological roles of keystone taxa in manipulating the microbiome.

Heavy metal contamination threatens soil health and ecosystem stability. Endophytic bacteria from metal-tolerant plants can enhance phytoremediation. In this study, twenty-four endophytic bacterial isolates were isolated from leaves and roots of Cynodon dactylon collected from a metal-contaminated industrial site in Islamabad, Pakistan. All isolates were screened for plant growth-promoting (PGP) traits and heavy metal (Zn, Pb, Cu, Cr) tolerance. Quantitative assays revealed that 95.8% of isolates solubilised phosphate (maximum zone 17mm by CDR11), all produced indole acetic acid (IAA) (3.2-14.7µg/mL) and ammonia (0.8-6.5µg/mL). Metal tolerance tests showed minimum inhibitory concentrations (MIC) of 50-100µg/mL. Isolates CDL3, CDL2 and CDR1 exhibited maximum tolerance to all four metals at 100µg/mL. Seed germination assays with Linum usitatissimum demonstrated significant (p < 0.05) increases in germination percentage (up to 91.1% by CDR6 vs. 66.6% control) and seedling vigour. 16S rRNA gene sequencing of six potential isolates identified them as Bacillus thuringiensis CDL2 (99.78%), Bacillus cereus CDL3 (99.90%), Bacillus cereus CDL5 (99.90%), Bacillus sp. CDL9 (98.52%), Bacillus sp. CDR1 (100%) and Bacillus subtilis CDR12 (99.90%). These results demonstrate that metal-resistant Bacillus endophytes from C. dactylon possess multiple PGP traits and significantly improve flax seed germination, highlighting their potential as bio-inoculants for phytoremediation of metal-polluted soils.

Isolation and characterisation of virulent bacteriophage targeting canola rhizosphere bacteria Klebsiella grimontii and Bacillus sp.

The shift toward sustainable agriculture has increased interest in biostimulants and in novel strategies for their delivery to crops. Key challenges include improving the stability, field performance, and environmental compatibility of these agents. This study investigates a circular economy approach to develop biobased carriers from cellulose and pectin for the delivery of two plant growth-promoting bacteria, Bacillus sp. LR01 and Rhizobium sp. GR12, and a phytoextract obtained from leafy vegetable by-products. Both bacterial strains exhibited distinct colonization patterns in the rhizosphere of lettuce and tomato. When incorporated into two biobased carriers (BC1 and BC2), Rhizobium sp. GR12 did not survive desiccation and was therefore alternatively encapsulated in alginate beads showing a survival rate of 108CFU/g of material for 28days of storage. The spore-forming Bacillus sp. LR01 maintained high viability in both formulations (107 to 109CFU/g) for 28days. The silica-enriched BC2 formulation was selected for biostimulant delivery in greenhouse trials for its improved structural integrity, while alginate was chosen as benchmark. Application of all three biostimulants as aqueous suspensions significantly enhanced lettuce growth increasing leaves biomass by 20% to 30%. Delivery via the selected carriers maintained bacterial viability and sustained rhizosphere colonization (106 to 108CFU/g of soil) but reduced or reversed plant growth-promotion effects. Conversely, phenol-related secondary metabolism responses were triggered only when bacteria were delivered through the carriers. Overall, biostimulant performance depended not only on successful delivery but appeared strongly related with the physiological compatibility of the carrier with the plant-soil system. KEY POINTS: • Waste-derived biobased materials were designed for biostimulants delivery. • Biostimulants provided as aqueous suspensions enhanced lettuce growth. • Biobased materials maintained microbial viability but reduced plant growth promotion.

