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BACKGROUND RESULTS CONCLUSION Xianju wheat paste, a traditional condiment in Hubei Province, China, possesses nutritional value and a distinctive taste profile. Nevertheless, there remains a dearth of comprehensive comprehension regarding the intricate interplay between the microbial population and its nutritional profile in Xianju wheat paste.It was determined that Xianju wheat paste harbors predominant microbial genera such as Bacillus, Staphylococcus and Aspergillus. The findings from high‐throughput sequencing analysis revealed the presence of 11 bacterial genera in Xianju wheat paste, with relative abundances exceeding 1%. These genera included Bacillus, Staphylococcus, Brevibacterium, Lactobacillus, Allorhizobium‐Neorhizobium‐Pararhizobium‐Rhizobium, Enterobacteriaceae, Pantoea, Brachybacterium, Klebsiella, Escherichia‐Shigella and Ochrobactrum. Furthermore, six fungal genera were identified with relative abundances greater than 1%, specifically Aspergillus, Zygosaccharomyces, Cutaneotrichosporon, Candida, Millerozyma and Rhizopus. The correlation analysis indicated a significant impact of the microbial community and nutritional flavor on the second phase of fermentation in Xianju wheat paste. The predominant bacterium Bacillus in Xianju wheat paste facilitated the production of free amino acids, whereas Staphylococcus exhibited a negative correlation with free amino acid levels. The quantity of volatile compounds in Xianju wheat paste progressively increased during fermentation, with the presence of typical aroma compounds 4‐vinyl‐2‐methoxyphenol significantly associated with Bacillus. This indicated Bacillus notably enhanced the production of aromatic substances. Furthermore, a strong correlation was observed between Staphylococcus and the 18 volatile organic compounds, highlighting their substantial contribution to these aroma compounds.This research indicates that the presence of microbial communities significantly contributes to the development of the nutritional flavor profile in Xianju wheat paste. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Amplifying small subunit (SSU) rRNA genes with universal primers in assessing microbial populations diversity, but target microorganisms are sometimes omitted due to inadequate primer coverage. Adding degenerate bases to primers can help, but existing methods are complex and time-consuming. This study introduces a user-friendly tool called "Degenerate primer 111" for adding degenerate bases to existing universal primers. By aligning one universal primer with one uncovered target microorganism's SSU rRNA gene, this tool iteratively generates a new primer, maximizing coverage for the target microorganisms. The tool was used to modify eight pairs of universal primers (515F Parada-806R Apprill, S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21, OP_F114-KP_R013, 27F-1492R, 341F-806R, OP_F066-KP_R013, 515F Parada-926R Quince, 616*F-1132R), and generated 29 new universal primers with increased coverage of specific target microorganisms without increasing coverage of non-target microorganisms. To verify the effectiveness of the improved primers, one set of original and improved primers (BA-515F-806R and BA-515F-806R-M1) was used to amplify DNA from the same sample, and high-throughput sequencing of the amplicons confirmed that the improved primers detected more microbial species compared to the original primers. Future researchers can use this tool to develop more personalized primers to meet their diverse microorganism detection needs. [ABSTRACT FROM AUTHOR]

[Display omitted] • Biofilters (BFs) can remove significant VMS loads from gas. • Low toluene concentrations (315–635 mg m−3) improved VMS removal. • Majority (87.7%) of VMS and toluene removal occurred in the initial BF section. • Toluene shaped microbial population, boosting VMS-degrading microorganisms. • Results underscore BF potential to reduce VMS concentration, requiring optimization. The removal of volatile methyl siloxanes (VMS) from landfill biogas is crucial for clean energy utilization. VMS are usually found together with aromatic compounds in landfill biogas of which toluene is the major representative. In the present study, two biofilters (BFs) packed with either woodchips and compost (WC) or perlite (PER) were used to study the (co–) removal of octamethyltrisiloxane (L3) and octamethylcyclotetrasiloxane (D4) from gas in presence and absence of toluene, used as a representative aromatic compound. The presence of low inlet toluene concentrations (315 ± 19 – 635 ± 80 mg toluene m-3) enhanced the VMS elimination capacity (EC) in both BFs by a factor of 1.8 to 12.6. The highest removal efficiencies for D4 (57.1 ± 1.1 %; EC = 0.12 ± 0.01 gD4 m-3 h-1) and L3 (52.0 ± 0.6 %; EC = 0.23 ± 0.01 gL3 m-3 h-1) were observed in the BF packed with WC. The first section of the BFs (EBRT = 9 min), where toluene was (almost) completely removed, accounted for the majority (87.7 ± 0.6 %) of the total VMS removal. Microbial analysis revealed the impact of VMS and toluene in the activated sludge, showing a clear selection for certain genera in samples influenced by VMS in the presence (X 2) or absence (X 1) of toluene, such as Pseudomonas (X 1 = 0.91 and X 2 = 12.0 %), Sphingobium (X 1 = 0.09 and X 2 = 4.04 %), Rhodococcus (X 1 = 0.42 and X 2 = 3.91 %), and Bacillus (X 1 = 7.15 and X 2 = 3.84 %). The significant maximum EC values obtained by the BFs (0.58 gVMS m-3 h-1) hold notable significance in a combined system framework as they could enhance the longevity of traditional physicochemical methods to remove VMS like activated carbon in diverse environmental scenarios. [ABSTRACT FROM AUTHOR]

