Search Results (413)

Nitzschia sp., a diatom isolated from Paposo (Antofagasta, northern Chile), was evaluated as a biological solution for removing kaolinite-type clay minerals from recycled process water in large-scale copper mining. Optimization of culture conditions to maximize extracellular polymeric substance (EPS) production revealed that supplementing with 0.1 gL⁻¹ of glucose yielded the highest EPS levels on day 17, reaching 1285 ± 58.9 mgL⁻¹ (control equal to 237.8 ± 34 mgL⁻¹ on day 17). However, maximum dry weight biomass productivity was achieved in the presence of sodium carbonate at a concentration of 1 gL⁻¹ (319 ± 12.5 mgL⁻¹d⁻¹), significantly exceeding the productivity of the control group (242.7 ± 5.4 mgL⁻¹d⁻¹). Notably, low glucose supplementation enhanced EPS synthesis. Application of control-derived EPS of 1 gL⁻¹ rapidly decreased kaolinite initial turbidity from ~2024 FNU to ~354 ± 0.74 FNU within one minute. Even more glucose-derived EPS (1 gL⁻¹) further reduced turbidity to ~22.2 ± 0.1 FNU at 5 min, achieving a flocculation efficiency of ~98.9% after 15 min. Genomic analysis and KEGG annotation identified abundant genes for EPS and carbohydrate metabolism, including numerous glycosyltransferases, glycoside hydrolases, and multiple copies of UDP-glucose 4-epimerase, consistent with strong polysaccharide-biosynthesis capacity. Physicochemical characterization (particle sizing, HPLC, SEM, zeta-potential and FT-IR) showed EPS comprised mainly of rhamnose, fucose, arabinose, xylose and glucose, featuring functional groups (–OH, C=O/COO–, O-acetyl, uronic/guluronic signatures) that interact with kaolinite to promote aggregation. These findings demonstrate that Nitzschia-derived EPS, especially from glucose-supplemented cultures, represent promising sustainable bioflocculants for treating kaolinite-contaminated recycled water in mining operations. Full article

Artisanal raw milk cheeses harbour complex microbial communities that drive cheese making and shape sensory quality. Previous work on Idiazabal cheese identified rennet as a major microbial source, although all reservoirs contributed to varying degrees. However, their impact in terms of enzyme-encoding genes related to technological quality of cheese remained unexplored. Building on that, this study draws on metagenome-assembled genomes (MAGs) from cheeses and dairy environments to comprehensively identify enzyme-encoding genes involved in key biochemical processes. In cheese MAGs (Lacticaseibacillus paracasei), protease-encoding genes were dominated by ATP-dependent metalloproteases (M41), carbohydrate-active enzyme-encoding genes (CAZymes) by glycoside hydrolases (GH) and glycosyltransferases (GT), while esterase, lipase, and related-enzyme-encoding genes were restricted to sparse ‘GDXG’, type-B and esterase D families. Dairy environments emerged as major reservoirs of enzyme-encoding genes, with notable differences among sample types (p ≤ 0.001). The richest sources of protease-encoding genes were grass (610 genes), linked primarily to Pantoea agglomerans, and rennet (318), mainly related to Basfia sp. and Moraxella sp., dominated by metalloproteases (M23, M38) and serine proteases (S15). The largest reservoirs of CAZyme-encoding genes were food contact surfaces (1550), associated mainly with Salinisphaera sp. and Dietzia sp., and rennet (1505), related to, e.g., Bacteroides pyogenes, Alloprevotella sp., and Lentilactobacillus buchneri. Food contact surfaces were also the richest source of esterase, lipase and related-enzyme-encoding genes (1209), mainly linked to Dietzia sp., Corynebacterium sp., and Brevibacterium aurantiacum. Similarly, aroma-related enzyme-encoding genes (e.g., oppA, pepA, GH13, esterase D) were consistently detected in environmental matrices. These results provide novel insights into dairy microbiomes as functional reservoirs of aroma precursors, revealing their relevance for artisanal PDO cheese production and future biotechnological applications. Full article