ABSTRACT Lipid-degrading bacteria play an important role in the removal of fats, oils and grease (FOG) from lipid-rich environments, contributing to environmental protection. In this study, five lipid-degrading bacterial strains were isolated from water samples and evaluated for extracellular lipase activity, degradation ability toward representative lipid substrates (olive oil, lard and salad oil) and COD reduction. Among them, Staphylococcus sp. FX-2-1 and Bacillus sp. MX-A1 exhibited consistently higher lipase activity (15.68–16.22 U/mL) and superior degradation efficiencies. A ratio-guided bacterial consortium was subsequently constructed using the two dominant strains. Intermediate inoculation ratios (2:1, 1:1 and 1:2) achieved higher degradation efficiencies than single-strain cultures and extreme ratios, reaching up to 85.0% within 12 h. The consortium maintained a consistent performance advantage over individual strains across increasing olive oil concentrations (1–8%, v/v), although absolute degradation efficiency declined at higher substrate concentrations. This study highlights the effectiveness of ratio-guided microbial consortia for efficient lipid degradation, providing insights for potential application in complex environments. Highlights Five lipid-degrading strains were isolated and showed the ability to utilize multiple lipid substrates. Two strains exhibited higher lipase activity and lipid removal performance. A ratio-guided consortium achieved a maximum removal efficiency of 85% within 12 h. Removal efficiency declined with increasing oil concentration but remained higher than individual strains. A performance-based approach for constructing microbial consortia under simulated lipid-rich conditions was proposed.

Cadmium (Cd) accumulation in rice poses a significant threat to food safety and human health. Plant growth-promoting endophytes (PGPEs) offer a promising strategy to mitigate Cd stress. Yet, the mechanisms underlying microbe-mediated reduction of Cd uptake, particularly through specific plant-microbe interactions, remain poorly understood. Here, we demonstrate that the root endophyte Bacillus sp. RE35, a Cd-tolerant and high-IAA producer isolated from rice, established an effective apoplastic niche and significantly enhanced Cd retention in roots through a multi-level mechanism. Successful colonisation of RE35 in the root apoplast, confirmed by the red fluorescent protein labelling, strain-specific gene quantification and colonisation-related genes analysis, promoted extensive root morphological remodelling via both de novo and salvage pathways of IAA biosynthesis under Cd stress. Notably, RE35 inoculation drastically reshaped Cd distribution, increasing cell wall-bound Cd by 64.7% while reducing shoot Cd accumulation by 24.1%-49.7%. This enhanced apoplastic trapping of Cd was attributed to a comprehensive cell wall remodelling program, activated through RE35-induced expression of plant receptor kinases (e.g., LRR-RLKs, LysM-RLKs) and the upregulation of key genes involved in the biosynthesis of pectin, hemicellulose and lignin. In parallel, RE35 modulated host Cd transport by downregulating influx transporter genes (OsNRAMP5, OsZIP5/9) and upregulating the vacuolar sequestration gene OsHMA3. Our findings reveal a Cd-responsive regulatory network where endophytes enhance apoplastic immobilisation by coordinating auxin signalling, receptor kinase activation and cell wall remodelling, providing a mechanistic basis for sustainable agriculture in contaminated environments.

High-altitude regions of the Pangi-Chamba Himalayas (PCH) provide a distinctive environment for isolating extremophilic lignocellulolytic bacteria. This study reports the isolation of lignocellulolytic enzyme-producing bacteria from decaying wood samples. Among 54 bacterial isolates, 24 demonstrated lignocellulose hydrolysis potential, producing laccase, xylanase, and cellulase enzymes. Eight morphologically distinct isolates belonging to the phylum Bacillota were selected for further experiments. Quantitative analysis identified Bacillus sp. PCH491 as an efficient producer of xylanase using alkaline-pretreated wheat straw, whereas Bacillus sp. PCH494 produced laccase using alkaline-pretreated sugarcane bagasse. Notably, Bacillus sp. PCH492 produced multiple enzymes, laccase, xylanase, and cellulase, using various agro-residues. Further, characterization of laccase and xylanase enzymes revealed activity across a broad pH (4.0-12.0) and temperature (4-90 ℃). Xylanase from Bacillus sp. PCH491 showed maximum activity (38.86IU/mL) at pH 7.0 and 50 ℃, whereas laccase from Bacillus sp. PCH494 reached peak activity (31.20IU/mL) at pH 3.0 and 50 ℃. SEM and FTIR analyses confirmed significant structural and functional group modifications in the biomass, highlighting these high-altitude isolates as robust candidates for industrial biorefineries.