Introduction: Sichuan south-road dark tea (SSDT) is generally produced through a series of processes, including fixing, rolling, pile fermentation, and drying, with microbial action during pile fermentation playing a crucial role in determining tea quality. The air within the SSDT pile fermentation plant (SSDTPP) is considered an important source of these microbes, but research in this area has been limited. Methods: In this study, air samples from SSDTPP were collected on the 1st (SSDT1), 12th (SSDT2), and 24th (SSDT3) days of pile fermentation and comprehensively analyzed by high-throughput sequencing. Results and discussion: The results revealed the presence of 2 and 24 phyla, 9 and 49 classes, 18 and 88 orders, 28 and 153 families, 38 and 253 genera, and 47 and 90 species of fungi and bacteria, respectively, across all samples. SSDT1 and SSDT2 individually had the highest fungal and bacterial diversity, while Aspergillus was the dominant genus throughout the pile fermentation with an abundance of 34.6%, 91.17%, and 67.86% in SSDT1, SSDT2, and SSDT3, respectively. Microbial populations in SSDT1 were predominantly involved in xenobiotic biodegradation and metabolism, amino acid metabolism, the biosynthesis of other secondary metabolites, etc. However, SSDT2 exhibited a higher prevalence of human disease-related functions. SSDT3 primarily focused on the metabolism of other amino acids and carbohydrate metabolism. Additionally, 104 genera and 22 species coexisted in both SSDTPP air and piled SSDT, suggesting that frequent microbial exchange may occur between them. These findings pave the way for microbial traceability during SSDT production and provide a foundation for further functional microbial research. [ABSTRACT FROM AUTHOR]

Slow Transit Constipation (STC) is characterized by impaired colonic motility, but its relationship with gut microbiota remains unclear. This study investigated the correlation between specific gut microbial populations and STC, focusing on the Lactobacillus acidophilus to Lactobacillus johnsonii (A/J) ratio. We used four rat groups: Control (CON), Loperamide-induced STC (LOP), antibiotic-treated (ABX), and antibiotic plus Loperamide (ABX + LOP). Fecal samples were analyzed using 16S rRNA gene sequencing, and serum metabolites were examined through LC–MS. The LOP group showed an increased A/J ratio, while ABX and ABX + LOP groups had decreased ratios. Notably, the ABX + LOP group did not develop STC symptoms. Metabolomic analysis revealed alterations in key metabolites across groups, including changes in levels of guanidinoacetate, glycine, l-glutamine, nicotine, and nicotinate d-ribonucleotide in the LOP group, and variations in l-glutamine, l-phenylalanine, l-tyrosine, histamine, d-ornithine, and lecithin in the ABX and ABX + LOP groups. Our findings suggest a correlation between the A/J ratio and STC development, offering insights into STC pathophysiology and potential microbiome-targeted therapies. [ABSTRACT FROM AUTHOR]

Pathogenic fungi can cause significant annual losses in the quality and quantity of fruits belonging to Rosaceae family during pre‐ and postharvest. Synthetic fungicides are considered the main method for controlling diseases in food crops; however, they pose a great risk to human health and to the environment. As a result, biological control methods, which are based on living microorganisms to reduce the population or to inhibit the growth of pathogens, have arisen as a safe alternative. In this review, we highlight the principal mechanisms (e.g., nutrition and space competition, mycoparasitism, induced resistance and growth enhancement, production of volatile organic compounds, and antibiosis) utilized by the most frequently reported non‐Saccharomyces biocontrol agents (BCAs) yeasts: Meyerozyma guilliermondii, Pichia membranifaciens, Wickerhamomyces anomalus, Metschnikowia pulcherrima, Hanseniaspora uvarum, and Aureobasidium pullulans, against the common pathogenic fungi found within Rosaceae family: Penicillium expansum, Botrytis cinerea, and Monilinia spp. Understanding BCAs' importance and mode of action is a necessary step in order to reduce the detrimental effect of spoilage fungi in the agriculture and food industry, by achieving a more sustainable and safer control of them. [ABSTRACT FROM AUTHOR]

Understanding the environmental drivers of microbial H 2 metabolisms is crucial for evaluating the risks for geological hydrogen storage. This study investigates how mineralogy and temperature affect H 2 consumption kinetics and metabolic activity of a microbial consortium containing methanogens, homoacetogens and sulfate reducers, incubated at 25, 34 and 40 °C under H 2 /CO 2 (80/20, v/v; 2 bars) with different rock powders (basalt, calcite, gypsum, and sandstone). The presence of gypsum favors sulfate reduction over methanogenesis and homoacetogenesis, especially at 25 °C. Methanogenesis is dominant at 34 and 40 °C with all sulfate-free mineralogies. At 25 °C, homoacetogenic bacteria are favored over methanogens and acetate production varies with the mineralogy. This suggests interactions of the microbial community with the rock powders, which may serve as a surface to form biofilms. These metabolic shifts are associated with radical changes in microbial populations, highlighting that ecosystems plasticity towards H 2 also depends on the mineralogical composition of the reservoir. • Both temperature and mineralogy affect H 2 consumption kinetics. • Gypsum powder favors sulfate reduction over methanogenesis and homoacetogenesis. • Low temperature favors homoacetogenesis over methanogenesis. • Proportions of methanogenesis and homoacetogenesis vary with the substrate mineralogy. • Metabolic shifts are associated with radical changes in microbial populations. [ABSTRACT FROM AUTHOR]