Daqu is the core saccharifying and fermenting agent in Baijiu production and a pivotal factor in flavor formation. Challenges that often hinder traditional strong-flavor Daqu brewing include low enzymatic activity and insufficient aroma. Therefore, we have developed a novel Daqu brewing system. Furthermore, we investigated the differences in flavor profiles between traditional and novel Daqu by performing headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). We comparatively analyzed the microbial communities, metabolic functions, and flavor compositions in the two Daqu types via absolute quantitative metagenomics. Functional microorganisms were significantly enriched in the novel Daqu, which exhibited enhanced carbohydrate metabolism and a highly robust acidic environment owing to the fostering of core functional genera such as Aspergillus, Saccharomyces, and Pediococcus. This significantly increased the aldehyde and organic acid levels, which resulted in pronounced aldehydic and acidic sensory characteristics. Carbohydrate-Active EnZyme (CAZy) profiling confirmed the significantly elevated abundance of glycoside hydrolases (GHs) and glycosyltransferases (GTs) in novel Daqu, which improved starch bioconversion and synthesis of flavor precursors. Thus, this study shows that novel Daqu promotes ethanol accumulation and the synthesis of flavor compounds like acetals by strengthening the core microbiota and metabolic networks. These findings provide a theoretical foundation for enriching the aromatic complexity of Baijiu. Full article

This study presents a high-quality chromosome-level genome assembly of Morchella sextelata (54.64 Mb, 26 pseudochromosomes) and systematically characterizes its genomic and evolutionary features. Phylogenetic analysis indicates that M. sextelata diverged early within the Morchella genus (~14.2 million years ago) and underwent substantial genomic remodeling, with 1124 expanded and 1961 contracted gene families. Enrichment analysis of rapidly expanded gene families highlights two prominent functional themes: genes associated with small molecule/ion binding and secondary metabolite biosynthesis, and genes linked to the Fanconi anemia pathway and DNA repair/recombination. Notably, 56.96% of the COG-annotated M. sextelata-specific genes encode retrotransposon-related proteins, and this enrichment coincides with the expansion of DNA repair systems—a pattern reminiscent of the “transposon domestication” model. Functional genomic analyses further reveal that the glycoside hydrolase system is dominated by GH5, GH43, and GH3 families, suggesting a predicted capacity for plant cell wall polysaccharide degradation, while 12 biosynthetic gene clusters indicate genetic potential for terpenoid and non-ribosomal peptide biosynthesis. These findings provide a valuable genomic resource for M. sextelata and offer new insights into the role of transposable element mediated remodeling in fungal genome evolution. Full article

The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe–phenotype association in waterfowl. Full article

The rumen microbiota plays a key role in nutrient fermentation and short-chain fatty acid (SCFA) production in ruminants. However, the impacts of different feeding regimes on rumen microbial composition, functional potential, and metabolic outputs remain unclear. In this study, rumen fluid samples were collected from 12 Longdong goats (Capra hircus), which were divided into four groups based on feeding regime and coat color: housed white goats (n = 3), housed black goats (n = 3), grazing white goats (n = 3), and grazing black goats (n = 3). Samples were analyzed using high-throughput sequencing combined with functional annotation (KEGG and CAZy) and targeted SCFA profiling. Distinct differences in microbial community composition were observed primarily between feeding regimes, with enrichment of taxa related to carbohydrate degradation and fermentation. Functional analyses revealed significant shifts in metabolic pathways, particularly those associated with carbohydrate metabolism, energy production, and glycan biosynthesis. Several glycoside hydrolase and glycosyltransferase families showed differential abundances across groups. Consistently, SCFA concentrations varied significantly among feeding regimes. Correlation analyses further demonstrated strong associations between key microbial taxa, functional pathways, and specific SCFAs. Overall, these results indicate that feeding regime, rather than coat color, plays a dominant role in shaping rumen microbial structure, functional capacity, and fermentation characteristics, providing insights into microbial mechanisms underlying rumen metabolism and informing feeding strategy optimization. Full article

