Search Results (367)

Koji production is a critical process that determines the flavor and quality of the final soy sauce product. However, the complex mechanisms underlying microbial metabolism and the evolution of the physicochemical environment still require further analysis. This study focuses on three parallel koji rooms in an industrialized koji fermentation process. This work tracked the dynamics of physicochemical indices, volatile flavor compounds, and microbial communities over a full 40 h cycle. Data integration and correlation analysis elucidated the close linkage between the microbial community, the fermentation environment, and flavor formation. Koji moisture declined gradually, with faster losses at later fermentation stages. This physiological dehydration arose from microbial metabolic heat, forced aeration and structural loosening of koji, not simple physical evaporation. System pH displayed a typical U-shaped trend across fermentation. Values dropped early, most likely driven by accumulating organic acids, before rising from mid to late fermentation. This pH rebound was tentatively attributed to ammonia release from proteolytic breakdown, which may neutralize acidic compounds. These observations cast doubt on the conventional assumption that organic acid levels may be reliably estimated solely from pH measurements. Physicochemical analysis showed continuous accumulation of amino acid nitrogen (0.6–0.9 g/100 g) and total acidity throughout fermentation. By contrast, reducing sugar concentrations differed across individual koji rooms, presumably owing to divergent microbial adaptation in early fermentation. A total of 77 common compounds were identified, among which 13 key odor-active compounds with OAV ≥ 1, such as 4-vinylguaiacol and 3-methylbutyraldehyde, constitute the characteristic flavor profile of soy sauce starter culture. High-throughput sequencing uncovered a distinct ecological pattern: eukaryotic communities, dominated by Aspergillus oryzae, converged under controlled regulation. While prokaryotic communities differentiated dynamically, driven by spatial heterogeneity in the semi-open fermentation environment. Spearman correlation analysis further indicated potential functional partitioning: high-abundance taxa (e.g., Aspergillus oryzae, Weissella) were predominantly associated with macromolecular substrate degradation, whereas rare low-abundance taxa (e.g., Alternaria) displayed significant correlations with the biosynthesis of key characteristic flavor compounds. This study clarifies the synergistic regulatory mechanisms linking physicochemical conditions, microbial metabolism, and flavor precursor formation during industrial koji production. The findings establish a scientific foundation for optimizing process parameters and achieving standardized quality control in soy sauce manufacturing. Full article

Benthic prokaryotic communities in deep-sea sediments remain poorly studied. They are constrained by organic matter availability and oxygenation in warm deep-sea ecosystems. Here, we investigated benthic prokaryotic communities and carbon uptake in deep Red Sea sediments (218–2415 m seafloor depth), where persistently warm (~21.5 °C) waters and a strong south–north productivity gradient co-occur. Sediment particulate organic carbon (POC), prokaryotic abundance (PA), and [¹³C]-D-glucose-based carbon uptake and uptake kinetics were examined in two sediment layers (0–1 and 4–5 cm), while bacterial communities were characterized using 16S rRNA gene sequencing of the 0–1 cm layer. Sediment POC, PA, and carbon uptake declined northward, consistent with reduced organic-carbon supply to the seafloor. Bacterial community composition differed significantly across the ~500 m depth associated with the Red Sea oxygen minimum zone (OMZ). Sediments from the relatively low-oxygen upper OMZ-range (200–500 m) had higher sediment POC and PA, and were enriched in putatively anaerobe-associated taxa, whereas deeper sediments (>500 m) below the OMZ exhibited more fragmented co-occurrence networks. These results suggest that organic-carbon availability defines the basin-scale metabolic backdrop, whereas bacterial community differentiation was more clearly resolved between upper OMZ-range and below-OMZ sediments than along latitude alone. Full article

