Search Results (2,308)

Buffalo mozzarella cheese whey (CW) and ricotta cheese exhausted whey (RCEW) are valuable by-products of the Mozzarella di Bufala Campana PDO production chain. This study characterized their microbial communities using an integrated culture-dependent and -independent approach. Metabarcoding analysis revealed that the dominance of lactic acid bacteria (LAB), including Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus, alongside diverse heat-resistant yeasts such as Cyberlindnera jadinii. Culture-based isolation identified subdominant lactic acid bacteria strains, not detected by sequencing, belonging to Leuconostoc mesenteroides, Enterococcus faecalis, and Enterococcus durans. These strains were further assessed for their probiotic potential. E. faecalis CW1 and E. durans RCEW2 showed tolerance to acidic pH, bile salts, and lysozyme, as well as a strong biofilm-forming capacity and antimicrobial activity against Bacillus cereus and Staphylococcus aureus. Moreover, bile salt resistance suggests potential functionality in cholesterol metabolism. These findings support the potential use of CW and RCEW as reservoirs of novel, autochthonous probiotic strains and underscore the value of regional dairy by-products in food biotechnology and gut health applications. Full article

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire in 2014. Twenty soil samples were collected for microbiological (10 cm depth) and physicochemical (30 cm) analysis. Basal respiration was measured using Stotzky’s method, nitrogen mineralization via Rawls’ method, and fungal diversity through culture-based identification and colony-forming unit (CFU) counts. Diversity was assessed using Simpson, Shannon–Weaver, and ACE indices. The soils presented low organic matter (0.70%) and nitrogen content (0.035%), with reduced biological activity as indicated by basal respiration (0.12 kg C ha⁻¹ d⁻¹) and mineralized nitrogen (5.61 kg ha⁻¹). Four fungal morphotypes, likely from the genus Aspergillus, were identified. Simpson index indicated moderate dominance, while Shannon–Weaver values reflected low diversity. Correlation analysis showed Aspergillus-3 was positively associated with moisture, whereas Aspergillus-4 correlated negatively with pH and sand content. The species accumulation curve reached an asymptote, suggesting an adequate sampling effort. Although no control site was included, the findings provide a baseline characterization of post-fire soil microbial structure and function in a dry tropical ecosystem. Full article

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole^®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing. Full article

Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant physiology and soil function through diverse molecular mechanisms. PGPB synthesizes indole-3-acetic acid (IAA) to stimulate root development and nutrient uptake and produce ACC deaminase, which lowers ethylene accumulation under stress, mitigating growth inhibition. They also enhance nutrient availability by releasing phosphate-solubilizing enzymes and siderophores that improve iron acquisition. In parallel, PGPB activates jasmonate and salicylate pathways, priming a systemic resistance to biotic and abiotic stress. Through quorum sensing, biofilm formation, and biosynthetic gene clusters encoding antibiotics, lipopeptides, and VOCs, PGPB strengthen rhizosphere colonization and suppress pathogens. These interactions contribute to microbial community recovery, an improved soil structure, and enhanced nutrient cycling. This review synthesizes current evidence on the molecular and physiological mechanisms by which PGPB enhance soil restoration in degraded agroecosystems, highlighting their role beyond biofertilization as key agents in ecological rehabilitation. It examines advances in nutrient mobilization, stress mitigation, and signaling pathways, based on the literature retrieved from major scientific databases, focusing on studies published in the last decade. Full article

To explore an industrial fermentation approach for traditional mung bean sour pulp, this study isolated core microorganisms including lactic acid bacteria and yeasts from naturally fermented samples and constructed a synthetic microbial community. The optimized community consisted of Lactiplantibacillus pentosus, Lactococcus garvieae, and Cyberlindnera jadinii at a ratio of 7:3:0.1 and was used to ferment cooked mung bean pulp with a material-to-water ratio of 1:8 and 1% sucrose addition. Under these conditions, the final product exhibited significantly higher levels of protein (4.55 mg/mL), flavonoids (0.10 mg/mL), polyphenols (0.11 mg/mL), and vitamin C (7.75 μg/mL) than traditionally fermented mung bean sour pulp, along with enhanced antioxidant activity. The analysis of organic acids, free amino acids, and volatile compounds showed that lactic acid was the main acid component, the bitter amino acid content was reduced, the volatile flavor compounds were more abundant, and the level of harmful compound dimethyl sulfide was significantly decreased. These results indicate that fermentation using a synthetic microbial community effectively improved the nutritional quality, flavor, and safety of mung bean sour pulp. Full article