Lentinula edodes (Berk.) Pegler, also known as Shiitake, is one of the most popular edible mushroom species containing high contents of polysaccharides, proteins and unique aroma, widely cultivated in China, Japan and Korea. A series of studies has been carried out on the extraction and active effect of the L. edodes polysaccharides, but the molecular mechanisms involved in the protein expression profiles during the whole life cycle are relatively unclear. This study employed an iTRAQ-MS/MS proteomic approach, combined with real-time quantitative PCR (qRT-PCR) and enzyme activity assays, to systematically analyze the protein expression profiles and their relationship with lignocellulose degradation in L. edodes across four key developmental stages: mycelia (SF), brown film formation (BF), primordia (YF), and fruiting bodies (MF). A total of 2043 proteins were identified, with 1188 being differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that metabolic processes, carbohydrate metabolism, and related pathways were significantly active during development. The study specifically focused on carbohydrate-active enzymes (CAZymes), identifying 197 CAZyme proteins classified into 78 families. Key families such as glycoside hydrolases (GHs) and carbohydrate esterases (CEs) played crucial roles in lignocellulose degradation. The enzymatic activities of major lignin-degrading enzymes (laccase, manganese peroxidase, and lignin peroxidase) were dynamically regulated across the developmental stages. qRT-PCR results largely corroborated the proteomic data, confirming the reliability of the protein expression profiles. This study provides a comprehensive, stage-resolved proteomic landscape of lignocellulose degradation during L. edodes development, revealing species-specific temporal dynamics, offering a valuable basis for understanding its growth and development, with implications for edible fungus cultivation and biomass conversion applications. Full article

This study investigated the impacts of diverse aeration processes (continuous aeration vs. intermittent aeration) and aeration rates on the aerobic composting process. The key properties examined include temperature, oxygen dynamics, lignocellulose degradation, humification, and the functional potential of carbohydrate-active enzymes (CAZymes) based on metagenomic analysis. Among all the treatments, continuous aeration at a low rate (CA_1.5) attained the highest level of lignocellulose degradation by balancing the thermophilic duration and oxygen supply. Conversely, intermittent aeration (IA_3) led to superior humus stabilization, with the ratio of humic acid to fulvic acid (H/F) increasing by 118.45% in comparison to the initial level. Low total ventilation in CA_1.5 and IA_3 facilitated an increase in the abundance of glycosyl transferases (GTs) genes. Notably, intermittent aeration (IA_3) synergistically augmented the activities of glycoside hydrolases (GHs) and GTs, propelling the efficient conversion of lignocellulose into stable humic substances. In conclusion, the aeration process influenced the functional potential of microbial CAZymes, thus exerting an influence on both the composting efficiency and the quality of the final product. Full article

Nigrospora musae ST1 is a newly identified pathogen responsible for leaf spot disease in Idesia polycarpa. In order to further advance our understanding of this strain and improve management strategies for the leaf spot disease, the PacBio Sequel II platform was used to perform whole-genome sequencing of N. musae ST1. The assembled genome comprised 42 contigs, with a total length of 49,259,803 bp and an average GC content of 56.23%. Functional annotation identified 12,063 protein-coding genes, including 125 Transporter Classification Database (TCDB)-related genes, 3600 pathogen host interaction (PHI) genes, 2503 Virulence Factor Database (DFVF)-related genes, and 722 genes encoding carbohydrate-active enzymes (CAZymes). Integrated analyses of the secretome, PHI, and DFVF databases revealed six secreted carbohydrate-active enzymes implicated in plant pathogenicity, including three glycoside hydrolases, two pectinate lyases, and one cutinase, potentially playing important roles in pathogenicity. A total of 77 secondary metabolite gene clusters were predicted. Comparative genomic analysis between N. musae ST1 and other Nigrospora species revealed differences in genome rearrangements in Nigrospora fungi. In conclusion, this study has clarified the whole-genome structural characteristics and evolutionary relationships of the newly reported pathogenic fungus, N. musae ST1. It provides a theoretical foundation for future investigations into the pathogenic mechanisms of N. musae ST1 infection in I. polycarpa, as well as potential targets for disease control. Full article