Microbial functional traits play a central role in regulating carbon mineralization efficiency (CME) in peatlands, yet how they respond to concurrent warming and atmospheric nitrogen deposition remains unclear. In this study, peat soils from three vegetation types (sedge, reed, and shrub) were subjected to controlled microcosm incubations simulating warming and nitrogen addition gradients. Microbial community composition and functional profiles were characterized using 16S rRNA high-throughput sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX) functional prediction, while dissolved organic matter (DOM) composition was analyzed via excitation–emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC) and fluorescence indices. Integrating correlation analysis, Random Forest, and partial least squares path modeling (PLS-PM) modeling, we identified microbial functional traits as key factors linking environmental changes to soil CME, with DOM serving as a substrate-mediated pathway. External nitrogen input primarily drove shifts in microbial functional composition, whereas warming modulated substrate utilization preferences and DOM turnover. The interaction between warming and nitrogen selectively reshaped microbial functional profiles, thereby jointly determining CME. Functional traits explained more variation in CME than taxonomic composition, indicating a “structure–function decoupling” under environmental change. These findings highlight the central role of microbial functional traits in peatland carbon transformation and suggest that the net response of peatland carbon emissions to future environmental change will depend critically on the balance between warming magnitude and nitrogen deposition levels. Full article

Nile tilapia (Oreochromis niloticus) is a major aquaculture species worldwide, yet bacterial infections remain a critical constraint to production sustainability. Although pathogen-associated dysbiosis has been widely described, most studies have focused exclusively on bacterial communities, overlooking the multi-kingdom nature of the intestinal microbiota. This study evaluated the impact of experimental Providencia vermicola infection on both prokaryotic and microeukaryotic intestinal communities under controlled conditions. Using 16S (V3–V4) and 18S (V9) rRNA amplicon sequencing, we compared healthy and infected fish and assessed taxonomic, structural, and predicted functional changes. Infection was associated with significant compositional shifts, including increased relative abundances of Bacteroidota and Proteobacteria and decreased relative abundances of Fusobacteriota and Patescibacteria. Concomitantly, microeukaryotic groups such as Protalveolata, Nematozoa, and Phragmoplastophyta were significantly reduced. Functional prediction revealed metabolic pathway reconfiguration consistent with infection-associated ecological disturbance. Together, these results suggest that the pathogen challenge is associated with coordinated changes in the intestinal microbiota as an integrated system across multiple microbial kingdoms rather than as isolated bacterial shifts. This study supports ecosystem-level interpretations of dysbiosis and highlights the importance of incorporating cross-domain analyses into health assessment strategies in aquaculture species. Full article

The application of nitrification inhibitors (Nis) with nitrogen fertilizers is increasingly used as a management strategy to improve nitrogen use efficiency in crop production systems. To evaluate the effects of Ni dicyandiamide (DCD) and 1,2,4-triazole (TZ) on the rhizosphere microbiome and strawberry yield (Fragaria × ananassa Duch.), a two-year field experiment was conducted with three treatments: unfertilized control (C), mineral nitrogen fertilizer (N) applied in two doses (40 + 40 kg N ha⁻¹ year⁻¹), and a single nitrogen application (80 kg N ha⁻¹ year⁻¹) combined with nitrification inhibitors (N + Ni). Soil microbiota were assessed using cultivation-based methods and metabarcoding of 16S rRNA and ITS2 regions. Total bacterial counts on complex media increased from 5.85 to 6.15 log CFU g⁻¹ in the N treatment, while remaining 5.89 in N + Ni. Microscopic fungi increased in fertilized treatments during spring but decreased in July of the second year. Microbial community composition differed among treatments, although sampling time explained a larger proportion of variability than fertilization. Relative abundance of Gemmatimonas decreased under N + Ni, whereas Nitrososphaera increased. Fungal Shannon diversity decreased in N + Ni, while prokaryotic diversity did not differ significantly. Despite similar levels of mineral nitrogen measured before harvest, strawberry yield increased significantly in the N + Ni treatment in the second year, reaching 109% higher values than the control and 80% higher than the N treatment. This may indicate that the fertilization regime including nitrification inhibitors influenced nitrogen availability earlier in the growing season. Full article