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix. Evolution experiments are beginning to explicitly address the impact of graph structures on mutant fixation. However, the assumptions of evolutionary graph theory differ from the conditions of modern evolution experiments, making the comparison between theory and experiment challenging. Here, we aim to bridge this gap by using our new model of spatially structured populations. This model considers connected subpopulations that lie on the nodes of a graph, and allows asymmetric migrations. It can handle large populations, and explicitly models serial passage events with migrations, thus closely mimicking experimental conditions. We analyze recent experiments in light of this model. We suggest useful parameter regimes for future experiments, and we make quantitative predictions for these experiments. In particular, we propose experiments to directly test our recent prediction that the star graph with asymmetric migrations suppresses natural selection and can accelerate mutant fixation or extinction, compared to a well-mixed population. Author summary: Predicting how mutations spread through a population and eventually take over is important for understanding evolution. Complex spatial structures are ubiquitous in natural microbial populations, and can impact the fate of mutants. Theoretical models have been developed to describe this effect. They predict that some spatial structures have mutant fixation probabilities that differ from those of well-mixed populations. Experiments are beginning to probe these effects in the laboratory. However, there is a disconnect between models and experiments, because they consider different conditions. In this work, we connect them through a new model that closely matches experimental conditions. We analyze recent experiments and propose new ones that should allow testing the effects of complex population spatial structures on mutant fate. [ABSTRACT FROM AUTHOR]

Microorganisms, including fungi, bacteria, cyanobacteria, and algae, frequently colonize the surfaces of cultural heritage materials. These biological agents can cause biodeterioration through various mechanisms, resulting in aesthetic alteration, physical disruption, or compromise of mechanical integrity. To assess the presence and diversity of microorganisms, a combination of microscopy techniques is commonly used in conjunction with results from both culture‐dependent and culture‐independent methods. However, microbial populations are often underestimated. To address this issue, microorganisms can be detected by their intrinsic fluorescence, which can be observed via fluorescence microscopy. This approach facilitates the mapping of the spatial arrangement of microorganisms and the understanding of colonization patterns, thereby complementing established imaging techniques and providing insight into the interactions of microbial communities with the substrate. Given the limited research in this area, we examine the potential of microorganism autofluorescence as a molecular tool for investigating biodeterioration in artistic and architectural heritage, with a particular focus on paper and stone materials. Identifying and understanding the diverse microbiota that may be present is crucial for developing tailored and effective preventive measures and conservation treatments, as some of the species discovered may pose significant risks to both artifacts and human health. [ABSTRACT FROM AUTHOR]

This study evaluates the efficacy of the Thiopaq bio-desulfurization system at the Daegu Bangcheon-ri Sanitary Landfill in Korea over 1 year focusing on operational insights and microbial dynamics. The system employs sulfur-oxidizing bacteria (SOBs) to convert hydrogen sulfide (H2S) in landfill gas (LFG) into elemental sulfur. Key findings include maintaining over 96% H2S removal efficiency despite operational challenges such as sulfur clogging and foam formation. Significant microbial community shifts were observed, with Thioalkalibacter halophilus remaining robust, Alkalilimnicola ehrlichii declining, and Halothiobacillus kellyi becoming more prominent, especially during new well installations with high thiol (methanethiol) concentrations. Scanning electron microscopy revealed distinct morphological characteristics of bio-sulfur under varying conditions contributing to process optimization. Our results underscore the necessity for continuous monitoring and adaptive management of microbial populations and system parameters to effectively handle fluctuating LFG compositions and operational conditions. This study provides substantial guidance for enhancing LFG quality and bio-sulfur production in large-scale landfills. [ABSTRACT FROM AUTHOR]

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations. [ABSTRACT FROM AUTHOR]

The gut barrier is essential for protection against pathogens and maintaining homeostasis. Macrophages are key players in the immune system, are indispensable for intestinal health, and contribute to immune defense and repair mechanisms. Understanding the multifaceted roles of macrophages can provide critical insights into maintaining and restoring gastrointestinal (GI) health. This review explores the essential role of macrophages in maintaining the gut barrier function and their contribution to post-inflammatory and post-infectious responses in the gut. Macrophages significantly contribute to gut barrier integrity through epithelial repair, immune modulation, and interactions with gut microbiota. They demonstrate active plasticity by switching phenotypes to resolve inflammation, facilitate tissue repair, and regulate microbial populations following an infection or inflammation. In addition, tissue-resident (M2) and infiltration (M1) macrophages convert to each other in gut problems such as IBS and IBD via major signaling pathways mediated by NF-κB, JAK/STAT, PI3K/AKT, MAPK, Toll-like receptors, and specific microRNAs such as miR-155, miR-29, miR-146a, and miR-199, which may be good targets for new therapeutic approaches. Future research should focus on elucidating the detailed molecular mechanisms and developing personalized therapeutic approaches to fully harness the potential of macrophages to maintain and restore intestinal permeability and gut health. [ABSTRACT FROM AUTHOR]

Organic vegetable production is needed worldwide to minimize the use of inorganic fertilizers, protect the environment, and produce healthy food. Accordingly, in the present study, the effects of organic granules on the productivity, quality, and nutrient uptake level of tomatoes and the fertility and microbial population of the soil were determined. Briefly, organic NPK granules and organic N, P and K-rich sources were compared with synthetic NPK granules and synthetic fertilizers administered at 100 and 75% of the recommended fertilizer levels. Among the various treatments applied, treatment with 100% of the recommended NPK using the synthetic NPK granules (Urea, DAP and MOP) led to higher growth, yield attributes, and yield (fruit yield, - 24.21 t/ha and stover yield, -15.01 t/ha) of tomato. This treatment also enhanced the nutrient uptake by tomato. However, quality parameters, such as total soluble solids (6.64%), titrable acidity (0.62%), ascorbic acid content (14.31 mg/100 g), lycopene content (3.54 mg/100 g), reducing sugars (3.11%), non-reducing sugars (1.02%), total sugar (4.13%), and shelf life (15.76 days) of tomato were higher with 100% of the recommended NPK from organic NPK granules than from synthetic granules. This treatment also enhanced the available nutrients and microbial population in the soil. Notably, the same trend was observed for tomatoes fertilized with 75 % of the recommended NPK. The lowest values were obtained with the absolute control. Based on the results of this experiment, the application of 100% of the recommended NPK using organic NPK granules is the best approach to improve the quality of tomato fruits and to enhance the soil fertility. [ABSTRACT FROM AUTHOR]