Acidic chitinase (Chia) degrades chitin, a structural polysaccharide in insect exoskeletons, and plays important roles in omnivorous and insectivorous mammals and birds. In birds, gene duplications have generated multiple Chia paralogs with functional divergence, but the molecular basis for this diversification remains unclear. Here, we characterized three chicken Chia paralogs (Chia1–3) and identified distinct pH-dependent enzymatic profiles. Chia1 is enzymatically inactive but was captured by chitin-affinity resin despite lacking a canonical chitin-binding domain, suggesting residual substrate interaction through the catalytic domain or a non-catalytic role. Chia2 exhibits maximal activity at pH 2.0, whereas Chia3 peaks at pH 5.0 and displays broader activity. Exon swapping and site-directed mutagenesis identified residues 104 (Ala in Chia2, Asp in Chia3) and 269 (His vs. Asn) as key contributors to pH-dependent activity differences. Reciprocal substitutions shifted pH profiles accordingly. Structural modeling and computational pKa predictions suggested that D213 and residue 269 may function as a pKa-regulating module influencing catalytic ionization. Comparative sequence analysis revealed lineage-specific conservation of these residues, consistent with adaptive divergence. Our findings show that limited amino acid substitutions can markedly modify pH-dependent enzymatic activity, providing mechanistic insight into how local residue variation contributes to the functional diversification of duplicated genes. Full article

The highly chitinolytic marine bacterium Vibrio jasicida KMM 6832, which exhibits potent antifungal activity, possesses an atypical Glycosyl Hydrolase family 19 (GH19) chitinase (ChitVjs). This is the first report of a GH19 gene in V. jasicida, an enzyme generally absent in this species and rare within the Harveyi clade. Phylogenetically, ChitVjs-like enzymes from the genera Vibrio and Aeromonas form a distinct cluster, separate from typical plant and bacterial GH19 counterparts. Despite high sequence identity (80–94%) with characterized homologs from V. parahaemolyticus and V. cholerae, ChitVjs is distinguished by its obligate halophilicity (optimum 0.3–0.4 M NaCl), an acidic isoelectric point (pI 4.72), and a broader cation-activation profile (K⁺, Ni²⁺, Ca²⁺, Cu²⁺, Co²⁺). The recombinant ChitVjs was produced in E. coli as a soluble 63 kDa protein. It functions as a stable, salt-dependent endo-chitinase/chitosanase, exhibiting optimal activity at 40 °C and pH 7.0. The enzyme displays high affinity for colloidal chitin (K_M 0.377 mg·mL⁻¹), is activated by DTT and Tween 80, and shows moderate stability in organic solvents. Furthermore, unlike its primarily catabolic relatives, ChitVjs suppresses conidial germination in marine-derived Aspergillus strains. These findings suggest that ChitVjs significantly contributes to the competitive fitness of V. jasicida KMM 6832 in high-salinity marine environments through both nutrient acquisition and antagonism. Full article

Cypripedium shanxiense S. C. Chen has high ornamental value; it relies on specific habitats and fungi. Wild C. shanxiense populations need urgent conservation because they are declining rapidly. This study investigated three wild C. shanxiense populations under different canopy densities in the Changbai Mountains, analyzing habitat characteristics and plant morphology. Tissue isolation methods, molecular identification techniques, and metagenomic approaches were applied separately to purify root-colonizing fungi and to investigate the composition and functions of rhizosphere fungi, thereby revealing the diversity of root mycobiome in C. shanxiense. Results revealed that C. shanxiense achieved the best growth when the canopy density was 85.29%, and the lowest growth was under 96.13% canopy density. Soil phosphorus and potassium contents reached their highest levels under 69.33% canopy density, while soil nitrogen and organic matter contents peaked at 85.29%. Soil organic matter and available nitrogen constitute the core nutrient factors for the growth of C. shanxiense. A total of 16 fungal strains were mainly enriched in the roots, all belonging to Ascomycota. Including numerous growth-promoting fungi and pathogenic fungi. The rhizosphere fungi were mainly enriched with Basidiomycota and Ascomycota. Functional genes related to replication, recombination, and repair, and Glycoside Hydrolases. This study clarifies the optimal growth conditions of this species and the dominant rhizosphere and root fungi, providing a scientific basis for the ecological restoration and conservation of rare species. Full article

