3 Biotech最新文献

We assessed the potential of Bacillus subtilis BSS.2162 to promote plant growth under water deficit conditions through genomic analyses and a greenhouse assay. The genome sequence has a total size of 4.1 Mb, with a GC content of 43.67%, harboring 4,077 coding sequences (CDSs) and 80 RNA genes. The strain exhibited a genetic framework specialized for tolerance to abiotic stresses, encompassing genes associated with antioxidant responses, sporulation, exopolysaccharide (EPS) production, osmoregulation, and homeostasis mechanisms. These featuress reflect the strain's adaptation to the Caatinga biome, an environment characterized by high temperatures and low rainfall, which exerts selective pressure on microbial communities, favoring microorganisms with specialized genetic and biochemical traits. Additionally, we identified CDSs associated with nutrient acquisition and metabolism, including phosphorus and potassium solubilization, nitrate assimilation, production of siderophores, and sulfur metabolism; tryptophan biosynthesis; and hydrolytic enzymes. These traits indicate a strong potential for plant growth promoting. Under greenhouse conditions, maize plants inoculated with BSS.2162 and exposed to complete water restriction showed a significant increase (p < 0.05) in all parameters evaluated, showing improvements ranging from 48% to 306% when compared to the control. Genomic analysis, combined with the greenhouse experiment, highlights BSS.2162 as a novel strain with potential to mitigate the effects of water deficit, highlighting the need for complementary approaches to validate its suitability for the development of a bioinoculant for cultivation in arid and semi-arid regions.

Papaya ringspot virus (PRSV), the causal agent of ringspot disease, is one of the most destructive pathogens affecting papaya, resulting in substantial (80-90%) yield losses worldwide. A critical knowledge gap persists in understanding the molecular determinants of the host tolerance to PRSV and the antiviral role of RNA silencing. As an RNA virus, PRSV exists as a quasi-species within its host, comprising a population of closely related mutant variants which interact dynamically with the plant RNA interference (RNAi) machinery. In infected plants, viral RNA assumes multiple forms- single-stranded RNA, double-stranded RNA, encapsidated RNA, and virus-derived small interfering RNAs (vsiRNAs) that collectively influence the viral persistence and host defence. Plants often harbor co-infections by multiple viral strains or variants; a phenomenon increasingly uncovered through high-throughput sequencing technologies. In this study, we performed a comparative small RNA sequencing analysis to characterize the vsiRNA populations in PRSV infected papaya plants and non-symptomatic (healthy) counterparts of two papaya genotypes- PRSV-tolerant Pusa Selection-3, PRSV-susceptible Pusa Majesty and a wild relative, Vasconcellea cauliflora. High-throughput sequencing generated ~ 238 million reads, from which vsiRNAs of 21, 22, and 24 nucleotides (nt) in length were abundantly detected and mapped across the PRSV genome. Notably, 21nt vsiRNAs were predominant, constituting 35-60% of vsiRNAs in PRSV-infected samples, whereas 22nt and 24nt vsiRNAs (15-35%) were more abundant in healthy plants and the wild relative, showing a consistent sense-strand polarity bias. Analysis of the 5'-end nucleotides of the antisense strand of vsiRNAs revealed a preferential presence of Adenine (A) or Uracil (U), suggesting selective Argonaute protein loading pattern. This study provides the first comparative insight into vsiRNA dynamics across susceptible, tolerant, and wild papaya genotypes, highlighting the complexity of host-virus interactions in PRSV pathogenesis and host defense. The findings advance the understanding of the RNAi-mediated antiviral defense mechanisms underlying PRSV tolerance and lay the groundwork for developing RNAi-based resistance strategies in papaya improvement programs.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04672-0.