A high-fat diet can modify the composition of gut microbiota, resulting in dysbiosis. Changes in gut microbiota composition can lead to increased permeability of the gut barrier, allowing bacterial products like lipopolysaccharides (LPS) to enter circulation. This process can initiate systemic inflammation and contribute to neuroinflammation. Empagliflozin (EF), an SGLT2 inhibitor-type hypoglycemic drug, has been reported to treat neuroinflammation. However, there is a lack of evidence showing that EF regulates the gut microbiota axis to control neuroinflammation in HFD models. In this study, we explored whether EF could improve neuroinflammation caused by an HFD via regulation of the gut microbiota and the mechanism underlying this phenomenon. Our data revealed that EF alleviates pathological brain injury, reduces the reactive proliferation of astrocytes, and increases the expression of synaptophysin. In addition, the levels of inflammatory factors in hippocampal tissue were significantly decreased after EF intervention. Subsequently, the results of 16S rRNA gene sequencing showed that EF could change the microbial community structure of mice, indicating that the abundance of Lactococcus , Ligilactobacillus and other microbial populations decreased dramatically. Therefore, EF alleviates neuroinflammation by inhibiting gut microbiota-mediated astrocyte activation in the brains of high-fat diet-fed mice. Our study focused on the gut-brain axis, and broader research on neuroinflammation can provide a more holistic understanding of the mechanisms driving neurodegenerative diseases and inform the development of effective strategies to mitigate their impact on brain health. The results provide strong evidence supporting the larger clinical application of EF. Schematic illustration of EF alleviates neuroinflammation via integrating analysis of the microbiota-gut-brain axis in high-fat diet-induced mice. [Display omitted] • RNA-seq and 16S rRNA were used to detect genes and flora species in HFD mice after administration of EF. • EF alleviates neuroinflammation via improved gut microbiota profile and affects the Akt-mTOR pathway. • The role of EF in ameliorating neuroinflammation induced by a HFD via the gut-brain axis were to investigated. [ABSTRACT FROM AUTHOR]

In recent years, the phenomenon of black–odorous water has occurred frequently, and constructed wetlands have been widely used as an effective means of treating black–odorous water. In order to achieve the goal of low-carbon and high-efficiency long-term clean-up of black–odorous water, the modular constructed wetland system was optimized in this study. The optimized modular constructed wetland consisted of aeration, denitrification, and phosphorus removal, of which the denitrification module was a sulfur–iron autotrophic denitrification unit and the phosphorus removal module was a polyaluminum chloride composite filler phosphorus-removal unit. Experimental findings indicated that modular systems with layout ratios of 1:3:1 (A) and 1:2:2 (B) exhibit outstanding performance in remediating contaminants from black–odorous water. Notably, system B demonstrated superior treatment efficiency. Under conditions of high pollution loading, system B consistently achieved stable removal rates for COD (95.79%), TN (91.74%), NH4+-N (95.17%), and TP (82.21%). The combination of along-track changes and high-throughput sequencing results showed that the synergies among the units did not produce negative effects during the purification process, and each unit realized its predefined function. Changes in the substrate and internal environment of the wetland units caused changes in the microbial populations, and the unique microbial community structure of the units ensured that they were effective in removing different pollutants. [ABSTRACT FROM AUTHOR]

The gut microbiota influences host metabolism and health, impacting diseases. Research into how diet affects gut microbiome dynamics in model organisms is crucial but underexplored. Herein, we examined how dietary adenine affects uric acid levels and the gut microbiota over five generations of Drosophila melanogaster. Wild-type W1118 flies consumed diets with various adenine concentrations (GC: 0%, GL: 0.05%, and GH: 0.10%), and their gut microbiota were assessed via Illumina MiSeq sequencing. Adenine intake significantly increased uric acid levels in the GH group > the GC group. Despite no significant differences in the alpha diversity indices, there were significant disparities in the gut microbiota health index (GMHI) and dysbiosis index (MDI) among the groups. Adenine concentrations significantly altered the diversity and composition of the gut microbiota. High adenine intake correlated with increased uric acid levels and microbial population shifts, notably affecting the abundances of Proteobacteria and Firmicutes. The gut microbiota phenotypes included mobile elements, gram-positive bacteria, biofilm-forming bacteria, and gram-negative bacteria. The significantly enriched KEGG pathways included ageing, carbohydrate metabolism, and the immune system. In conclusion, adenine intake increases uric acid levels, alters gut microbiota, and affects KEGG pathways in Drosophila across generations. This study highlights the impact of dietary adenine on uric acid levels and the gut microbiota, providing insights into intergenerational nutritional effects. [ABSTRACT FROM AUTHOR]