Microplastics (MPs) and nanoplastics (NPs) can affect microbial abundance and activity, likely by damaging cell membrane components. While their effects on anaerobic digestion are known, less is understood about their impact on microbes involved in contaminant bioremediation. Chlorinated volatile organic contaminants (CVOCs) such as tetrachloroethene (PCE) and explosives like hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) are common in the environment, and their bioremediation is a promising cleanup strategy. This study examined how polystyrene (PS) and polyamide 6 (PA6) MPs and NPs influence CVOC and RDX biodegradation. PS particles did not inhibit the CVOC-degrading community SDC-9, but PA6 MPs impaired the reductive dechlorination of trichloroethene (TCE) to cis-1,2-dichloroethene (cis-DCE), causing a “cis-DCE stall” with no further conversion to vinyl chloride (VC) or ethene. Only 45% of TCE was dechlorinated to cis-DCE, and Dehalococcoides mccartyi abundance dropped 1000-fold in 35 days with PA6 MPs. In contrast, neither PA6 nor PS MPs and NPs affected RDX biotransformation. These results highlight the significant impact of PA6 MPs on CVOC biodegradation and the need to consider plastic pollution in environmental management. Full article

This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice–frog–loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 10⁴ individuals/667 m²), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice–frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice–frog–loach integrated systems was determined to be 1.0 × 10⁴ individuals/667 m². This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities. Full article

In a greenhouse experiment, we examined the behavior of biochar in arable soil to demonstrate that these supplements can boost soil carbon storage, as well as to track changes in microbial biomass and identify the microbial communities that use these biochars. In order to ascertain if biochar can consistently alter soil microbial activities, we studied the impact of biochar combination treatments on 16S rRNA gene diversity. In soil treated with biochar, there was a rise in the relative abundance of taxa belonging to the phyla Actinobacteria and Gemmatimonadetes, despite the overall diversity decreasing with biochar addition. According to all of these observations, pyrogenic carbon has a major effect on the composition of the soil microbial community and enriches keystone taxa within the parent soil microbial community. Certain species experienced increases throughout the biochar-amended incubation period, despite the total diversity declining following biochar amendments. The phyla Actinobacteria and Gemmatimonadetes increased in the relative abundance of bacteria in soil treated with biochar, according to DNA sequencing of these species. In summary, these findings show that biochar significantly impacts the constitution and composition of the soil microbial community and enriches important taxa within the parent soil microbial community. Full article

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization. Full article

Landslides are a common geological hazard in mountainous areas, causing significant damage to ecosystems and production activities. Near-natural ecological restoration is considered an effective strategy for post-landslide recovery. To investigate the impact of near-natural restoration strategies on the recovery of plant communities and soil in landslide-affected areas, we selected landslide plots in Lantian County at 1, 6, and 11 years post-landslide as study sites, surveyed plots undergoing near-natural restoration and adjacent undisturbed control plots (CK), and collected and analyzed data on plant communities and soil properties. The results indicate that vegetation succession followed a path from “human intervention to natural competition”: species richness peaked at 1 year post-landslide (D_m = 4.2). By 11 years, dominant species prevailed, with tree species decreasing to 4.1 ± 0.3, while herbaceous diversity increased by 200% (from 4 to 12 species). Soil recovery showed significant temporal effects: total nitrogen (TN) and dehydrogenase activity (DHA) exhibited the greatest increases after 1 year post-landslide (132% and 232%, respectively), and by 11 years, the available nitrogen (AN) in restored plots recovered to 98% of the CK levels. Correlations between plant and soil characteristics strengthened over time: at 1 year, only 6–9 pairs showed significant correlations (p < 0.05), increasing to 21–23 pairs at 11 years. Near-natural restoration drives system recovery through the “selection of native species via competition and activation of microbial functional groups”. The 6–11-year period post-landslide is a critical window for structural optimization, and we recommend phased dynamic regulation to balance biodiversity and ecological functions. Full article