The Himalayas offer a unique environment for the study of microbial diversity and their response to biotic and abiotic factors, enhancing knowledge on ecological processes under altitudinal control in subalpine forests. This study investigates the impact of altitude on bacterial diversity and soil physico-chemical properties of Himalayan subalpine coniferous forests at four different regions-Sillery Gaon (S1; 1829 m), Gangotri (S2; 3415 m), Kausani (S3; 1890 m) and Gwal Dam (S4; 1940 m). Using 16S rDNA amplicon sequencing, soil microbial diversity of the said subalpine ecosystems were explored. Physico-chemical studies of the soil samples showed that S1 had the highest moisture content (25.66 ± 0.26%) and C:N ratio (136.26 ± 5.4) while S4 had the highest TOC (22.78 ± 1.2%), TKN (0.7373 ± 0.043%) and available phosphate content. Results indicated presence of diverse microflora from various phyla, including Actinomycetota (7.52% in S2, 7.98% in S3), Planctomycetota (53.36% in S1, 51.09% in S3), Proteobacteria (14.3% in S1, 18.28% in S3, 14.96% in S4), and Verrucomicrobiota (18.75% in S2 and 21.88% in S4). Proteobacteria was the dominant phyla in mid (S4) and lower (S1, S3) subalpine forest soils, suggesting enhanced abundance due to human intervention at these altitudes. Multivariate analysis revealed a positive correlation between altitude, precipitation, moisture content, soil pH, organic carbon, nitrogen and phosphate contents with the presence of Proteobacteria and Actinomycetota phyla. The study highlights the connection between microbial communities and soil physicochemical properties, and the intricate interplay of biotic and abiotic factors affecting the microbial community composition in a unique region at different elevations.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04608-8.

Advanced glycation end products (AGEs) are key molecular mediators implicated in diabetic neuropathy (DN), although their exact mechanisms and therapeutic implications remain unclear. This review systematically integrates current evidence on AGE formation, AGE-RAGE signaling, oxidative stress, and emerging interventions in DN. A comprehensive literature search was conducted across PubMed, Scopus, Web of Science, and Google Scholar, in accordance with the PRISMA guidelines. Studies addressing biochemical, molecular, and clinical aspects of AGEs in DN were identified, screened, and qualitatively analyzed. Evidence consistently shows that AGEs promote neuronal and vascular injury through both receptor-dependent (AGE-RAGE-NF-κB/oxidative stress) and receptor-independent (protein crosslinking and matrix stiffening) mechanisms. Clinical data reveal significant associations between elevated AGE levels and DN severity, although differences in assay methods and diagnostic criteria limit direct comparisons. Antiglycation and antioxidant therapies, including aminoguanidine, carbonyl scavengers, and RAGE antagonists, have demonstrated neuroprotective potential in preclinical studies but have yielded variable results in human trials. AGEs play a central yet multifactorial role in DN by coupling metabolic stress with neuroinflammation and structural damage. Standardization of AGE detection techniques, longitudinal human studies, and rigorously designed translational trials are essential to advance their diagnostic and therapeutic potential.

This review synthesizes recent advances in the integration of omics, synthetic biology, and artificial intelligence (AI) to deepen understanding of plant-microbe interactions and support sustainable agriculture. Omics approaches have provided molecular-level insights into microbial diversity, functional genes, and regulatory pathways shaping rhizosphere dynamics. Synthetic biology has enabled the design of microbial strains and synthetic communities (SynComs) with enhanced traits such as nutrient solubilization, stress tolerance, and pathogen suppression, offering targeted solutions for crop improvement. AI-driven tools have accelerated these advances by enabling predictive modelling, multi-omics data integration, and real-time phenotyping, while also enhancing disease forecasting and microbiome-informed crop management. The combined application of these technologies demonstrates potential for the rational design of next-generation plant growth-promoting rhizobacteria and synthetic microbial consortia optimized for diverse agroecosystems. Key challenges remain in translating laboratory findings to field conditions, ensuring biosafety of engineered microbes, and addressing ethical and regulatory issues. Addressing these barriers through interdisciplinary frameworks and responsible innovation will pave the way for climate specific high-yielding, and sustainable cropping systems.

The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.

Liver fibrosis is a progressive pathological condition characterised by excessive deposition of extracellular matrix components, primarily driven by chronic liver injury and activation of hepatic stellate cells. This pathological remodelling disrupts hepatic architecture and function, and if left untreated, may advance to cirrhosis, liver failure, or hepatocellular carcinoma, a major contributor to global morbidity and mortality. Flavonoids are a diverse group of polyphenolic compounds found in plants, known for their antioxidant, anti-inflammatory, antiviral, and hepatoprotective properties. Their beneficial effects on liver health have been widely explored in preclinical and clinical studies. Apigenin (4',5,7-Trihydroxyflavone) is a naturally occurring flavonoid (specifically a flavone) widely distributed in fruits, vegetables, and herbs, especially in parsley, celery, chamomile, and oranges. It has gained significant scientific attention due to its antioxidant, anti-inflammatory, neuroprotective, and hepatoprotective properties. Preclinical studies demonstrate that apigenin mitigates fibrogenesis by attenuating oxidative stress, suppressing pro-inflammatory cytokine production, and inhibiting HSC activation. Mechanistically, it modulates multiple signalling pathways and molecular targets such as TGF-β1/Smad, NF-κB, PI3K/AKT, PPARα, GSK3β, MAPK, MLKL, Nrf-2/Keap1, and NLRP3 inflammasome, thereby exerting a multitargeted antifibrotic response. Furthermore, apigenin's ability to restore redox homeostasis and regulate apoptotic signalling underscores its therapeutic potential. Considering the potential of apigenin in modulating these mediators, the present study was conceptualised to study the mechanistic interplay underlying its anti-fibrotic effects. By investigating these interconnected pathways, this study will provide foundational insights that will enable future researchers to address existing gaps and further elucidate apigenin's potential in liver fibrosis.

