Search Results (1,902)

The purpose of this work was to obtain specialized enrichment cultures from an original extreme acidophilic consortium of extremely acidophilic microorganisms and to study their microbial community composition and biotechnological potential. At temperatures of 25, 35, 40 and 50 °C, distinct enrichments of extremely acidophilic microorganisms used in the processes of bioleaching sulfide ores were obtained using nutrient media containing ferrous sulfate, elemental sulfur and a copper sulfide concentrate as nutrient inorganic substrates, with and without the addition of 0.02% yeast extract. The microbial community composition was studied using the sequencing of the V3–V4 hypervariable region of the 16S rRNA genes. The different growth conditions led to changes in the microbial composition and relative abundance of mesophilic and moderately thermophilic, strict autotrophic and mixotrophic microorganisms in members of the genera Acidithiobacillus, Sulfobacillus, Leptospirillum, Acidibacillus, Ferroplasma and Cuniculiplasma. The dynamics of the oxidation of ferrous iron, sulfur, and sulfide minerals (pyrite and chalcopyrite) by the enrichments was also studied in the temperature range of 25 to 50 °C. The study of enrichment cultures using the molecular biological method using the metabarcoding method of variable V3–24 V4 fragments of 16S rRNA genes showed that enrichment cultures obtained under different conditions differed in composition, which can be explained by differences in the physiological properties of the identified microorganisms. Regarding the dynamics of the oxidation of ferrous ions, sulfur, and sulfide minerals (pyrite and chalcopyrite), each enrichment culture was studied at a temperature range of 25 to 50 °C and indicated that all obtained enrichments were capable of oxidizing ferrous iron, sulfur and minerals at different rates. The obtained enrichment cultures may be used in further work to increase bioleaching by using the suitable inoculum for the temperature and process conditions. Full article

Sustainability represents a significant global challenge, requiring a balance between environmental impact and the use of natural resources. White biotechnology, which uses microorganisms and enzymes for environmentally friendly products and processes, offers promising solutions to support a growing population. Within this context, the yeast Yarrowia lipolytica stands out, so we investigated the generation of biomass from two wild strains (ATCC 9773 and NRRL Y-50997) using different carbon sources. Additionally, protein content and amino acid profiles were assessed via standardized analytical methods to evaluate their potential as nutritional yeasts. Both strains demonstrated potential as nutritional yeasts, with biomass productivities of up to 35.5 g/L and 42 g/L, respectively. The protein content was high, with 58.8% for ATCC 9773 and 58.2% for NRRL Y-50997. Furthermore, the strains presented essential amino acid contents of 62.6% and 41.5%, with lysine being the most abundant amino acid. These findings underscore the versatility and productivity of Y. lipolytica, highlighting its potential for sustainable biotechnological applications such as single-cell protein production. 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

Straw returning (ST) significantly improves soil quality and profoundly impacts soil microorganisms. However, the effects of different ST application amounts on the soil bacterial community remain unclear, and more studies on optimal ST application amounts are warranted. This study aimed to investigate the bacterial diversity and composition, as well as physicochemical properties, of soil in a corn field with 5-year ST amounts of 0, 3, 4.5, 5, and 6 t/hm², respectively. The results indicated that ST significantly reduced soil bulk density and increased soil pH and nutrients. Meanwhile, ST had a significant effect on the bacterial composition, and the bacterial diversity increased significantly after ST. The relative abundance of Proteobacteria and Acidobacteria increased dramatically, whereas that of Actinobacteria significantly decreased after ST. The amount of ST had threshold effects on soil physicochemical properties and the dominant bacterial phyla. Moreover, the co-occurrence networks indicated that bacterial stability first increased and then decreased with the increase in ST amounts. Soil organic carbon and total nitrogen concentrations were the main drivers of bacterial diversity, whereas soil pH and total nitrogen concentrations were the main drivers of bacterial composition. This study strengthens the fact that ST amounts have threshold effects on the soil physicochemical properties and soil microorganisms, and ST amounts of 3–5 t/hm² were appropriate. Full article

Rare earth elements and yttrium (REY) are critical metals underpinning high-technology industries. Marine deposits have attracted growing interest due to their abundant REY reserves and high grades. This review synthesizes current knowledge on sources, distribution, and enrichment mechanisms of marine REY, with a particular focus on the role of microorganisms in REY phase transitions, fractionation, and enrichment. We highlight the largely untapped potential of marine-specific microbial strains and critically assess their influence on REY cycling. Key research challenges are proposed, followed by actionable directions to advance understanding of microbial–REY interactions. This review aims to deepen insights into marine REY cycling and support the sustainable development of deep-sea REY resources, emphasizing the need to integrate molecular-scale microbial processes into marine REY biogeochemical models. 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

Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources. Full article

There is a growing body of research showing that Alzheimer’s disease (AD) is related to enteric dysbacteriosis. Exercise can be effective in alleviating AD, but the effects that exercise has on the gut microbiota in AD patients needs to be further studied. Through this study, we aimed to investigate the differences in the diversity of gut microorganisms between AD model mice and wild-type mice and the effect that treadmill exercise has on the composition of the gut microbiota in both types of mice. C57BL/6 wild-type mice were randomly divided into a sedentary control group (WTC) and an exercise group (WTE); APP/PS1 double transgenic mice were also randomly divided into a sedentary control group (ADC) and an exercise group (ADE). After the control group remained sedentary for 12 weeks and a 12-week treadmill exercise intervention was adopted for the exercise group, the rectal contents were collected so that they could undergo V3-V4 16S rDNA sequencing, and a comparative analysis of the microbial composition and diversity was also performed. The alpha diversity of the gut microbiota in AD mice was lower than that in wild-type mice, but exercise increased the gut microbial diversity in both types of mice. At the phylum level, the dominant microorganisms in all four groups of mice were Bacteroidetes and Firmicutes. There was an increase in the Bacteroidetes phylum in AD mice. Treadmill exercise reduced the abundance of Bacteroidetes in both groups of mice, whereas the abundance of Firmicutes increased. At the genus level, Muribaculaceae, the Lachnospiraceae_NK4A136_group, Alloprevotella, and Alistipes were in relatively high abundance. Muribaculaceae and Alloprevotella were in greater abundance in AD mice than in wild-type mice, but both decreased after treadmill exercise. Through performing linear discriminant analysis effect size (LEfSe), we found that the dominant strains in AD mice were Campilobacterota, Helicobacteraceae, Escherichia–Shigella, and other malignant bacteria, whereas exercise resulted in an increase in probiotics among the dominant strains in both types of mice. Although gut microbial diversity decreases and malignant bacteria increase in AD mice, treadmill exercise can increase gut microbial diversity and lead to the development of dominant strains of probiotics in both types of mice. These findings provide a basis for applying exercise as a treatment for AD. Full article

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

Straw-returning is an effective way to improve straw utilization efficiency and reduce environmental pollution. Various straw-returning methods exist; however, their effects on soil microbial diversity and community composition in cool regions have been little studied. This study investigated the changes of soil microbial diversity and community composition under three straw-returning methods, i.e., straw mulching, straw mulching and overturning, straw crushed and mixed, as compared to straw removal as control. The results showed that straw-returning could alter the soil microbial community composition and abundance compared with straw removal. Alpha diversity analysis showed that straw mulching treatment, and straw crushed and mixed treatment significantly increased the diversity of both soil bacteria and fungi compared with straw mulching and overturning treatment. Moreover, this study preliminarily screened Trichoderma, Chaetomium and Streptomyces as potential straw-degrading microorganisms. This study provides basis for further enhancement of straw degradation by using soil microorganisms and sheds light on future work for improving straw degradation efficiency. Full article

Foodborne diseases are the most common causes of illness worldwide. Bacterial pathogens, including Staphylococcus aureus, are often involved in foodborne disease and pose a serious threat to human health. S. aureus is commonly found in humans and a variety of animal species. Staphylococcal enteric disease, specifically staphylococcal food poisoning (SFP), accounts for numerous gastrointestinal illnesses, through the contamination of food with its enterotoxins, and its major impact on human health imposes a heavy economic burden in society. Commonly, antibiotics and antimicrobials are used to treat SFP. However, a range of complications may arise with these treatments, impeding the control of S. aureus diseases specifically caused by methicillin-resistant S. aureus (MRSA). Natural alternative options to control S. aureus diseases, such as bacteriophages, plant-based antimicrobials, nanoparticle-based or light-based therapeutics, and probiotics, are promising in terms of overcoming these existing problems as they are environmentally friendly, abundant, unlikely to induce resistance in pathogens, cost-effective, and safe for human health. Recent findings have indicated that these alternatives may reduce the colonization and infection of major foodborne pathogens, including MRSA, which is crucial to overcome the spread of antibiotic resistance in S. aureus. This review focuses on the present scenario of S. aureus in foodborne disease, its economic importance and current interventions and, most importantly, the implications of natural antimicrobials, especially probiotics and synbiotics, as alternative antimicrobial means to combat pathogenic microorganisms particularly, S. aureus and MRSA. Full article

