Search Results (607)

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article

True slime molds (Eumycetozoa) remain under-explored globally, particularly in water-logged forest habitats. Despite evidence suggesting a high biodiversity potential in the Knyszyn Forest of north-eastern Poland, no systematic effort had previously been undertaken there. In the present survey, plant substrates from eight swampy sub-compartments were incubated for over four months, resulting in the detection of fifteen slime mold species. Four of these taxa are newly reported for northern and north-eastern Poland, while several have been recorded only a handful of times in the global literature. These findings underscore how damp, nutrient-rich conditions foster Eumycetozoa and demonstrate the effectiveness of moist-chamber culturing in revealing rare or overlooked taxa. Current evidence shows that, although slime molds may occasionally colonize living plant or fungal tissues, their influence on crop productivity and tree vitality is negligible; they are therefore better regarded as biodiversity indicators than as pathogens or pests. By establishing a replicable framework for studying water-logged environments worldwide, this work highlights the ecological importance of swamp forests in sustaining microbial and slime mold diversity. Full article

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

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

Background/Objectives: Gut microbiota research has gained momentum in recent years broadening knowledge of microbial components and their potential effects on health and well-being. Strong association between explicit microbes and metabolic diseases associated with obesity and type 2 diabetes mellitus, gastrointestinal disorders, neurodegenerative diseases, and even cancers have been established. Akkermansia muciniphila is a budding next-generation probiotic that plays an important role in systemic metabolism, intestinal health, and immune regulation, establishing strong implications for its use as a potent therapeutic intervention in diverse diseases. This project aimed at evaluating whether bacterial cell extracts of VH Akkermansia muciniphila (Vidya Strain; VS) can stimulate insulin secretion in INS-1 pancreatic beta cells and GLP-1 secretion in NCI-H716 human L-cells, both established in vitro models for studying metabolic regulation. Methods: Cultured VH Akkermansia muciniphila extracts were administered in a dose-dependent manner on INS-1 cells, and glucose-stimulated insulin secretion (GSIS) was measured via ELISA. Treated Human L-cell lines (NCI-H716) were analyzed for GLP-1 secretion. Results: Our study demonstrated that VH Akkermansia muciniphila extracts modestly increase insulin secretion from INS-1 beta cells and, more notably, induce a robust, dose-dependent rise in GLP-1 secretion from NCI-H716 L-cells, with the highest dose achieving over a 2000% increase comparable to glutamine. Conclusions: These findings suggest that VH A. muciniphila extracts may offer metabolic benefits by enhancing GLP-1 release, highlighting their potential for managing type 2 diabetes and obesity. Full article

Background/Objectives: Selective serotonin reuptake inhibitors (SSRIs), widely prescribed for anxiety disorders, may negatively impact the gut microbiota, contributing to dysbiosis. Considering the gut–brain axis’s importance in mental health, probiotics could represent an effective adjunctive strategy. This study evaluated the effects of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on microbiota composition, metabolic activity, and immune markers in fecal samples from patients with anxiety on SSRIs, using the SHIME^® (Simulator of the Human Intestinal Microbial Ecosystem) model. Methods: The fecal microbiotas of four patients using sertraline or escitalopram were inoculated in SHIME^® reactors simulating the ascending colon. After stabilization, a 14-day probiotic intervention was performed. Microbial composition was assessed by 16S rRNA sequencing. Short-chain fatty acids (SCFAs), ammonia, and GABA were measured, along with the prebiotic index (PI). Intestinal barrier integrity was evaluated via transepithelial electrical resistance (TEER), and cytokine levels (IL-6, IL-8, IL-10, TNF-α) were analyzed using a Caco-2/THP-1 co-culture system. The statistical design employed in this study for the analysis of prebiotic index, metabolites, intestinal barrier integrity and cytokines levels was a repeated measures ANOVA, complemented by post hoc Tukey’s tests to assess differences across treatment groups. For the 16S rRNA sequencing data, alpha diversity was assessed using multiple metrics, including the Shannon, Simpson, and Fisher indices to evaluate species diversity, and the Chao1 and ACE indices to estimate species richness. Beta diversity, which measures microbiota similarity across groups, was analyzed using weighted and unweighted UniFrac distances. To assess significant differences in beta diversity between groups, a permutational multivariate analysis of variance (PERMANOVA) was performed using the Adonis test. Results: Probiotic supplementation increased Bifidobacterium and Lactobacillus, and decreased Klebsiella and Bacteroides. Beta diversity was significantly altered, while alpha diversity remained unchanged. SCFA levels increased after 7 days. Ammonia levels dropped, and PI values rose. TEER values indicated enhanced barrier integrity. IL-8 and TNF-α decreased, while IL-6 increased. GABA levels remained unchanged. Conclusions: The probiotic combination of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 modulated gut microbiota composition, metabolic activity, and inflammatory responses in samples from individuals with anxiety on SSRIs, supporting its potential as an adjunctive strategy to mitigate antidepressant-associated dysbiosis. However, limitations—including the small pooled-donor sample, the absence of a healthy control group, and a lack of significant GABA modulation—should be considered when interpreting the findings. Although the SHIME^® model is considered a gold standard for microbiota studies, further clinical trials are necessary to confirm these promising results. Full article

