Search Results (10,225)

Kombucha fermentation is driven by a Symbiotic Culture of Bacteria and Yeast (SCOBY), a cellulose-rich biofilm that hosts a complex microbial consortium. While most kombucha studies focus on the liquid beverage, the SCOBY pellicle itself remains underexplored, particularly with respect to species-level microbial resolution and its intrinsic biological activities. In this study, a commercial kombucha SCOBY was characterized using full-length 16S rRNA gene and ITS amplicon sequencing based on Oxford Nanopore Technology, enabling species-level taxonomic resolution. In parallel, hydroalcoholic and aqueous extracts of dried SCOBY biomass were evaluated for in vitro antioxidant activity (DPPH and ABTS assays), antidiabetic-related enzyme inhibition (α-glucosidase and dipeptidyl peptidase-4, DPP4), and anti-aging-related enzyme inhibition (tyrosinase and elastase). The SCOBY bacterial community was strongly dominated by acetic acid bacteria, with Komagataeibacter saccharivorans and Acetobacter tropicalis accounting for more than 60% of total reads, reflecting a biofilm structure optimized for cellulose production and oxidative metabolism. The yeast community showed marked unevenness, with Brettanomyces bruxellensis representing over 80% of reads, consistent with its known role in ethanol production and stress tolerance within kombucha systems. In vitro assays revealed that hydroalcoholic SCOBY extracts consistently exhibited higher biological activity than aqueous extracts across all tested assays. However, both extracts showed substantially lower potency than purified reference compounds, indicating moderate but measurable bioactivity typical of complex fermented matrices. These findings support the potential valorization of SCOBY as a fermentation-derived biomaterial and functional ingredient while underscoring the need for further chemical characterization, mechanistic studies, and biological validation beyond enzyme-based assays. Full article

Microbial inoculation represents an environmentally friendly biocontrol strategy that can enhance soil quality, improve crop growth efficiency, and promote sustainable agriculture. However, the long-term effects and ecological safety of non-native microbial inoculants in soil remain uncertain. Here, we explore and evaluate a safer and potentially more effective inoculation strategy—the reintroduction of native microbiota—to maintain agricultural ecosystem health. Native microbiota were extracted from black soil in northeastern China and reintroduced into the indigenous soil. Two treatments were established: original soil (control) and original soil with a mixture of native microbiota, each with nine replicates. Soil samples were collected at 0, 21, and 90 days post-inoculation. Using high-throughput sequencing and agronomic chemical analyses, we dynamically monitored soil nitrogen, phosphorus, and potassium contents, as well as microbial community composition. Crops were harvested at day 90 to measure dry weight, fresh weight, and SPAD values. The results revealed that the number of colonizing species was lower than the number of inoculated species, yet crop agronomic traits and chemical composition were significantly improved, particularly SPAD values and total phosphorus content. Soil abiotic factors exhibited limited resistance but retained partial recovery capacity, showing a notable increase in readily available potassium at days 0 and 21. Native microbiota inoculation promoted positive synergistic interactions within the microbial community. Furthermore, this study underscores the practical significance of cultivable microorganisms in agricultural applications. Collectively, our findings demonstrate the feasibility of native microbiota reintroduction, highlighting its potential to optimize soil microbial communities, enhance soil properties, and improve crop performance, thereby providing a scientific basis for soil remediation and sustainable agriculture. Full article

Photosynthetic algae–microbial fuel cells (PAMFCs) are attractive for energy-positive wastewater treatment and carbon mitigation. However, PAMFC performance under continuous flow is often constrained by limited cathodic electron-acceptor supply and unstable photosynthetic biofilms, while the extent to which cathode interfacial engineering can stabilize diurnal power output and assimilative NH₄⁺–N removal remains unclear. In this study, the sponge-like and petal-like ZnO_0.2-NiO@rGO-modified carbon fibers (ZnO_0.2-NiO@rGO-pCFs and ZnO_0.2-NiO@rGO-pCFp) and pre-fabricated carbon felt (pCF) were used as cathode materials to construct three sets of PAMFC systems. Under light–dark cycling, the engineered cathodes reached steady operation within about 6.5 d and increased the steady-state voltage to approximately 0.35 V, compared with approximately 0.08 V for pCF. Under continuous-flow conditions, cathodic NH₄⁺–N removal exhibited a stable diurnal rhythm, with higher removal during illumination at about 43–51% than in the dark at about 29–30%, consistent with algal assimilation as the primary nitrogen sink, while cathode modification mainly improved the cathodic microenvironment and response stability. Compared with pCF, the ZnO_0.2–NiO@rGO cathode enriched a more even, Chlorophyta-dominated algal biofilm with an approximate relative abundance of 80%, indicating that its selective interfacial environment favors biofilm stabilization and sustains in situ oxygen production and cathodic electron-acceptor supply. Consequently, the composite cathode enhanced voltage output and stabilized light-enhanced, assimilative NH₄⁺–N removal under aeration-free operation, while establishing an interpretable link between electrochemical performance and 18S rDNA-derived community assembly features, thereby providing a low-cost cathode design basis for nitrogen removal in wastewater treatment. Full article