Hexavalent chromium [Cr(VI)] removal was evaluated using two facultative anaerobic bacteria isolated from a microbial mat near a chromite mining site: Bacillus sp. S9 (Gram-positive) and Enterobacter sp. Z11 (Gram-negative). Both strains effectively removed Cr(VI) under anaerobic conditions, with total removal efficiencies of 98.3 ± 0.6% and 97.2 ± 0.9%, respectively. The bacteria reduced Cr(VI) to trivalent chromium [Cr(III)], with this reduction occurring extracellularly in the supernatant, on cell surfaces, and intracellularly. Chromate reductase assays and spectroscopic analyses confirmed the predominant biological reduction of Cr(VI) to Cr(III), with minor formation of elemental chromium [Cr(0)]. Surface analyses showed Cr deposition on the surface of Bacillus sp. S9 (13.3 ± 0.5%) and Enterobacter sp. Z11 (33.9 ± 2%), with functional groups such as OH-NH, methyl-C-H, C = O/COO, C-N, N-H, PO43-, metal–O, and Cr(VI)–O bonds contributing to biosorption. Both strains secreted approximately two-fold more extracellular polymeric substances (EPS) after exposure to Cr(VI), thereby enhancing metal binding. Intracellular Cr accumulation was also observed, with a total amount of 3.9 ± 0.3 mg L⁻¹ in Bacillus sp. S9 and 6.4 ± 0.3 mg L⁻¹ in Enterobacter sp. Z11. These results demonstrate that facultative anaerobes from microbial mats effectively reduce, adsorb, and accumulate Cr species, underscoring their potential application in bioremediation of Cr-contaminated environments under varying oxygen conditions.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13205-026-04841-9.

Due to high Sulphur content of coals in Meghalaya, India, coal mining in this region generates huge amount of acidic waste characterized by low pH and leaching of toxic heavy metals which is a major environmental problem. This study involves isolating native Bacillus species from samples of active and abandoned Rat-hole coal mines in order to mitigate these phenomena. These species were then evaluated for significant bioremediation potential in the form of heavy metal binding and adsorption, as well as raising acidic pH to pH 8.0 (basic) under in vitro conditions. Sixteen (16) isolates were initially screened to develop the microbial consortia and five isolates (05) were finally selected for this study (sites specific) based on highest heavy metal resistance, and the ability to reverse or increase acidic pH. The isolates demonstrated resistance to the heavy metals under investigation (iron, cadmium, and chromium) with minimum bactericidal concentrations ranging from 1600mg/L to 2000mg/L of Fe, 128mg/L to 1024mg/L of Cd, and 64mg/L to 256mg/L of Cr. The lowest acidic pH the isolates could grow in in vitro conditions was pH 5.0, at 37°C, 150rpm shaking with or without metal. On average, Bacillus sp. KH5M11 and Bacillus sp. KHCL13 have the better binding and removal percentage (%) of iron (99.89 ± 0.066 and 99.87 ± 0.098) respectively. Lysinibacillus sp. SK18-4 have better removal percentage (%) of Chromium (79.903 ± 17.702), followed by Bacillus sp. KHCL13 (76.14 ± 12.233). Bacillus sp. KHCL13 (97.715 ± 1.040) and Bacillus sp. KH5M11 (97.363 ± 1.260) have better removal percentage (%) of Cadmium, as compared to other isolates. Amongst the consortia, the removal percentage, does not show significant differences in heavy metal removals. The iron removal percentage (%) of Consortia-A22ED9 is 92.08 ± 10.281, and Consortia-B18-4M11 is 89.597 ± 10.829. The chromium removal percentage (%) of Consortia-A22ED9 is 74.15 ± 12.906 and Consortia-B18-4M11 is 77.467 ± 12.420. However, both the consortia have similar removal percentage (%) for cadmium. Consortia-A22ED9 removed 97.587 ± 0.958% and Consortia-B18-4M11 removed 97.673 ± 0.475% of Cd respectively. Metal binding was confirmed by FTIR and SEM-EDX analysis, where distinct peaks and clear spectral pointed out to a specific cell surface functional groups and heavy metals binding. In all cases, the average cells optical density (OD-600) for all five isolates was high, ranges from 1.99 to 2.3 for isolates and 2.2 to 2.3 for consortia while the average pH remains relatively above pH 5.0, ranging from pH 5.4 to pH 6.23 for isolates and pH 5.7 to pH 6.3 for consortia. The study concluded that the bioremediation potential of the isolates under said condition was commendable both as individual isolates and in consortia and the possible mechanisms of bioremediation is through adsorption and binding of heavy metal and not solely because of metals precipitation. We hope with minimum manipulation of coal mines acidic condition these Bacillus spp. may become employable in bioremediation of heavy metal and control of acidic pH generation. However, our study is limited only to the in vitro as we do not have chance to carry out field trial which would be the future aspects of these beautiful findings. Much more study may be done on this field for practical applications.