Antibiotic-induced dysbiosis in the fish gut causes significant adverse effects. We use fecal microbiota transplantation (FMT) to accelerate the restoration of florfenicol-perturbed intestinal microbiota in koi carp, identifying key bacterial populations and metabolites involved in the recovery process through microbiome and metabolome analyses. We demonstrate that florfenicol disrupts intestinal microbiota, reducing beneficial genera such as Lactobacillus, Bifidobacterium, Bacteroides, Romboutsia, and Faecalibacterium, and causing mucosal injuries. Key metabolites, including aromatic amino acids and glutathione-related compounds, are diminished. We show that FMT effectively restores microbial populations, repairs intestinal damage, and normalizes critical metabolites, while natural recovery is less effective. Spearman correlation analyses reveal strong associations between the identified bacterial genera and the levels of aromatic amino acids and glutathione-related metabolites. This study underscores the potential of FMT to counteract antibiotic-induced dysbiosis and maintain fish intestinal health. The restored microbiota and normalized metabolites provide a basis for developing personalized probiotic therapies for fish. Analysis of microbiome and metabolome reveals that fecal microbiota transplantation accelerates the restoration of florfenicol-disturbed gut microbiota in koi carp and identifies key microbial taxa and metabolites involved in this recovery process. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is a promising and efficient biological nitrogen removal process, which can economically treat wastewater without organic supplement and aeration. However, to date, the insufficient nitrite in wastewater is the foremost problem encountered in anammox process. This restriction hinders full-scale application of anammox worldwide. Nitrite can be provided by innovative processes such as autotrophic denitrification and denitrifying anaerobic methane oxidation (DAMO). Therefore, the synergy between them and anammox is feasible means to solve the bottleneck. This review unravels the advantages and operating strategies of autotrophic denitrification, DAMO and their coupled processes with anammox. Besides, different electron donors such as reductive sulfur, iron, hydrogen, manganese and methane are analyzed in the two processes. The characteristics of microbial populations and their synergies in microbial communities are deciphered, and nitrogen removal contributions through different microbes are also highlighted. Still, nitrogen conversion pathways are clarified in the processes with different electron donors, and metabolic mechanisms of both autotrophic denitrifiers and DAMO microbes are revealed. Finally, the challenges to be focused in autotrophic denitrification and DAMO processes are proposed, and future perspectives on their coupled process with anammox are also put forward. [ABSTRACT FROM AUTHOR]

Wheat starch fermentation slurry is the main substrate for producing Ganmianpi, a traditional Chinese fermented wheat starch-based noodle. In the present work, the microbial population dynamics and metabolite changes in wheat starch fermentation slurry at different fermentation times (0, 1, 2, 3, and 4 days) were measured by using high-throughput sequencing analysis and headspace solid-phase microextraction gas chromatography–mass spectrometry (HS-SPME/GC-MS) methods. The texture and sensory properties of Ganmianpi made from fermented starch slurry are also evaluated. The results showed that Latilactobacillus curvatus and Leuconostoc citreum were the dominant bacteria in wheat starch fermentation slurry, while Saccharomyces cerevisiae and Kazachstania wufongensis were identified as the main species of fungi. With the extension of fermentation time, the reducing sugar content first increased and then decreased, when the titratable acidity content showed an increasing trend, and the nonvolatile acid was significantly higher than the volatile acid. A total of 62 volatile flavor compounds were identified, and the highest content is alcohols, followed by acids. Fermentation significantly reduced the hardness and chewiness of Ganmianpi, and increased its resilience and cohesiveness. Ganmianpi made from fermented starch slurry for two and three days showed a higher sensory score than other samples. The present study is expected to provide a theoretical basis for exploiting the strains with potential for commercial application as starter cultures and quality improvement of Ganmianpi. [ABSTRACT FROM AUTHOR]

Integrated pest management (IPM) is a comprehensive approach to managing diseases, focusing on combining various strategies to reduce pathogen populations effectively and in an environmentally conscious way. We investigated the effects of IPM on beneficial microbial populations and its relationship with pathogen populations in both direct-seeded rice (DSR) and transplanted rice (TR) systems. This study demonstrates that IPM practices have significantly higher populations of beneficial microbes, such as Trichoderma harzianum and Pseudomonas fluorescens, and lower level of the pathogen Fusarium verticillioides compared to non-IPM (farmer practices). The average mean population of T. harzianum was 6.38 x 10³ CFU/g in IPM compared to 3.22 x 10³ CFU/g in non-IPM during 2019 in TR at Bambawad. P. fluorescens mean population in 2019 was significantly higher in IPM (4.67 x 10³ CFU/g) than in non-IPM (3.82 x 10³ CFU/g) at the Karnal location in DSR. The F. verticillioides populations were significantly lower in IPM fields (9.46 x 10³ CFU/g) compared to non-IPM fields (11.48 x 10³ CFU/g) during 2017 at Haridwar in TR. Over three years, a significant increase in the populations of beneficial microbes in IPM plots was observed in all three locations of both TR and DSR, highlighting the sustainable impact of IPM practices. Disease dynamics analysis revealed that IPM effectively managed key diseases in both DSR and TR systems, with significant correlations between microbial density and disease severity. A significant positive correlation was recorded between F. verticillioides population and bakanae incidence at all three locations. Sheath blight incidence was negatively correlated with P. fluorescens population in both TR and DSR. In DSR, bacterial blight and brown spot diseases are reduced with the increased population of T. harzianum. Bioagents T. harzianum and P. fluorescens reduced disease incidence, underscoring the role of beneficial microbes in disease suppression and their importance for sustainable production using IPM practices. [ABSTRACT FROM AUTHOR]