The combined effects of organic pollutants and vertical soil gradients on microbial community assembly in long-term contaminated sites remain insufficiently understood. In this study, high-throughput sequencing was employed to characterize prokaryotic communities across depth-resolved soil profiles at a contaminated site in Tianjin, China. Microbial diversity, taxonomic composition, and predicted functional traits varied significantly with soil depth and pollutant distribution. Surface soils exhibited higher richness and diversity, with Shannon, Sobs, and PD indices decreasing with depth (p = 0.020, p = 0.002, and p < 0.001, respectively). Redundancy analysis showed that the first two axes explained 89.91% of the total variance, indicating strong associations between microbial community structure and environmental variables. Community differentiation was related to pollutant type, with aromatic hydrocarbons more strongly linked to surface assemblages and chlorinated compounds associated with deeper horizons. Although the overall abundance of predicted metabolic genes decreased with depth, the distribution of major functional categories, including pathways related to organic matter degradation, remained comparatively stable. Co-occurrence network analysis revealed a progressive decline in network connectivity and complexity along the vertical gradient, with the number of edges decreasing from 853 (L1) to 447 (L3) and average degree decreasing from 16.404 to 9.122. These findings highlight depth-related environmental filtering as a key mechanism structuring microbial communities under long-term organic contamination and provide a scientific basis for optimizing depth-specific in situ bioremediation strategies, such as targeting aromatic hydrocarbon degradation in surface soils and chlorinated compound remediation in deeper layers. Full article

The study of microorganisms inhabiting extreme environments offers a valuable opportunity to explore their potential ecological roles. This study aimed to reveal and compare the microbial taxonomic diversity of largely unexplored permafrost regions located in different climatic zones (dry and wet) in the Chilean Andes, separated by thousands of kilometers. Permafrost active layer samples were collected from the Ojos del Salado (Atacama Desert) and the Torres del Paine (Patagonia) from different sampling depths. Illumina 16S rRNA gene-based amplicon sequencing revealed that the Andean permafrost active layer provides diverse habitats for distinct microbial communities, with higher taxonomic diversity of Bacteria than Archaea. The wet Patagonian Andes samples showed higher diversity, with a greater abundance of Chloroflexota and Bacteroidota, while the dry Ojos del Salado samples were dominated by Actinomycetota, indicating desiccation stress. Archaea were classified as ammonia-oxidizing members of the Thermoproteota phylum. Beta-diversity analyses suggested that differences in environmental conditions (mainly available moisture) contributed more to community structure differentiation than geographical distances. Nevertheless, the effect of sampling depth on microbial diversity was insignificant. Full article

Background/Objectives: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation. Methods: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3–V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect. Results: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed. Conclusions: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players. Full article

The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats. Full article

“Rotten” sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season. Full article

Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery. Full article

Hot springs represent unique geothermal ecosystems where extreme physicochemical conditions intersect with remarkable microbial diversity and metabolic innovation. These natural laboratories harbor specialized communities of thermophilic and hyperthermophilic microorganisms that have evolved exceptional adaptations to elevated temperatures, extreme pH, and high salinity. This review synthesizes current understanding of hot spring systems as multifunctional natural resources, examining their roles in fundamental microbiology, biotechnology, and sustainable development. We explore the ecological principles governing microbial community assembly, the taxonomic and functional diversity of prokaryotic and eukaryotic microorganisms, and the genomic mechanisms underlying thermophilic adaptation. Hot springs yield enzymes revolutionizing molecular biology and industrial catalysis, bioactive metabolites with pharmaceutical potential, and novel bioremediation capabilities including plastic degradation. Beyond biological significance, these systems contain valuable minerals and rare earth elements, supporting an emerging bioeconomy integrating wellness tourism, bioprospecting, and sustainable resource extraction. However, critical knowledge gaps remain regarding viral ecology, horizontal gene transfer, eukaryotic diversity, and climate change impacts. We emphasize that hot springs merit renewed interdisciplinary attention as model systems for understanding extremophile physiology, early life evolution, and the development of nature-based biotechnological solutions. Realizing their full potential requires balanced management strategies that preserve ecosystem integrity while enabling responsible utilization of these irreplaceable geobiological resources. Full article

Transitional water bodies are coastal areas of strategic naturalistic and socio-economic importance, and highly vulnerable to increased anthropic pressure. A monitoring study was performed in the transitional area of Lake Faro (Cape Peloro Lagoon, Italy), where specimens of the threatened species Pinna nobilis (Mollusca, Bivalvia) constitute a resident community, as a part of a wider research program aiming to preserve this organism in the context of safeguarding lake biodiversity. Five surface water samplings with a two-month frequency were carried out at four selected stations, three of which were located in the inner part of the lake and one control station outside, in a canal connecting the lake to the Messina Straits. Trophic conditions (total suspender matter, nutrients and chlorophyll-a) and the main environmental variables (temperature, salinity, dissolved oxygen) were measured. Insights into the total prokaryotic abundance and metabolism via the extracellular enzymatic activities (i.e., leucine aminopeptidase; beta-glucosidase and alkaline phosphatase) were obtained. The dataset indicated that microbial and trophic dynamics were associated with the abundance of the P. nobilis population. These parameters, moreover, proved to represent a suitable tool for characterizing the environmental health status of transitional areas, as well as for implementing new effective strategies for sustainable resource management. Full article

