Introduction Genetic diversity and population structure are critical for understanding species distribution, environmental adaptability, and responses to anthropogenic disturbances. Dendrocalamus longispathus , a commercially and ecologically important bamboo species in North East India, remains understudied in terms of its population genetics. This study aims to assess the genetic diversity and structure of this species across its natural range in Mizoram and Tripura. Methods Leaf samples were collected from 12 populations and analyzed using 13 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including number of alleles, allelic richness, heterozygosity, and inbreeding coefficients, were estimated. Population structure was examined using Bayesian analysis, Neighbor-Joining method based genetic clustering, and principal coordinate analysis (PCoA). Results The analysis revealed moderate genetic diversity, with mean number of alleles (Na = 2.84), effective alleles (Ne = 1.87), and expected heterozygosity (He = 0.362). Observed heterozygosity (Ho = 0.234) was lower than expected, indicating inbreeding, supported by a positive inbreeding coefficient (F IS = 0.306). Populations from Mizoram exhibited higher allelic richness compared to those from Tripura. AMOVA showed that 70% of genetic variation occurred within populations and 30% among populations (F ST = 0.297), indicating very high levels of genetic differentiation with low gene flow (Nm = 0.86). Bayesian analysis identified three genetic clusters (K = 3), with most populations clearly structured except one admixed population. Overall, pattern of genetic clustering between population was largely aligned with geographic proximity. Discussion The findings indicate moderate genetic diversity, very high genetic differentiation, and robust genetic structure in D. longispathus populations, with evidence of limited gene flow and inbreeding. These results highlight the need for targeted conservation strategies and the use of genetically diverse populations for plantation and sustainable management programs.

Establishing links between biosynthetic gene clusters in fungi and their secondary metabolites: A case study of Aspergillus.

Sansalvamides are a class of bioactive cyclodepsipeptides recognized for their potent antitumor properties. In this study, genome mining of an endophytic fungus Fusarium sp. R1 led to the identification of a unique nonribosomal peptide synthetase (NRPS) gene cluster (san), which consists of 5 core genes and 14 auxiliary tailoring genes. Chemical investigation of strain R1 resulted in discovery of one new noncyclic sansalvamide derivative 1 together with three analogues (2-4). Using CRISPR-Cas9-mediated gene knockout, we disrupted the san cluster for the first time, abolishing production of compounds 1-4 and confirming its functional indispensability. Transcriptomic analysis unveiled a GDSL-like lipase/acylhydrolase (sanP) responsible for catalysis of a key ring-opening step followed by the production of 1 and 2. Antifungal assays revealed that compounds 3 and 4 possessed pronounced activity against the phytopathogenic fungus Alternaria solani with inhibition rates of 66.7 and 77.0%, respectively. In addition, compound 4 exhibits excellent inhibitory activity against tumor cell lines HCT-116 and MCF-7/ADR with IC50 values of 0.71 and 12.50 μM, respectively, indicating its potential application in agrochemical and pharmaceutical industry. Simultaneously, these results showed that the role of the macrocyclic scaffold of sansalvamides is essential for antifungal effect and the N-methylation of these chemicals could improve efficiency.

New insights into heterotrophic nitrification-aerobic denitrification during efficient pyridine degradation by Rhodococcus pyridinivorans WN2.

Steviol glycosides (SGs), intensely sweet diterpenoids found in Stevia rebaudiana (stevia), exhibit natural variation in composition that influences taste quality and commercial value. However, the genetic and cellular mechanisms underlying this variation remain poorly understood. We aimed to uncover how haplotype-level diversity and cell-type-specific gene expression contribute to SG profile diversity in stevia. We generated a chromosome-scale reference genome and conducted integrative multi-omics analyses combining haplotype-resolved population genomics, single-nucleus RNA sequencing, and imaging mass spectrometry. These approaches were applied to a diverse panel of breeding lines and a segregating population to associate genetic variants with SG composition and expression patterns. We identified a physically linked cluster of UGT76G glycosyltransferase genes whose structural and regulatory polymorphisms drive major differences in SG composition. Restricted expression of UGT91D4 to specific subsets of mesophyll and epidermal cells further constrained the biosynthesis of high-value SGs, such as rebaudioside D and rebaudioside M. Functional divergence among UGT76G paralogs was supported by sequence, expression, and structural modeling data. Our findings define a multi-allelic and spatially coordinated regulatory architecture underlying SG biosynthesis in stevia. These insights provide a foundation for haplotype-guided breeding and metabolic engineering strategies aimed at improving stevia sweetness quality and yield.