Despite the essential role of soil microbial communities in driving nutrient cycling within alpine meadows, their distribution patterns along elevational gradients and their responses to environmental changes remain largely unexplored. To investigate this, soil samples were collected from five elevations (3300–4500 m) in the northeastern Qinghai–Tibet Plateau to analyze bacterial community composition and diversity, as well as their associations with soil physicochemical properties and enzyme activities. The results showed significant variation in bacterial community composition and diversity across elevations. Actinomycetota, Pseudomonadota, and Acidobacteriota were the dominant phyla at all sampling sites. Community diversity, measured by the Shannon index, generally increased with elevation, peaking at 4500 m and lowest at 3300 m. Pearson correlation analysis and redundancy analysis (RDA) indicated that soil bacterial community structure was significantly correlated with both soil nutrient factors and enzyme activities. Among these variables, total potassium, available phosphorus, catalase, and urease were strongly correlated with bacterial community differentiation. In addition, PERMANOVA results showed that elevation was the primary factor driving community variation, explaining a substantial proportion of the variation in community composition at a statistically significant level. Overall, this study highlights the distribution of bacterial communities in alpine meadow soils along an elevational gradient and their environmental associations, providing foundational data for understanding microbial community responses to environmental changes in alpine ecosystems. Full article

Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment. Full article

Bioconversion of lignocellulosic biomass into edible, nutrient-rich products using low-cost forestry waste offers substantial ecological and economic benefits. Composting forestry waste as a substrate for oyster mushroom (Pleurotus ostreatus) cultivation is an effective recovery strategy. However, the specific microbial-driven mechanisms by which nitrogen sources regulate lignocellulose degradation and compost quality during forestry waste composting for Pleurotus ostreatus substrate preparation remain to be elucidated. We evaluated three organic nitrogen sources (bran, soybean meal, and chicken manure) and one inorganic source (diammonium phosphate, DAP) during composting of forest-waste-based substrates. Composting performance and cultivation outcomes were assessed using physicochemical analyses, lignocellulose degradation measurements, high-throughput sequencing of bacterial 16S rRNA and fungal ITS, and biological efficiency. Organic nitrogen sources enhanced compost temperature and lignocellulose degradation by providing sustained nitrogen release, promoting stable colonization of core microbial communities and cooperative bacteria–fungi networks. In contrast, inorganic nitrogen resulted in slower heating, minimal lignocellulose degradation (0.75%), and unstable, competition-dominated microbial networks. Nitrogen sources indirectly shaped microbial communities by regulating the C/N ratio, pH, and electrical conductivity. Lignocellulose degradation and bacterial diversity significantly influenced mushroom biological efficiency, with bacterial diversity strongly regulating degradation rates. The forest waste–bran treatment achieved the highest biological efficiency (78.35%). These findings offer a practical strategy for optimizing forestry waste bioconversion into fungal protein. Full article