Water environments and sediments are important reservoirs for antibiotic resistance genes (ARGs). Under the pressure of antibiotics, ARGs can transform between microorganisms. Lanthanum-modified bentonite (LMB) is a phosphorus passivation material with good prospects in water environment restoration. After a treatment with LMB, the phosphorus forms in water and sediments will change, which may have an impact on microorganisms and the transmission of ARGs. To investigate the effects of LMB and antibiotics on ARGs and bacterial communities in sediment and aquatic environments, LMB and tetracycline (Tet) were added individually and in combination to mixed samples of sediment and water. The results showed that the addition of either LMB or Tet increased the abundance of intI1 and tetA genes in both the sediment and water, with the Tet addition increasing ARGs to more than 1.5 times the abundance in the control group. However, when LMB and Tet were present simultaneously, the abundance of ARGs showed no significant difference compared to the control group. Tet and LMB also affected the bacterial community structure and function in the samples and had different effects on the sediment and water. A correlation analysis revealed that the potential host bacteria of the intI1 and tetA genes were unclassified_Geobacteraceae, Geothrix, Flavobacterium, Anaeromyxobacter, and Geothermobacter. These findings indicate that Tet or LMB may increase the dissemination of ARGs by affecting microbial communities, while LMB may reduce the impact of Tet through adsorption, providing a reference for the safety of the LMB application in the environment and its other effects (alleviating antibiotic pollution) in addition to phosphorus removal. Full article

Background/Objectives: We evaluated the diabetic foot ulcer (DFU) microbiome in clinical situations identified as risk factors for a worse outcome and explored the roles of the most abundant microorganisms. Methods: A prospective multicenter cohort of diabetic patients with DFU were followed up for 6 months. We obtained a DFU tissue biopsy for microbiome analysis at the baseline visit. Genomic DNA was extracted (QIAamp DNA Mini Kit, Qiagen, Hilden, Germany) and quantified (QuantiFluor dsDNA System, Promega, Madison, WI, USA), with analysis of bacterial communities focusing on relative abundances (RA) and on alpha and beta diversity. Results: Overall, 59 DFUs were analyzed. DFUs of long duration (≥4 weeks) presented a higher RA of Gammaproteobacteria compared with ulcers of short duration (p = 0.02). Non-infected DFUs had a higher proportion of Actinobacteriota phyla than infected DFUs and, particularly, a higher RA of Corynebacterium genera (means ± SD: 0.063 ± 0.14 vs. 0.028 ± 0.13, respectively; p = 0.03). Regarding the pathogenic role of Staphylococcus aureus, DFUs with low S. aureus bacterial loads (<10⁶ CFU/mL) compared with those with high loads (≥10⁶ CFU/mL) showed a higher Corynebacterium RA (0.045 ± 0.08 vs. 0.003 ± 0.01, respectively; p = 0.01). Conclusions: In clinical situations associated with poor DFU outcomes, we observed a predominance of Gammaproteobacteria in the microbiome of long-duration ulcers and a higher RA of Corynebacterium in non-infected DFUs. An inverse relationship between the predominance of Corynebacterium and the S. aureus bacterial load in DFUs was also noted, which may suggest these commensals have a modulatory role. Further studies should explore the clinical utility of microbiome analysis for DFUs. Full article

Climate change can have a direct impact on the decomposition of organic matter, as well as indirect effects on peatland vegetation (including carnivorous plants) and the microbial communities associated with this environment. The activity of microbes varies depending on the type of peatland they inhabit. Because some microorganisms are highly sensitive, they can be used as indicators of climate change. However, there is still little knowledge of how changes in the temperature of the environment can affect the microbiome of carnivorous plants. The study was conducted to test the following hypotheses: (1) The effect of rising water temperature on the qualitative and quantitative structure of the microbiome of carnivorous peatland plants depends on the type of peatland; (2) habitats with a higher trophic status stimulate the development of microbial communities in the water, but are an unfavourable habitat for the development of the microbiome of plant traps. Irrespective of the type of peatland, the species richness of microorganisms was much higher in the water than in the traps. As the temperature increased, there was an increase in the abundance of bacteria, heterotrophic flagellates, and testate amoebae, which was much more pronounced in the peat bog than in the carbonate fen. Full article

In this study, to enhance the concentration of caproic acid generated from maize straw fermentation and clarify the structures of bacterial and fungal communities within the serially subcultured rumen microbial fermentation system, maize straw was used as the substrate. In a continuous subculture system, the impacts of ethanol addition on pH and gas production were explored, with a focus on the caproic acid yield in the final (eighth generation) generation and alterations in bacterial and fungal communities. The results showed that the relative abundances of unidentified_Clostridiales, Shuttleworthia, and Syntrophococcus in ethanol-driven caproic acid production were enriched by 5.36-fold, 2.61-fold, and 2.25-fold, respectively. This consequently increased the concentration of caproic acid in the fermentation broth to 1492 mg/L, representing a 3.7-fold increase. These findings are highly significant for the high-value utilization of maize straw waste to produce caproic acid via the carboxylic acid platform using rumen microorganisms in industrial processing. Full article