Using Bacillus sp. TR2 to form nano-BioMnOx to improve 4-chlorophenol rhizoremediation.

Encapsulated Bacillus sp. THPS1, a novel thermophilic probiotic, enhances productivity and metabolic health in laying hens.

The molecular transformation of microplastic-derived dissolved organic matter regulates the bioavailability of conventional microplastic.

The key role of extracellular polymeric substances from indigenous Bacillus sp. X-113 in facilitating uranium immobilization

Optimization, partial characterization, and application of a biosurfactant produced by the wheat endophytic Bacillus sp. WL2-23.

Comprehensive characterization and genome-resolved insights into the probiotic potential of Bacillus sp. KNSH39 isolated from Litopenaeus vannamei intestine.

The severe, long-lastingharm caused by plastic pollution to marineecosystems and coastal economies has led to the development of biodegradableplastics; however, their limited decomposition in marine environmentsremains a challenge. Here, technologies are presented for creating3D-bioprinted living materials as a proof of concept for bioplasticdegradation, with specific use in marine environments. The approachdeveloped here integrates the halotolerant bioplastic-degrading bacterium Bacillus sp. NRRL B-14911 into alginate-based bio-ink toprint an engineered living material (ELM) termed a “bio-sticker.”Quantification of bacteria viability reveals that bioprinted marinebacteria survive within biostickers for more than 3 weeks. The rateat which the biostickers degrade the bioplastic polyhydroxybutyrate(PHB) can be tuned by altering biosticker biomass concentration, bioplasticconcentration, or incubation temperature. Biostickers that are transferredto a different PHB sample still retain high biodegradation activity,demonstrating their reusability. Strain sweep oscillatory tests demonstratethat the biostickers display predominantly viscoelastic behavior.Monotonic tensile tests indicate that the elastic modulus and theadhesion of the biostickers are not negatively impacted by bacteriagrowth or incubation temperature. This work paves the way for thedevelopment of ELMs to facilitate the inclusion of bioplastics withinthe blue economy, promoting the emergence of more sustainable andeco-friendly materials.

Polyhydroxyalkanoates (PHAs) are biodegradable microbial polyesters that represent a promising sustainable alternative to petroleum-based plastics. Salterns, hypersaline environments, are recognized as significant sources of halotolerant microorganisms that can produce PHAs in high-salinity conditions; however, Vietnamese saltern ecosystems have not been extensively investigated. This research aimed to isolate and initially characterize salt-tolerant bacteria capable of synthesizing PHAs from the Hon Khoi saltern in Khanh Hoa Province, Vietnam. A total of 37 halotolerant bacterial isolates were obtained, and potential PHA-producing strains were initially screened using Sudan Black B and Nile Blue A. TEM microscopy was then employed to confirm the existence of PHA granules. Furthermore, FTIR spectroscopy and GC-MS/MS spectrometry were utilized to analyze the chemical structure and monomer composition of the extracted polymers. Six isolates were identified as PHA-producing bacteria, including Salinivibrio sp. HK101 and HK116, Halomonas sp. HK105, Priestia sp. HK125 and HK142, and Bacillus sp. HK130. These strains exhibited growth across 3-10% NaCl and temperatures from 25 to 45 °C. Priestia sp. HK142 and Salinivibrio sp. HK101 exhibited the most substantial PHA accumulation, achieving 50.72 ± 1.83% and 42.07 ± 1.8% of DCW, respectively. These results indicate that the Hon Khoi saltern represents a promising source of halotolerant PHA-producing bacteria with potential relevance for future biopolymer production studies.