The complex pathophysiological mechanism of end-stage renal disease (ESRD) has not been fully understood. Cuproptosis is a newly discovered type of programmed cell death. Therefore, this study attempts to clarify the relationship between cuproptosis-related genes (CRGs) and the phenotype of ESRD. The National Center for Biological Information Gene Expression Omnibus database was applied to obtain the GSE37171 dataset comprising whole-genome microarray analysis of peripheral blood samples. A 3:1 case-control design was employed with 75 ESRD patients and 20 healthy controls who were frequency-matched for age, sex, and ethnicity. Based on differentially expressed genes (DEGs) and genes related to cuproptosis, CRGs were identified. Thereafter, we explored two different subpopulations based on the cuproptosis gene and analyzed their expression and immune infiltration. Genes specific to the CRG cluster were identified through the weighted gene co-expression network analysis algorithm, and the best prediction model was determined and verified by four machine learning methods. The study identified 14 differentially expressed CRGs, among which ATP7B, SLC31A1, LIAS, LIPT1, DLD, MTF1, CDKN2A, DBT, and DLST had relatively high expression levels in the ESRD samples. Compared with the control group, expression levels of FDX1, DLAT, PDHA1, PDHB, and GLS were significantly lower in the ESRD group, and CRGs played a key role in the regulation of immune infiltration in ESRD. Two cuproptosis-related molecular clusters were identified in the ESRD samples. Cluster2 was more correlated with the immune infiltration of ESRD. By analyzing the intersection points between CRG cluster and key genes of ESRD, a total of 888 specific DEGs were identified. Functional differences related to specific DEGs were further explored using gene set variation analysis. Five significant genes (SMC5, USP47, USP53, AGA, and DMXL1) were identified by the support vector machine model as key predictors for ESRD disease risk, achieving an area under the curve (AUC) of 1.00 in internal validation. However, external validation in independent cohorts is required prior to clinical application. Individual gene analysis showed an AUC >0.81 in discriminating ESRD patients from healthy controls, and the expression of all 5 genes in ESRD patients was significantly lower than in the control group. This study clarified the relationship between CRGs and the phenotype of ESRD, analyzed their specific roles in the immune microenvironment, and obtained a predictive model, providing new insights for the study of its potential therapeutic targets.

Bacillus velezensis HZ33, isolated from the potato rhizosphere, exhibits significant inhibitory activity against Rhizoctonia solani AG-3, the pathogen causing potato black scurf. To determine the antifungal compounds responsible for this inhibitory effect, we optimized the fermentation process and conducted bioassay-guided fractionation. Whole-genome sequencing revealed that this strain harbors 12 known biosynthetic gene clusters for secondary metabolites, indicating substantial biosynthetic potential. To enhance the yield of antifungal substances, single-factor experiments and response surface methodology were used to optimize the fermentation conditions. Among the crude extracts obtained from fermentation supernatant, the hydrochloric acid-precipitated fraction exhibited the strongest antifungal activity. This extract was fractionated by Mitsubishi Chemical Industries gel column chromatography and Sephadex gel chromatography, purified by high-performance liquid chromatography, and characterized by high-resolution mass spectrometry and nuclear magnetic resonance. Two cyclic lipopeptides (marihysin A and B) and 10 surfactin derivatives were identified. Notably, this is the first report of marihysin A and B in B. velezensis. Among these, marihysin B showed the highest yield (43.04 mg L-1) and the strongest antifungal activity against R. solani AG-3, with an EC50 of 9.78 μg mL-1. Furthermore, marihysin B demonstrated preventive and curative efficacy against potato black scurf. Its primary mechanism of action involves disrupting hyphal structure and cell membrane integrity, as well as inducing the accumulation of reactive oxygen species. This study presents the first evidence that marihysin B, the most active constituent of B. velezensis HZ33, has strong biocontrol potential against the potato black scurf pathogen, providing a basis for developing new biocontrol agents and fungicide lead compounds. © 2026 Society of Chemical Industry.

The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts-natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as 'greenbeards' (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.

Multifaceted metabolic engineering of Streptomyces hygroscopicus for milbemycins overproduction.

Fungal ribosomally synthesized and post-translationally modified peptides (F-RiPPs): Biosynthesis, genome mining, structural diversity, and translational potential as targeted anticancer ADC payloads.