Transport emissions are a major source of urban polycyclic aromatic hydrocarbons (PAHs), posing risks to human health. While plant leaves and their epiphytic microbes contribute to PAH degradation, how plant traits and environmental factors affect this process remains unclear. This study examined 20 tree species in Beijing’s traffic corridors to explore PAH enrichment on leaves and the structure of phyllospheric bacterial communities. Results show that leaf area, morphology, and sampling height significantly influenced bacterial community assembly. Normalized Stochasticity Ratio (NST) analysis indicated that deterministic processes dominate on medium-sized leaves (11.8–40.1 cm²), simple leaves, and those below 2.3 m or above 3 m in height, whereas stochastic factors prevail on nano leaves, compound leaves, and leaves at low-position (<2.3 m). Although low-molecular-weight PAHs (2–4 rings) were predominant in leaves, Mantel tests revealed significant positive correlations between bacterial communities and high molecular weight PAHs (4–6 rings), such as benz(a)anthracene, benzo[e]pyrene, and picene. Spearman analysis identified 10 dominant bacterial taxa with PAH degradation potential, including Kocuria rosea, Serratia symbiotica, Massilia sp. WG5, and seven unclassified species from Hymenobacter, Sphingomonas, Roseomonas, Curtobacterium, and Deinococcus. Functional Annotation of Prokaryotic Taxa(FAPROTAX) prediction further associated 14 species across six genera, including Acinetobacter, Nocardioides, Gordonia, Rhodococcus, Clostridium_sensu_stricto_18, and Geobacter, with PAH degradation function. This work clarifies the composition and function of phyllospheric PAH-degrading bacteria in an urban traffic environment, offering a theoretical basis for enhancing degradation via bacterial consortia, biosurfactants, and optimized plant selection. Full article

Arid and semi-arid soils represent extreme habitats where microbial life is constrained by high temperature, low water availability, salinity, and nutrient limitation, yet these ecosystems harbor unique bacterial communities that sustain key ecological processes. To explore the diversity and functional potential of prokaryotic assemblages in Algerian drylands, we compared soils from three contrasting sites: The Oasis of Djanet (RM1), the hyper-arid Tassili of Djanet desert (RM2), and the semi-arid El Ouricia forest in Sétif (RM3). Physicochemical analyses revealed strong environmental gradients: RM2 exhibited the highest pH (8.66), electrical conductivity (11.7 dS/m), and sand fraction (56%), whereas RM3 displayed the greatest moisture (10.9%), organic matter (7.6%), and calcium carbonate (20.7%) content, with RM1 generally showing intermediate levels. High-throughput 16S rRNA gene sequencing generated >60,000 effective reads per sample with sufficient coverage (>0.99). Alpha diversity indices indicated the highest bacterial richness and diversity in RM2 (Chao1 = 3144, Shannon = 10.0), while RM3 showed lower evenness and the dominance of a few taxa. Across sites, 66 phyla and 551 genera were detected, dominated by Actinobacteriota (38–45%) and Chloroflexi (13–44%), with Proteobacteria declining from RM1 (17.5%) to RM3 (3.3%). Venn analysis revealed limited overlap, with only 58 operational taxonomic units shared among all sites, suggesting highly habitat-specific communities. Predictive functional profiling (PICRUSt2, Tax4Fun, FAPROTAX) indicated metabolism as the dominant functional category (≈50% of KEGG Level-1), with carbohydrate and amino acid metabolism forming the metabolic backbone. Notably, transport functions (ABC transporters), lipid metabolism, and amino acid degradation pathways were enriched in RM2–RM3, consistent with adaptation to osmotic stress, nutrient limitation, and energy conservation under aridity. Collectively, these findings demonstrate that Algerian arid and semi-arid soils host diverse, site-specific bacterial communities whose functional repertoires are strongly shaped by soil chemistry and climate, highlighting their ecological and biotechnological potential. Full article