Almond decline and dieback have become significant challenges in newly established orchards, with symptoms including internal necrosis, canker, and external gummosis. This work aims to explore the potential fungal and bacterial causative agents through metabarcoding and traditional culture plate isolation across six almond cultivars. Our results emphasize the multifactorial nature of almond decline and dieback, with possible co-infections by opportunistic fungi and bacteria playing a central role. Classical isolation identified 47 fungal species or genera, including Diaporthe amygdali, Diplodia corticola, Phytophthora sp., and several Fusarium species. Almond metabarcoding revealed a more diverse microbial community, highlighting the prevalence of soilborne pathogens such as Neocosmospora rubicola, Dactylonectria estremocensis, and Plectosphaerella niemeijerarum. Soil metabarcoding suggested that these pathogens likely originate from nursery substrates or soils shared with other crops, such as olives and vineyards, that serve as a source of inoculum. ‘Soleta’ generally presented lower richness when compared to the other tested cultivars, suggesting a higher degree of biotic stress and decreased plant resilience. This study highlights the value of integrating NGS approaches to comprehensively study complex diseases and the need for further research on pathogen interactions and cultivar susceptibility for the future development of new sustainable, targeted management strategies in almond orchards. Full article

Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial diversity, starter cultures, and interactions, such as competition and quorum sensing, shape food ecosystems. Diverse biosensor platforms, including electrochemical, optical, piezoelectric, thermal, field-effect transistor-based, and lateral flow assays, offer distinct advantages tailored to specific food matrices and microbial targets, enabling rapid and sensitive detection. Biosensors have been developed for detecting pathogens in real-time monitoring of fermentation and tracking spoilage. Control strategies, including bacteriocins, probiotics, and biofilm management, support food safety, while decontamination methods provide an additional layer of protection. The integration of new techniques, such as nanotechnology, CRISPR, and artificial intelligence, into Internet of Things systems is enhancing precision, particularly in addressing regional food safety challenges. However, their adoption is still hindered by complex food matrices, high costs, and the growing challenge of antimicrobial resistance. Looking ahead, intelligent systems and wearable sensors may help overcome these barriers. Although gaps in standardization and accessibility remain, biosensors are well-positioned to revolutionize food microbiology, linking ecological insights to practical solutions and paving the way for safer, high-quality food worldwide. Full article

Biochar and seaweed fertilizers could improve soil quality and promote plant growth. However, the key soil factors and microbial mechanisms that drive maize growth in coastal saline–alkali soils remain unclear. A soil culture experiment was designed with four treatments—no organic fertilizer (CK), single seaweed fertilizer (F), single biochar (B), and combined application of seaweed fertilizer and biochar (BF)—to investigate the effects of biochar and seaweed fertilizer on maize growth and its mechanism. The results showed that B and BF significantly increased maize aboveground biomass by 8.86% and 17.28% compared to CK, respectively. The soil organic carbon, total nitrogen, available nitrogen, available phosphorus, available potassium content, and pH of B and BF were significantly increased. Bacterial diversity increased under B and BF, while fungal richness decreased under BF. The changes in the fungal community were mainly affected by soil available nitrogen, but there was no significant correlation between bacterial communities and these indicators. Pearson correlation analysis suggested that the bacterial Chao1 index was significantly positively correlated with maize growth indicators, soil available phosphorus, and available potassium, as well as the bacterial PD whole tree index with leaf area and available phosphorus. The fungal Shannon index was significantly negatively correlated with maize plant height, leaf area, SPAD, aboveground biomass, and soil total nitrogen and available nutrients. Overall, biochar and seaweed fertilization could significantly promote maize growth by improving soil chemical properties and microbial communities in coastal saline–alkali soils. Full article

This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed. Full article

Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at −1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds. Full article

As consumer demand for quality fish products continues to rise, quality has become a key factor in market competition. Ecological aquaculture research is exploring various farming methods to balance high-quality demand with environmental protection. This study compared three aquaculture models—cage culture (CG), recirculating aquaculture (RAG), and rice–fish co-culture (RG)—by analyzing muscle quality (AOAC, GC-MS), intestinal microbiota (16S rRNA), and liver metabolism (LC-MS) to assess their effects on M. albus. In terms of muscle quality, the RG group showed increased levels of EPA and DHA, reduced muscle moisture and crude lipid content, and enhanced crude protein accumulation. The crude protein content was significantly higher in the RAG group than in the CG group (p < 0.05). The RG group also had the highest levels of total, essential, and umami amino acids, followed by the RAG and CG groups. In terms of intestinal microbiota, the RG group had the highest microbial diversity and stability, with increased abundance of Firmicutes and Bacteroidetes and decreased levels of Proteobacteria. Compared to the CG, the RAG group also showed increased microbial diversity and a reduction in pathogenic genera. Liver metabolomics analysis demonstrated that the RG group had significant advantages over the CG group in amino acid, lipid, and energy metabolism. The RAG group exhibited upregulation of glycerophospholipid metabolism and a decrease in oxidative stress marker levels. Overall, the RG group enhanced muscle quality and optimized intestinal and liver metabolism in M. albus. Full article