Sustainable alternatives to fish meal are increasingly required to minimize the environmental impact of aquaculture feeds. This study focuses on incorporation of microalgae Spirulina platensis and Chlorella vulgaris in rainbow trout's (Oncorhynchus mykiss) feed replacing 25 and 50% of fish meal present in standard formulation and reaching total microalgae proportion in feed, respectively 5 and 10%. It was demonstrated that trout with initial weight 45 and 65 g has significantly improved growth (weight and length) when fed with microalgae supplemented feed. The highest gains in length and weight in both groups were observed using 5% S. platensis feed, with average wight increase up to 28% compared to the control. Incorporation of microalgal biomass has significantly improved the chemical composition of trout's filet, due to increase in concentration of certain PUFA (including DHA, EPA, Omega-3, Omega-6), carotenoids, vitamins and iron. Enhanced filet pigmentation was also observed. Histological analysis showed a significant improvement in villi diameter and goblet cell count in pyloric appendages and proximal intestine. To sum up, partial fish meal substitution with microalgae has significantly improved trout growth performance and product quality and has strong potential to reduce the environmental impact associated with overfishing.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04666-y.

One of the most attractive solutions to deal with global Zinc-deficiency problem is Zn-biofortification of wheat using a combination of Zn-solubilizing bacteria (ZSB) and ZnO-nanoparticles. This study compared commonly used Zn-fertilizer, bulk-ZnO and nano-ZnO by functionalizing both with Alizarin Red S (ARS) to track their passage into plant tissues in a ZSB environment. Mung bean and wheat were grown in the presence of these functionalized ZnO. Mung bean tissues exhibit higher intensity of pink/purple color (ARS) when grown with functionalized ZnO-NPs as opposed to bulk-ZnO indicating a higher ZnO-uptake. SEM-EDX analysis of roots and shoots grown with ZnO-NPs revealed a higher Zn-weight% of 0.76% and 0.16%, respectively compared to 0.50% and 0.04%, respectively obtained with bulk-ZnO. This was further confirmed with dithizone staining and AAS analysis. Migration of bulk-ZnO and ZnO-NPs along a soil column was also checked. The results suggested that the use of ZnO can be reduced by half if nano-ZnO is used instead of bulk-ZnO. When the influence of ZnO-NPs on plant-growth-promoting activities of ZSB was checked, low concentration (5 µg/ml) was found to enhance multiple PGP-activities, increase germination and vegetative growth. While high concentration (500 µg/ml) were inhibitory. Cytotoxicity of ZnO was also checked using Allium cepa assays. Higher concentration of ZnO (500 µg/ml) significantly decreased mitotic-index, increased total abnormalities percentage, and dead cells population. This study for the first time reports a holistic approach to understand the passage of ZnO-NP into plant tissues in a ZSB environment and consequent increase in plant growth and Zn content.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04606-w.

Glucansucrases are the key biocatalysts in the industrial production of glucans. This study initially investigated glucansucrase production using the honey isolate Bacillus subtilis EGY1 followed by optimizing the enzyme productivity in which the optimized activity was 15-fold higher than the estimated initial activity. Moreover, the enzyme was immobilized using a carrier matrix of egg white protein (EWP) incorporated into pectin beads, activated with polyethyleneimine (PEI) and glutaraldehyde (GA). The optimal conditions for egg white protein and PEI concentrations, as well as pH, were determined using Box-Behnken design in which the estimated optimal conditions were EWP concentration of 1% and PEI processing conditions of 2.5% PEI concentration and 9.4 pH. At these optimal conditions, the immobilized enzyme exhibited high immobilization yield (93.87%) and efficiency (94.95%). Surface morphology, structural elements, and functional groups were analyzed using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy. The immobilized enzyme demonstrated improved activity at alkaline pH (up to pH 9) and high temperatures (up to 75 °C), with reduced activation energy, approximately one-third that of the free enzyme. In addition, it retained > 50% activity after four reuse cycles.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04609-7.