Introduction: Inside oil and gas pipelines, native microbial communities and different solid compounds typically coexist and form mixed deposits. However, interactions between these deposits (primarily consisting of mineral phases) and microorganisms in oil and gas systems remain poorly understood. Here, we investigated the influence of magnetite (Fe3O4), troilite (FeS), and silica (SiO2) on the microbial diversity, cell viability, biofilm formation, and EPS composition of an oil-recovered multispecies consortium. Methods: An oilfield-recovered microbial consortium was grown for 2 weeks in separate bioreactors, each containing 10 g of commercially available magnetite (Fe3O4), troilite (FeS), or silica (SiO2) at 40°C ± 1°C under a gas atmosphere of 20% CO2/80% N2. Results: The microbial population formed in troilite significantly differed from those in silica and magnetite, which exhibited significant similarities. The dominant taxa in troilite was the Dethiosulfovibrio genus, whereas Sulfurospirillum dominated in magnetite and silica. Nevertheless, biofilm formation was lowest on troilite and highest on silica, correlating with the observed cell viability. Discussion: The dissolution of troilite followed by the liberation of HS- (H2S) and Fe2+ into the test solution, along with its larger particle size compared to silica, likely contributed to the observed results. Confocal laser scanning microscopy revealed that the EPS of the biofilm formed in silica was dominated by eDNA, while those in troilite and magnetite primarily contained polysaccharides. Although the mechanisms of this phenomenon could not be determined, these findings are anticipated to be particularly valuable for enhancing MIC mitigation strategies currently used in oil and gas systems. [ABSTRACT FROM AUTHOR]

Introduction: Panax notoginseng, a medicinal herb in China, is attacked by several pathogens during its cultivation. Dazomet (DZ) is a soil fumigant that is effective in controlling soil-borne pathogens, but its long-term effects on P. notoginseng growth and soil properties are unknown. Methods: We conducted field experiments over two consecutive years to assess the impact of three concentrations of DZ fumigation (35 kg/666.7 m2, 40 kg/666.7 m2, and 45 kg/666.7 m2) on soil physicochemical properties, microbial diversity, and P. notoginseng growth. Correlation analyses were performed between microbial community changes and soil properties, and functional predictions for soil microorganisms were conducted. Results: DZ fumigation increased total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, and ammonia nitrogen levels in the soil. DZ fumigation promoted the nutrient accumulation and improvement of agronomic traits of P. notoginseng, resulted in a 2.83-3.81X yield increase, with the highest total saponin content increasing by 24.06%. And the 40 kg/666.7 m2 treatment had the most favorable impact on P. notoginseng growth and saponin accumulation. After DZ fumigation, there was a decrease in the relative abundance of pathogenic fungi such as Fusarium, Plectosphaerella, and Ilyonectria, while beneficial bacteria such as Ramlibacter, Burkholderia, and Rhodanobacteria increased. The effects of fumigation on soil microorganisms and soil physicochemical properties persisted for 18 months post-fumigation. DZ fumigation enhanced the relative abundance of bacteria involved in the biosynthesis of secondary metabolites and arbuscular mycorrhizal fungi, reduced the relative abundance of plant-animal pathogenic fungi, reduced the occurrence of soil-borne diseases. Conclusion: In conclusion, DZ fumigation enhanced soil physicochemical properties, increased the proportion of beneficial bacteria in the soil, and rebalanced soil microorganism populations, consequently improving the growth environment of P. notoginseng and enhancing its growth, yield, and quality. This study offers a theoretical foundation for DZ fumigation as a potential solution to the continuous cropping issue in perennial medicinal plants such as P. notoginseng. [ABSTRACT FROM AUTHOR]

Water reservoir sediments represent a distinct habitat that harbors diverse microbial resources crucial for nitrogen cycling processes. The discovery of resuscitation promoting factor (Rpf) has been recognized as a crucial development in understanding the potential of microbial populations. However, our understanding of the relationship between microorganisms containing rpf-like genes and nitrogen-cycling functional populations remains limited. The present study explored the distribution patterns of rpf-like genes and nitrogen-cycling genes in various water reservoir sediments, along with their correlation with environmental factors. Additionally, the co-occurrence of rpf-like genes with genes associated with the nitrogen cycle and viable but non-culturable (VBNC) formation was investigated. The findings indicated the ubiquitous occurrence of Rpf-like domains and their related genes in the examined reservoir sediments. Notably, rpf-like genes were predominantly associated with Bradyrhizobium, Nitrospira, and Anaeromyxobacter, with pH emerging as the primary influencing factor for their distribution. Genera such as Nitrospira, Bradyrhizobium, Anaeromyxobacter, and Dechloromonas harbor the majority of nitrogen-cycling functional genes, particularly denitrification genes. The distribution of nitrogen-cycling microbial communities in the reservoir sediments was mainly influenced by pH and NH4 +. Notably, correlation network analysis revealed close connections between microorganisms containing rpflike genes and nitrogen-cycling functional populations, as well as VBNC bacteria. These findings offer new insights into the prevalence of rpf-like genes in the water reservoir sediments and their correlation with nitrogen-cycling microbial communities, enhancing our understanding of the significant potential of microbial nitrogen cycling. [ABSTRACT FROM AUTHOR]

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the "mobilome," potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs. [ABSTRACT FROM AUTHOR]

Simple Summary: The water environment in Laizhou Bay has experienced mild eutrophication in recent years, impacting the interactions between environmental factors, microorganisms, and aquatic species. The metagenomic analysis of 142 samples from various water layers revealed that Oplegnathus punctatus mariculture significantly increases microbial abundance and complexity in the culture area. These alterations were more noticeable in sediments compared to seawater. Cyanobacteria and Candidatus Micrarchaeota in seawater, and Actinobacteria and Thaumarchaeota in sediments show notably higher abundances in the mariculture area, indicating shifts in microbial community structure due to aquaculture practices. Antibiotic resistance genes (ARGs) in sediments are highly sensitive to environmental variables, particularly oxygen solubility and salinity. This indicates that Oplegnathus punctatus mariculture can impact the occurrence and spread of antibiotic resistance in marine ecosystems. The study underscores the intricate and dynamic relationships between microorganisms, environmental conditions, and ARGs, highlighting the need for region-specific strategies in managing marine resources sustainably. (1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism–environment–ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources. [ABSTRACT FROM AUTHOR]