Edible insects are gaining traction worldwide; however, the existing data regarding their microbiological quality remain inadequate. This study investigated the bacterial communities and microbiological quality of five types of frozen edible insects commercially available in Thailand. Amplicon sequencing revealed Firmicutes (Bacillota) and Proteobacteria (Pseudomonadota) as the main phyla across all samples; Bacteroidota was predominant in house crickets, Actinobacteriota in silkworms, and Desulfobacterota was exclusively found in house and mole crickets. Culture-based assays showed total viable counts, lactic acid bacteria, yeasts–molds, and spore-formers ranging from 3.41–6.58, 2.52–7.41, 1.83–5.62, to 2.00–4.70 log CFU·g⁻¹, respectively. In some samples, Enterobacteriaceae and Escherichia coli, key hygiene indicators, reached 5.05 and 2.70 log CFU·g⁻¹, respectively. Among foodborne pathogens, presumptive Bacillus cereus was found to vary from <1.70 to 3.93 log CFU·g⁻¹, while Clostridium perfringens and Staphylococcus aureus were under the quantitation limit, and Salmonella was absent. Overall, the results indicate significant variation in microbial diversity and quality among different insect types. The high levels of microbial hygiene indicators and foodborne pathogens in some samples raised food safety concerns and point to the need to develop or implement production guidelines and microbiological criteria for frozen edible insects to ensure food safety. Full article

Urban soils are subject to intense anthropogenic disturbance, often resulting in biodiversity loss and reduced ecosystem functionality. However, rhizospheric microbial communities help maintain critical soil-ecosystem services, supporting urban soil resilience. This study evaluated the diversity of culturable bacteria associated with the rhizospheres of Pennisetum clandestinum and Pseudelephantopus spicatus in green areas of Medellín, Colombia, under contrasting levels of anthropic pressures. Rhizospheric and non-rhizospheric soils were sampled near automotive mechanic sites, and bacterial communities were assessed through plate counting and morphological characterization. Alpha, beta, and rarefaction diversity indices were applied to evaluate culturable morphotypes. P. clandestinum supported a more diverse and complex rhizospheric microbiome, particularly in non-exposed soils, while P. spicatus hosted less diverse communities under similar conditions. Diversity indices effectively distinguished microbial patterns, demonstrating the utility of culture-based methods for microbial community assessment. As a first step in microbial bioprospecting workflows, these methods allow for the rapid screening of culturable diversity and support decision-making for the selection of promising environments, plant species, and microbial isolates. This approach can inform urban soil threats, the promotion of beneficial plant–microbe interactions, and the identification of bioindicator species for soil health monitoring in a framework for the management of green areas. Full article

In the African Sahel, fonio (Digitaria sp.) is a cereal crop that alleviates mid-season hunger before other main crops are harvested. As fonio is valued for its ability to grow under low nutrient and drought conditions, it was hypothesized that it may contain endophytic bacteria that can tolerate such extreme stress. White fonio seeds were obtained from a dry environment (Mali) and a moderate rainfall environment (Guinea). Plants were grown indoors on field soil mixed with sand to mimic Sahelian soils, grown at 30 °C, and exposed to drought, optimal water, and low nitrogen stress conditions. In total, 73 cultured bacteria were classified using full-length 16S rRNA sequencing followed by searching three 16S reference databases. Selected strains were tested in vitro for tolerance to relevant abiotic stresses. Including nine isolates from seeds, the candidate root/shoot endophytes spanned 27 genera and 18–39 top-match species. Several well-known nitrogen-fixing bacteria were cultured, including Ensifer. Leaves were dominated by Bacilli (spore-formers known to withstand dry conditions). There were five root isolates of Variovorax. Leifsonia was isolated from the leaves and showed 100% sequence identity with seed isolates, suggestive of transmission from seed to shoot. In vitro experiments showed that seed isolates, including Leifsonia, survived diverse abiotic stresses relevant to the Sahel. Combined, these results suggest that white fonio hosts stress-tolerant microbiota, and points to Leifsonia as a candidate seed-to-plant transmitted endophyte, pending confirmation by future whole genome sequencing. This microbial collection serves as a starting point for long-term experiments to understand stress tolerance in this under-studied crop. Full article