Hemp (Cannabis sativa L.) is an important crop, yet little is known about how herbivory and soil microbial communities interact to influence plant performance. In this study, two hemp cultivars, BaOx and Cherry Citrus, were grown under identical greenhouse conditions and exposed to naturally occurring background populations of the two-spotted spider mite (Tetranychus urticae). Plant traits were measured, and rhizosphere soil was sampled for 16S rRNA gene sequencing to compare bacterial community composition and diversity between cultivars. Spider mite injury was assessed using a standardized 0–5 visual damage scale commonly applied in integrated pest management studies. Although the cultivars did not differ significantly in growth traits, Cherry Citrus experienced significantly less spider mite damage than BaOx, suggesting greater tolerance or resistance to herbivory under shared conditions. Rhizosphere bacterial communities differed markedly between cultivars despite identical soil and environmental conditions. BaOx rhizospheres were enriched in Actinobacteria, including taxa associated with decomposition and antimicrobial compound production, whereas Cherry Citrus rhizospheres were enriched in Alphaproteobacteria, particularly nitrogen-cycling and root-associated taxa such as Rhizobium and Reyranella. Alpha diversity metrics did not differ between cultivars; however, beta diversity analyses revealed significant cultivar-level separation, particularly in phylogenetic community structure. Because herbivore pressure and microbial communities were not experimentally manipulated, this observational study identifies ecological associations rather than direct causal relationships. Nevertheless, the results demonstrate that hemp cultivar identity is associated with distinct rhizosphere microbiomes and differential susceptibility to spider mite damage. These findings highlight the potential for integrating cultivar selection and microbiome-informed strategies into sustainable pest management programs for hemp. Full article

Honey bees are exposed to a wide range of environmental and ecological stressors that threaten individual health and colony sustainability. Growing evidence suggests that many of these stressors converge on a common target: the gut microbiome and its metabolic functions. The honey bee microbiome–metabolome axis represents a central regulatory system linking microbial symbionts with host nutrition, detoxification, immune competence, neural signaling, and social behavior. This review synthesizes current knowledge on how major stressors—including pesticides, antibiotics, pathogens, nutritional imbalance, thermal stress, habitat change, and environmental contaminants—reprogram honey bee chemistry by disrupting microbial community structure and, importantly, microbial and host metabolic pathways. We highlight recurring patterns consistent with functional dysbiosis, characterized by impaired energy metabolism, reduced production of short-chain fatty acids, altered amino acid and lipid metabolism, compromised antioxidant and detoxification capacity, and weakened immune regulation. However, much of the current evidence is correlative and derived from short-term or laboratory-focused studies; longitudinal and multi-site field validation of causal links remains limited. Importantly, emerging multi-omics studies suggest that profound metabolic disturbances can occur even when taxonomic changes in the microbiome are modest, emphasizing the need to move beyond descriptive community profiling toward functional and mechanistic assessments. We further discuss how stress-induced metabolic reprogramming at the individual level scales up to influence behavior, division of labor, and colony-level resilience. Finally, we propose a conceptual model illustrating how diverse stressors converge to disrupt the microbiome–metabolome axis, potentially leading to functional dysbiosis and host impairment. Full article

Soil-borne diseases have become increasingly serious due to continuous planting. Soil fumigation may be inadequate because of the persistence of soil-borne pathogens on ginger seed rhizome. A combined strategy of soil fumigation and seed rhizome disinfection would be necessary to achieve synergistic control. In this study, the approach of soil fumigation with chloropicrin (CP) coupled with seed rhizome disinfection (Copper, Cu) was first adopted to evaluate the synergistic effects on soil physicochemical properties, enzyme activities and microbial communities, and therefore reveal mechanisms for soil microecological health and crop yield promotion. The results showed the comprehensive strategy could reduce NO₃⁻-N content, and the activities of soil enzymes, while increased NH₄⁺-N content, EX-Cu, and OXI-Cu content, which were positively correlated with ginger yield but negatively correlated with soil-borne pathogens and plant mortality. On the other hand, there was a reduction in bacterial diversity and richness, which was positively correlated with the abundance of soil-borne pathogens. Moreover, some beneficial soil microorganisms’ relative abundance (such as Firmicutes, Actinobacteria, Bacillus, and Sphingomonas.) was increased. The strategy decreased the abundance of Fusarium spp. and Phytophthora spp. by 49.41–90.07% and 43.34–89.21%, respectively. Compared with other treatments, the combination decreased the ginger mortality by 5.70–57.02% and increased the growth of ginger plants and yield by 3.58–139.96%, and 13.11–399.74%, respectively. This study highlights a prospect to promote ginger growth and yield by blocking the transmission of primary infection pathogens in ginger cultivation and improving soil ecological environment. Full article