Cyanobacteria, among the most ancient and versatile microorganisms on Earth, thrive across different aquatic ecosystems, ranging from freshwater to marine environments. In addition to being important producers of structurally diverse secondary metabolites, these photosynthetic prokaryotes are crucial to the global cycling of carbon and nitrogen. With their wide range of biological activities, such as antibacterial, antiviral, anticancer, and anti-inflammatory properties, cyanobacterial metabolites are attractive options for use in biotechnology and medicine. In addition, some cyanometabolites have toxic properties that affect aquatic ecosystems and present problems for human health and water quality. This dual significance for ecology and biomedicine emphasizes how crucial it is to do systematic research on cyanobacterial metabolites. The chemical diversity, biological roles, and biosynthetic origins of cyanobacterial secondary metabolites are summarized in this review, with a focus on their translational potential and ecological responsibilities. Innovative approaches for accelerating metabolite discovery and characterization are also covered, including recent developments in metabolite profiling, genome mining, and artificial intelligence (AI)-assisted biosynthetic gene cluster prediction. The present review integrate ecological, biochemical, and computational perspectives emphasizes the cyanobacteria is ongoing significance as sources of bioactive chemicals for environmental sustainability, pharmaceutical research, and biotechnology.

Towards the targeted activation of silent biosynthetic gene clusters by chemical elicitors.

Development of a GMO-free de novo lager yeast with reduced phenolic off-flavor production through interspecific hybridization and UV mutagenesis.

Soil microbial communities play a pivotal ecological role in contaminated environments. However, conventional metagenomic approaches struggle to distinguish between "potential function holders" and "in situ metabolically active executors". Here, we employed a method combining fluorescent d-amino acid labeling, fluorescence-activated cell sorting, and metagenomics (FDAA-FACS-Metagenomics) to capture and profile active microbes in complex soils. The secondary addition of As(V) and Sb(V) enhanced the community's reductive activity toward these metalloids, reshaping the active assemblages. Clostridium was markedly enriched, and several low-abundance members were activated as true executors of the reduction process. MAGs recovered via FDAA-FACS revealed an active core community with functional partitioning: some taxa participated directly in As(V)/Sb(V) reduction, while others contributed to community stability through tolerance and metabolic support. Notably, a Desulfitobacteriaceae genome (MAG29) harbored both arrAB and anrAB gene clusters, a complete Wood-Ljungdahl carbon fixation pathway, and nitrogen fixation genes. These genomic features suggest the potential for a multifunctional metabolic lifestyle involving metalloid reduction, carbon fixation, and nitrogen transformation. Such metabolic versatility may enable MAG29 to contribute to coupled carbon-nitrogen cycling and metalloid transformation under contaminated environmental conditions. These findings emphasize the important ecological roles of rare, metabolically active microbes in metalloid transformation and soil ecosystem functioning.

This study aimed to isolate and characterize autochthonous lactic acid bacteria (LAB) from naturally fermented yak milk (NFYM) in the western Sichuan Plateau, focusing on their ability to metabolize diverse prebiotic oligosaccharides and their potential as synbiotic starter cultures with probiotic properties. Twenty LAB isolates representing eight species were obtained from eleven NFYM samples. Metabolic screening revealed strain- and species-specific utilization of seven prebiotic oligosaccharides. Leuconostoc pseudomesenteroides YT830 efficiently metabolized fructo- (FOS), xylo- (XOS), and isomalto-oligosaccharides (IMO), reducing pH to 5.13, 4.66, and 5.12, respectively, after 72h. Whole-genome sequencing (2.17 Mbp, 2 244 CDSs) identified 60 carbohydrate-active enzymes and 182 genes involved in carbohydrate transport and metabolism, along with multiple gene clusters for oligosaccharide degradation. Strain YT830 exhibited promising in vitro survival rates in simulated gastric (68.3%) and intestinal (90.7%) fluids, strong DPPH (95.9%) and hydroxyl radical (87.4%) scavenging, and antimicrobial activity against Escherichia coli and Staphylococcus aureus, and no transferable antibiotic resistance genes. Leu. pseudomesenteroides YT830 combines versatile oligosaccharide metabolism with favorable in vitro probiotic properties and a favorable safety profile, supporting its application as a starter culture for synbiotic fermented yak milk products.

Secondary metabolites as multifunctional molecular weapons: New mechanistic insights into how entomopathogenic fungi suppress insect immunity.