Stipagrostis pennata is an important plant in desert ecosystems. Its seed-endophytic bacteria may play a critical role in plant growth and environmental adaptation processes. This study systematically analyzed the community composition and potential plant growth-promoting (PGP) functions of seed-endophytic bacteria associated with S. pennata. The results showed that while the overall diversity of bacterial communities from different sampling sites was similar, significant differences were observed in specific functional genes and species abundances. Nine endophytic bacterial strains were isolated from the seeds, among which Bacillus altitudinis strain L7 exhibited phosphorus solubilizing capabilities, nitrogen fixing, IAA production, siderophore generation, and multi-hydrolytic enzyme activities. Additionally, the genomic sequencing of L7 revealed the key genes involved in plant growth promotion and environmental adaptation, including Na⁺ efflux systems, K⁺ transport systems, compatible solute synthesis genes, and the gene clusters associated with nitrogen metabolism, IAA synthesis, phosphate solubilization, and siderophore synthesis. Strain L7 exhibits salt and osmotic stress tolerance while promoting plant growth, providing a promising candidate for desert microbial resource utilization and plant biostimulant development. Full article

Integrated rice–crayfish (Oryza sativa–Procambarus clarkii) co-culture (RC) systems have gained prominence due to their economic benefits and ecological sustainability; however, the interactions between soil properties and microbial communities in such systems remain poorly understood. This study evaluated the effects of the RC systems on soil physicochemical characteristics and microbial dynamics in paddy fields of southern Henan Province, China, over the 2023 growing season and subsequent fallow period. Using a randomized complete design, rice monoculture (RM, as the control) and RC treatments were compared across replicated plots. Soil and water samples were collected post-harvest and pre-transplanting to assess soil properties, extracellular enzyme activity, and microbial community structure. Results showed that RC significantly enhanced soil moisture by up to 30.2%, increased soil porosity by 9.6%, and nearly tripled soil organic carbon compared to RM. The RC system consistently elevated nitrogen (N), phosphorus (P), and potassium (K) throughout both the rice growth and fallow stages, indicating improved nutrient availability and retention. Elevated extracellular enzyme activities linked to carbon, N, and P cycling were observed under RC, with enzymatic stoichiometry revealing increased microbial nutrient limitation intensity and a shift toward P limitation. Microbial community composition was significantly altered under RC, showing increased biomass, a higher fungi-to-bacteria ratio, and greater relative abundance of Gram-positive bacteria, reflecting enhanced soil biodiversity and ecosystem resilience. Further analyses using the Mantel test and Random Forest identified extracellular enzyme activities, PLFAs, soil moisture, and bulk density as major factors shaping microbial communities. Redundancy analysis (RDA) confirmed that total potassium (TK), vector length (VL), soil pH, and total nitrogen (TN) were the strongest environmental predictors of microbial variation, jointly explaining 74.57% of the total variation. Our findings indicated that RC improves soil physicochemical conditions and microbial function, thereby supporting sustainable nutrient cycling and offering a promising, environmentally sound strategy for enhancing productivity and soil health in rice-based agro-ecosystems. Full article

Ecological restoration in the cold and high-altitude mining areas of the Qinghai–Tibet Plateau is faced with dual challenges of extreme environments and insufficient microbial adaptability. This study aimed to screen local microbial resources with both extreme environmental adaptability and plant-growth-promoting functions. Local fungi (DK; F18-3) and commercially available bacteria (B0) were used as materials to explore their regulatory mechanisms for plant growth, soil physicochemical factors, microbial communities, and metabolic profiles in the field. Compared to bacterial treatments, local fungi treatments exhibited stronger ecological restoration efficacy. In addition, the DK and F18-3 strains, respectively, increased shoot and root biomass by 23.43% and 195.58% and significantly enhanced soil nutrient content and enzyme activity. Microbiome analysis further implied that, compared with the CK, DK treatment could significantly improve the α-diversity of fungi in the rhizosphere soil (the Shannon index increased by 14.27%) and increased the amount of unique bacterial genera in the rhizosphere soil of plants, totaling fourteen genera. Meanwhile, this aggregated the most biomarkers and beneficial microorganisms and strengthened the interactions among beneficial microorganisms. After DK treatment, twenty of the positively accumulated differential metabolites (DMs) in the plant rhizosphere were highly positively associated with six plant traits such as shoot length and root length, as well as beneficial microorganisms (e.g., Apodus and Pseudogymnoascus), but two DMs were highly negatively related to plant pathogenic fungi (including Cistella and Alternaria). Specifically, DK mainly inhibited the growth of pathogenic fungi through regulating the accumulation of D-(+)-Malic acid and Gamma-Aminobutyric acid (Cistella and Alternaria decreased by 84.20% and 58.53%, respectively). In contrast, the F18-3 strain mainly exerted its antibacterial effect by enriching Acidovorax genus microorganisms. This study verified the core role of local fungi in the restoration of mining areas in the Qinghai–Tibet Plateau and provided a new direction for the development of microbial agents for ecological restoration in the Qinghai–Tibet Plateau. Full article