Fertilization is a regular management approach that can enhance soil fertility and stimulate the proliferation of beneficial microorganisms. However, the prolonged influence of fertilization practices on soil quality, microbial functional characteristics, and the underlying mechanisms still remain incompletely understood. In this study, we examined the impact of various fertilization strategies on the soil quality index (SQI) and community-level physiological profiles (CLPP) during two crop seasons (maize and soybean, respectively) in a 45-year field trial. Four treatments were implemented: unfertilized control (CK), inorganic nitrogen–phosphorus–potassium fertilizer (NPK), organic fertilizer (M), and organic–inorganic fertilization (MNPK). Results showed that across both seasons, NPK application reduced soil pH and the McIntosh index, whereas organic amendments (M and MNPK) notably enhanced total and available nutrients, SQI, microbial biomass, and enzyme activities. CLPP analysis revealed that organic fertilization significantly enhanced microbial metabolic activity and functional diversity, particularly boosting the utilization of carbohydrates (20–38%) and carboxylic acids (18–36%). Random forest modelling indicated available potassium (AK) as the primary driver of carbon metabolic activity in both seasons, revealing its critical role in regulating microbial functions. Functional metabolic diversity during the maize season was most strongly influenced by microbial entropy (qMB), whereas in the soybean season, it was available nitrogen (AN). Additionally, organic fertilization led to an indirect improvement in SQI during the maize and soybean seasons by increasing microbial biomass. In conclusion, the study underscored the importance of long-term organic fertilization for improving soil quality and provided empirical evidence to maintain the sustainable practices of agriculture in Northeast China. Full article

Microplastics are persistent contaminants in coastal wetlands, yet the mechanisms of their microbial transformation remain poorly understood. This study examined the interactions between a wetland sediment-derived microbial consortium and polyethylene terephthalate (PET) fibers over a 60-day incubation. After 60 days, the consortium caused a PET weight loss of 13.7 ± 0.9%, whereas the abiotic control showed a less than 2% loss. The water contact angle decreased from 77.5 ± 1.2° to 75.8 ± 0.4°, suggesting enhanced surface hydrophilicity. Multi-scale surface analyses (SEM, WCA, and FTIR) confirmed progressive microbial colonization, increased surface roughness, and enhanced hydrophilicity through microbially mediated modification. High-throughput 16S rRNA sequencing unveiled a distinct community succession; PET exerted selective pressure that reduced alpha-diversity while enriching specific functional taxa such as Acinetobacter and Pseudomonas. Moreover, isolation and co-culture assays confirmed the importance of synergistic microbial interactions in PET transformation, with co-culture of four representative isolates causing 9.2 ± 0.1% PET weight loss, compared with only 1.7–3.2% in monocultures. These findings underscore the intrinsic natural attenuation potential of wetland ecosystems and provide a critical scientific basis for developing nature-based management strategies. By identifying key functional taxa and PET-associated transformation pathways, this work supports the establishment of early-warning mechanisms to safeguard the ecological integrity and soil health of coastal World Natural Heritage sites like the Tiaozini Wetland. Full article

Bioturbating animals move around large amounts of sediment, changing its physicochemical properties and biogeochemical processes. The present study assessed the role of the ghost shrimp Lepidophthalmus louisianensis, a major coastal bioturbator in the Northern Gulf of Mexico, in the fate of crude oil after the 2010 Deepwater Horizon blowout. Experiments were conducted in greenhouse mesocosms, with or without ghost shrimp and with or without added oil, reflecting mild surface or subsurface oiling in a beach environment. To evaluate the hydrocarbon-degradation potential of the sediment microbial community, a respirometric radiotracer assay was conducted with ¹⁴C naphthalene as a model polycyclic aromatic hydrocarbon (PAH) compound. Oil augmentation led to a substantial increase in the PAH degradation potential of mesocosm sediments, which was further enhanced by the presence of the bioturbator. However, bioturbation alone, without previous oil exposure, did not enhance naphthalene degradation. 16S rRNA gene analyses showed that there were no significant changes in the microbial community composition associated with either bioturbation, oil augmentation, or both. This study demonstrated bioturbation- and oil-exposure-related enhancement in hydrocarbon degradation in mildly oiled sediment, and indicated that this may be due to an increased expression of PAH degrading activities in the preexisting community of hydrocarbon-degrading bacteria rather than resulting from a shift in the microbial community composition. Full article

The dynamic interaction between plants and their root-associated microbiota represents a sophisticated and profound biological communication that regulates plant development and the formation of adaptation to the surrounding environment. These interactions function as critical regulators of multiple physiological processes, finally influencing soil fertility and agricultural productivity. Plants have evolved epigenetic networks that regulate beneficial plant–microbe interactions through regulating immune responses, gene regulation, and metabolite production to enhance stress tolerance and soil adaptation. These regulations collectively govern microbial colonization patterns while establishing reciprocal feedback loops through root exudate–microbe interactions. This review systematically updates contemporary advances in understanding how epigenetic modifications shape rhizosphere microbiome composition and function, and discusses their potential applications in enhancing the yield and quality of horticultural crops, as well as in mitigating continuous cropping obstacles. Full article