Rural black-odorous waterbodies (RBOWBs) represent a critical environmental challenge in China, yet the vertical stratification of sedimentary bacterial communities and its underlying drivers remain poorly understood. This study combined 16S rRNA gene amplicon sequencing across five sediment depths (0–125 cm) with shotgun metagenomic analysis of surface sediments to investigate bacterial diversity, composition, and functional potential in typical rural black-odorous systems of Dongming County, Shandong Province. Results showed a clear decline in bacterial richness with increasing sediment depth, with the surface layer (0–25 cm) exhibiting 1.2–1.9 times higher diversity than deeper strata. Community composition displayed distinct vertical zonation: Chloroflexi and Thiobacillus dominated surface layers and were linked to carbon hydrolysis and desulfurization, whereas Bacillus and nitrifying bacteria prevailed in deeper anoxic layers. Metagenomic analysis revealed high genetic potential for carbohydrate metabolism, amino acid biosynthesis, and sulfur-nitrogen cycling, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) being particularly abundant. Statistical correlations identified total phosphorus (TP₁), dissolved oxygen (DO), and pH of the overlying water—rather than sediment intrinsic nutrients—as the primary environmental factors associated with microbial functional stratification. These findings provide a mechanistic understanding of vertical microbial zonation in rural black-odorous sediment and offer a microbiological basis for developing depth-resolved sustainable remediation strategies. Full article

Two marine bacteria, designated strains 4Alg 33^Tand 3Alg 14/1, were isolated from brown (Saccharina japonica) and green (Ulva fenestrata) macroalgae, respectively. These isolates were aerobic Gram-negative rods exhibiting a gliding motility. The 16S rRNA gene phylogenetic analysis clearly showed their belonging to the genus Formosa, the family Flavobacteriaceae, and the phylum Bacteroidota. The closest relatives of the new strains were Formosa undariae KCTC 32328^T (99.05%), Formosa arctica IMCC 9485^T (99.05%) and Formosa agariphila KMM 3901^T (98.96%). The ANI and dDDH values between the two new strains were 97.9% and 85.3%, respectively. The AAI values between 4Alg 33^T and Formosa type strains ranged from 80.1% (Formosa haliotis MA1^T) to 91.4% (F. undariae KCTC 32328^T). The cellular fatty acid and polar lipid profiles of the new isolates were generally similar to those of the type strains of Formosa species. The genomes of 4Alg 33^T and 3Alg 14/1 are represented by a circular chromosome of 4,157,724 bp and 4,316,096 bp in size with 3536 and 3879 protein-coding genes, respectively. They shared a DNA G+C content of 34.3 mol% and comprised four rrn operons. The pangenome of the genus Formosa belongs to the open type and is characterized by an abundance of CAZymes. The proportion of CAZyme genes in novel genomes was more than 5%, with a prevalence of glycoside hydrolase genes, suggesting great potential for utilizing marine-derived polysaccharides. Based on the results of polyphasic characterization, the two algal isolates represent a distinct species lineage within the genus Formosa, for which we propose the name Formosa bonchosmolovskayae sp. nov. with the type strain 4Alg 33^T (= KMM 3963^T = KCTC 72008^T). In addition, we have proposed to transfer Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 to the genus Xanthomarina Vaidya et al. 2015 as Xanthomarina maritima comb. nov. and Xanthomarina arctica comb. nov. based on a combination of the genomic and phenotypic characteristics. Full article

For 12 isolates of Ilyonectria mors-panacis and 4 isolates of Ilyonectria robusta, the number of genes in the secretome showed a negative correlation with growth rates in culture, especially for small secreted non-cysteine-rich and cysteine-rich proteins, and several proteases and lipases, while it was positively correlated with genes for six CAZyme classes/modules and other proteases and lipases. However, this significant correlation with growth rate was influenced by the I. robusta isolates mostly having faster growth rates than the I. mors-panacis isolates on PDA, indicating a species-level difference. The only significant relationship of gene number to virulence was a positive correlation with genes for secreted glycoside hydrolases in families 18 and 78, and this was related to differences between isolates, even if only I. mors-panacis isolates were examined, indicating a difference within species. Glycoside hydrolase family 18 includes chitinase-like proteins, endo-β-N-acetylglucosaminidases, lectins, and xylanase inhibitors, which could help suppress triggered immunity by the host and regulate fungal xylanase activity. Glycoside hydrolase family 78 contain α-L-rhamnosidases that can cleave flavonoid glycosides, saponins, and ginsenosides, which could degrade antimicrobial compounds produced as a host response during infection. These results indicate that the number of certain classes of secreted enzymes could be a factor in both growth rate in culture and virulence. Full article