Iron deficiency limits legume production on calcareous soils, and commonly used synthetic iron chelates (e.g., Fe-EDTA) are effective but non-biodegradable and may mobilize toxic metals. Microbial siderophores offer an environmentally sound alternative, yet their direct application as biofertilizers remains underexplored. Here, we evaluated the iron-carrying siderophore produced by Amycolatopsis lurida strain 407 as a biofertilizer for chickpea. Siderophore extracts were quantified and characterized by the CAS assay, Fe (III)-ICP-OES, Arnow and FeCl₃ tests, UV-Vis spectroscopy, and genome mining (antiSMASH). Results indicate strain 407 secretes a mixed catecholate-hydroxamate siderophore whose UV-Vis spectrum (200-600nm) matches mirubactin C and is supported by a mirubactin-like biosynthetic gene cluster in its closest type strain. When applied to chickpea, the Fe + siderophore from strain 407 increased root dry weight and yielded the highest shoot biomass (28g/ plant), pod/plant (41 pods), and seed/pod (36 seeds), outperforming chemical iron fertilizer, Fe-EDTA/ Sequestrin 138 (22g, 24 pods, 24 seeds). Furthermore, seed soluble protein (20mg/g dry seed) was 17% higher than with Sequestrin 138. In this study, for the first time, findings show the mirubactin-like Fe-siderophore from A. lurida 407 enhances plant growth and seed quality and represents a promising, eco-friendly alternative to synthetic iron fertilizers.

Double-edged sword: Aspergillus flavus as a threat to food safety and a resource for biotechnology.

Echinocandin B (ECB), a fungal non-ribosomal lipopeptide, serves as the exclusive natural precursor of the front-line antifungal anidulafungin. Despite its clinical importance, ECB production remains suboptimal due to incomplete understanding of its biosynthesis mechanism. The global regulator LaeA has been implicated in secondary metabolite production, yet its specific role in ECB biosynthesis remains unexplored. To address this, we successfully constructed laeA deletion and overexpression strains, and demonstrated that LaeA functionally couples morphological development with ECB productivity. Transcriptomic analysis revealed LaeA directly activated the sterigmatocystin cluster via pathway-specific regulator AflR, but indirectly influenced ECB through iron-heme cofactor synchronization rather than direct gene cluster activation. LaeA overexpression upregulated siderophore iron transporters and heme biosynthetic genes, with supplementation of Fe2 + or 5-ALA further boosting titers to 2487 ± 123 and 2697 ± 16mg/L, respectively. To overcome P450s catalytic constraints, we screened out a novel cytochrome P450 reductase CPR2 as the optimal redox partner. Co-expression of CPR2 with bacterial hemoglobin VHb achieved synergistic enhancement, improving the ECB titer to 3170 ± 41mg/L. This study provided a practical strategy for improving ECB production and offering insights into the versatile regulatory modes of global secondary metabolite regulators.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) continue to provide a rich source of structurally diverse and bioactive natural products, yet radical S-adenosylmethionine (rSAM)-catalyzed C-C bond formation remains unexplored in lanthipeptide biosynthesis. Here, we report the discovery of azepinopeptide A, a new class of lanthipeptides featuring an unprecedented tetrahydropyrrolo[1',2':1,2]azepino[3,4-b]indole scaffold formed through rSAM-catalyzed cross-linking of adjacent Trp1 and Pro2 residues. This unusual sp2-sp3 C-C bond formation, which has not been observed in any previously characterized rSAM enzyme-catalyzed RiPP, is mediated by a distinct subclass of lanthipeptide rSAM enzymes. Biochemical reconstitution and mutational analyses demonstrate that these enzymes exclusively recognize the mature, leader-free lanthipeptide substrate and lack both the RiPP recognition element and the auxiliary iron-sulfur cluster that are essential in other RiPP rSAM systems. Computational structural analysis, supported by in vivo co-expression studies, reveals a specialized binding pocket capable of accommodating the lanthipeptide substrate and positioning the catalytic [4Fe-4S] cluster deep within the pocket. This arrangement provides a basis for the observed regioselectivity and strict requirement for leader peptide removal. Azepinopeptides A and B exhibit potent neuroprotective activity at low concentrations comparable to that of the positive control, 3-n-butylphthalide. Bioinformatic analyses further uncover hundreds of related biosynthetic gene clusters, highlighting the prevalence of this biosynthetic strategy. Together, these findings expand the catalytic repertoire of rSAM enzymes and introduce a new platform for the biosynthetic generation of medium-sized ring peptide architectures with therapeutic potential.