This study investigated the effects of isoacid supplementation on in vitro rumen fermentation characteristics, nutrient degradability, and bacterial community diversity in yaks using corn silage–highland barley straw-based substrates. An in vitro fermentation experiment was conducted with a substrate consisting of 80% whole-plant corn silage and 20% highland barley straw. Treatments included a control (without isoacids) and four isoacid supplemental levels (0.1%, 0.2%, 0.3%, and 0.4% of substrate dry matter, DM), each with six replicates. A 72 h in vitro gas production experiment was performed to measure cumulative gas production, fermentation parameters, nutrient degradability, and bacterial community diversity. Cumulative gas production increased by 12.96% with 0.2% isoacid supplementation compared to the control (p < 0.05). The contents of microbial protein (MCP), acetate, propionate, and total volatile fatty acids (TVFA) exhibited quadratic responses to the increasing isoacid dosage (p < 0.05). Specifically, MCP content reached a maximum of 0.76 mg/mL with 0.2% isoacids, representing a 31.03% increase compared to the control (p < 0.05). TVFA content was highest (146.85 mmoL/L) at 0.2% isoacid supplementation, with a 16.40% increase compared to the control (p < 0.05). Acetate content increased by 17.99% (p < 0.05), while propionate tended to increase with 0.2% isoacid supplementation (p = 0.08). Supplementation with 0.2% and 0.4% isoacids did not alter the bacterial composition and diversity (p > 0.05). However, at the genus level, g_Ruminococcus, g__Elusimicrobium, g_norank_f_Atopobiaceae, g_norank_o_Coriobacteriales, and g_Romboutsia were identified as differential biomarkers showing significant responses to isoacid supplementation (p < 0.05). Mantel-test analysis revealed positive correlation between g_Ruminococcus abundance and NH₃-N content (r < 0.4, p < 0.05); g_Romboutsia abundance and acetate content (r < 0.40, p < 0.05); g_Defluviitaleaceae_UCG-011 abundance and both NH₃-N content and the pH of rumen fluid (r < 0.40, p < 0.05); g_norank_o_Coriobacteriales abundance and rumen pH (r < 0.40, p < 0.01). Supplementation with 0.2% isoacids to corn silage–barley straw substrates improved in vitro rumen fermentation characteristics in yaks, which was associated with altered abundances of key bacterial genera including g_Ruminococcus, g__Elusimicrobium, g_norank_f_Atopobiaceae, g_norank_o_Coriobacteriales. Full article

Petroleum hydrocarbons remain major environmental contaminants, and understanding the mechanisms governing their biodegradation is essential for designing effective remediation plans. The strategy in this article is slightly different from other cases in the literature. Such literature models require, for their elaboration, a significant number of experiments; the number of experimental determinations is at least proportional to the square of the number of constants introduced in the mathematical expressions. For this reason, the strategy followed in this article is different—starting from a set of experiments carried out and presented in a coherent and published manner, a simple methodology for building specific and minimal models, which will allow solving specific problems, was effectively developed. This study develops a nonlinear mathematical structure, expressed as a system of coupled differential equations, that simultaneously describes the degradation of petroleum hydrocarbons and the dynamics of hydrocarbon-degrading bacteria and fungi in soil–sludge mixtures. The model was calibrated using experimental data obtained from biopiles prepared with different volumetric ratios of contaminated soil and sewage sludge. Approximate analytical solutions were derived and the distributed constants were evaluated. For a consistent discussion, the analytical solutions were assessed against numerical desk simulations performed with a classical fourth-order Runge–Kutta method, which accurately reproduced the nonlinear behavior of the specific system. This numerical approach was chosen in order to overcome the proper difficulties encountered in this strategy implementation. The results show that the soil–sludge ratio strongly influences biodegradation efficiency, while kinetic parameters determine whether microbial communities evolve toward a stationary regime or accelerated contaminant removal. The combined analytical–numerical framework provides a robust predictive tool for optimizing mixture composition and improving the design of bioremediation treatments for petroleum-contaminated soils. Full article