Chemosynthetic microorganisms facilitate microbialite development in many caves throughout the world. In Youqin Cave and Tian'e Cave, located in the Carboniferous–Triassic carbonates on the South China Block, five Quaternary speleothems (stalagmite, stalactite and cave pearl) that are 2.3 to 11.0 cm long were examined for their petrographic, geochemical and microbiological features to reveal how chemotrophs contribute to microbialite growth. In the speleothems, millimetre‐sized stromatolites, thrombolites and calcified microbial mats are characterized by alternating light, calcitic microlaminae and dark, clay and organic‐rich calcite microlaminae. Filamentous (reticulate, smooth, nodular and helical), coccoid and bacilliform microbes, originally carried into the caves from surface soils, are more common in the dark microlaminae/clots than in the light microlaminae. 16S rRNA gene sequencing shows that the biotas in the microbialites are dominated by chemoorganotrophic heterotrophic bacteria, including primarily Sphingomonas, Crossiella and Acinetobacter, and rare Archaea. Diverse metabolic pathways of these prokaryotes, including ureolysis, denitrification and nitrite ammonification, contributed to increases in localized pH and/or dissolved inorganic carbon in these microenvironments, prompting carbonate precipitation. Development of the cave microbialites was probably controlled by the evolution of the cave microbial community as environmental conditions changed. Microbialite growth was probably mediated by the microorganisms that flourished on the speleothem surfaces during periods of low drip water rates and slow calcite precipitation. The change from microstromatolites to microthrombolites was probably linked to a decrease in cell populations in the microbial communities. These cave microbialites provide clear insights regarding the biogenicity and growth mechanisms of chemosynthetic microbialites. Given their association with chemolithotrophic activities that can date back to the Meso‐Archean, cave microbialites provide insights into the biogenicity and growth mechanisms of chemosynthesis‐based microbialites throughout geological history. [ABSTRACT FROM AUTHOR]

The rubber tree is an economically important tree planted in many tropical countries. While rubber planting has improved the livelihoods of growers, it has also resulted in soil degradation. However, systematic studies on assessment of soil health and its management in rubber plantations are limited. The present study explored whether intercropping of Michelia macclurei (an ornamental evergreen tree) in rubber plantation could help conserve soil health compared to traditional monoculture practice with randomised complete block design. The rubber tree density was the same in monoculture and intercropping, with the addition of Michelia macclurei in intercropping. The effects of soil properties and microbial communities was used to analyse two different planting patterns of rubber monoculture and rubber intercropping using soil sampling from field plots. The study investigated variation in soil physical structure, soil moisture, soil nutrients, soil microbes, and enzyme activities in two types of rubber plantations viz. a monoclonal plantation without intercrop (RM) and a plantation with Michelia macclurei as an intercrop (RAS). The results from above study showed an increase in soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (AN), available phosphorus (AP), nitrate nitrogen (NN) and total potassium (TK) in plantation with intercrop as compared to monoclonal plantation without intercrop. When comparing the corresponding values of RM to RAS, bacteria and total microbial abundance of RAS increased on average by 75.51% and 48.42%, respectively. In addition, after the transition from rubber monoculture to rubber agroforestry, the annual average of SOC, TN, AP, TK nutrients and pH in soil increased by 10.94%, 4.25%, 14.53%, 1.34% and 9.74%, respectively. Soil water content, soil bulk density and soil porosity were not significantly different between RM and RAS treatments. Sucrase activity and cellulase activity also increased in the RAS intercropping system. These results show that intercropping promotes soil organic matter and microbial communities and enhances soil enzyme activities. These findings indicate that rubber intercropping creates healthy soil environments conducive to tree growth and improves the ecosystem sustainability of rubber plantations. Healthier and stronger rubber trees may increase rubber production and provide sustainable management of plantations in the future. [ABSTRACT FROM AUTHOR]

The present study assessed the influence of the preceding crop (crotalaria or corn) on the bromatological, digestibility and microbiological aspects of the EMBRAPA 139 black oat hay (Avena strigosa) cultivar. A randomized block design was used, with subplots divided according to time, whereby the preceding crop (crotalaria or corn) was allocated to the main plot and hay storage times (baling, 30, 60 and 90 days of storage) to the subplots, with five repetitions. Crotalaria as predecessor resulted in lower indigestible fiber and higher protein contents in black oat hay, both in acid detergent, as well as higher pH. Corn as the preceding crop provided better hay digestibility due to lower neutral detergent insoluble protein content and higher in vitro neutral detergent fiber digestibility. The preceding crop did not significantly affect the drying time of forage and the microorganism population. [ABSTRACT FROM AUTHOR]

Background: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances. Results: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions. Conclusions: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes. [ABSTRACT FROM AUTHOR]

Breast cancer (BrCa) is the most prevalent malignant tumor in women and one of the leading causes of female mortality. Its occurrence and progression are influenced by various factors, including genetics, environment, lifestyle, and hormones. In recent years, the gut microbiota has been identified as a significant factor affecting BrCa. The gut microbiota refers to the collective population of various microorganisms in the human gastrointestinal tract. Gut microbiota is closely associated with human health and disease development, participating in crucial physiological functions such as digestion, metabolism, immune response, and neural regulation. It has been found to influence the occurrence and treatment of BrCa through a variety of mechanisms. This article aims to review the immunomodulatory role of the gut microbiota in the development and treatment of BrCa. [ABSTRACT FROM AUTHOR]

The knowledge of the different population‐level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia‐oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long‐read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long‐reads located within the flexible genomic islands (fGIs) identified by their under‐recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third‐generation sequencing metagenomics. [ABSTRACT FROM AUTHOR]

Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining the variation available in a population. One such environmental dependency is the inverse relationship between mutation rates and population density in many microbial species. Here, we determine the mechanism responsible for this mutation rate plasticity. Using dynamical computational modelling and in culture mutation rate estimation, we show that the negative relationship between mutation rate and population density arises from the collective ability of microbial populations to control concentrations of hydrogen peroxide. We demonstrate a loss of this density-associated mutation rate plasticity (DAMP) when Escherichia coli populations are deficient in the degradation of hydrogen peroxide. We further show that the reduction in mutation rate in denser populations is restored in peroxide degradation-deficient cells by the presence of wild-type cells in a mixed population. Together, these model-guided experiments provide a mechanistic explanation for DAMP, applicable across all domains of life, and frames mutation rate as a dynamic trait shaped by microbial community composition. In some bacteria, mutation rates depend on environmental factors such as population density. This study uses simulation-guided experiments to show that denser microbial populations detoxify their environment more efficiently, resulting in a reduced rate of mutation. [ABSTRACT FROM AUTHOR]

This experiment was carried out to investigate the effect of bioactive peptides derived from casein on performance, nutrient digestibility, enzyme activity and intestinal microbial population in broiler chickens. In this study, 350 1‐day‐old male Ross 308 broiler chicks were distributed among 35 pens in a completely randomized design with seven treatments, five replicates and 10 chicks in each replicate. The experimental treatments included: basal diet without any additives (control), basal diet + Avilamycin antibiotic, basal diet + 200, 400, 600, 800 and 1000 mg of peptides per kg of diet. Results showed no significant effects of the experimental treatments on weight gain and feed conversion ratio during the starter period, but there was a significant improvement in weight gain in grower, finisher and whole periods in chicks fed with diet containing 1000 mg/kg peptides (p < 0.05). Adding peptides improved intestinal morphology (in duodenum and ileum) (p < 0.05). Supplementation of casein peptides significantly reduced thiobarbituric acid reactive substances concentration in breast and thigh meat. The activity of amylase, lipase and protease enzymes improved in treatments containing 800 and 1000 mg peptides in comparison to the control treatment. The use of casein‐peptides increased intestinal Lactobacillus and decreased Coliform populations. [ABSTRACT FROM AUTHOR]

Biological agents used to treat severe psoriasis may alter the gut microbiota, though current knowledge is limited. This study examines whether switching from TNFα inhibitors, from which patients had reduced or lost effect, to brodalumab, an IL-17 inhibitor, affects the gut microbiota in patients with psoriasis and how these changes correlate with the clinical variables of psoriasis severity and depressive symptoms. Fecal samples from patients were collected before the treatment switch and 12 weeks after the switch and were analyzed for the microbiota composition using next-generation sequencing targeting the V3–V5 region of the 16S rRNA gene, followed by bioinformatics analysis. No significant changes in overall gut microbiota composition were observed after the treatment switch, although individual variations in the Firmicutes/Bacteroidetes ratio were noted, and no significant correlations with clinical variables were found. These findings suggest that short-term changes in gut microbiota in patients with psoriasis are limited and that dysbiosis may be influenced by the interplay of various microbial populations rather than specific taxa. This study provides a foundation for further research into the effects of biological treatments on the gut microbiota in patients with psoriasis. [ABSTRACT FROM AUTHOR]

The present study aimed to develop a system using a combination of enzymatic and microbial degradation techniques for removing phenol from contaminated water. In our prior research, the HRP enzyme extracted from horseradish roots was utilized within a core-shell microcapsule to reduce phenolic shock, serving as a monolayer column. To complete the phenol removal process, a second column containing degrading microorganisms was added to the last column in this research. Phenol-degrading bacteria were isolated from different microbial sources on a phenolic base medium. Additionally, encapsulated calcium peroxide nanoparticles were used to provide dissolved oxygen for the microbial population. Results showed that the both isolated strains, WC1 and CC1, were able to completely remove phenol from the contaminated influent water the range within 5 to 7 days, respectively. Molecular identification showed 99.8% similarity for WC1 isolate to Stenotrophomonas rizophila strain e-p10 and 99.9% similarity for CC1 isolate to Bacillus cereus strain IAM 12,605. The results also indicated that columns using activated sludge as a microbial source had the highest removal rate, with the microbial biofilm completely removing 100% of the 100 mg/L phenol concentration in contaminated influent water after 40 days. Finally, the concurrent use of core-shell microcapsules containing enzymes and capsules containing Stenotrophomonas sp. WC1 strain in two continuous column reactors was able to completely remove phenol from polluted water with a concentration of 500 mg/L for a period of 20 days. The results suggest that a combination of enzymatic and microbial degrading systems can be used as a new system to remove phenol from polluted streams with higher concentrations of phenol by eliminating the shock of phenol on the microbial population. [ABSTRACT FROM AUTHOR]

Geothermal features, such as hot springs and mud volcanoes, host diverse microbial life, including many extremophile organisms. The physicochemical parameters of the geothermal feature, such as temperature, pH, and heavy metal concentration, can influence the alpha and beta diversity of microbial life in these environments, as can spatiotemporal differences between sites and sampling. In this study, water and sediment samples were collected and analyzed from eight geothermal sites at Yellowstone National Park, including six hot springs, a mud volcano, and an acidic lake within the same week in July 2019, and these geothermal sites varied greatly in their temperature, pH, and chemical composition. All samples were processed and analyzed with the same methodology and taxonomic profiles and alpha and beta diversity metrics determined with 16S rRNA sequencing. These microbial diversity results were then analyzed with respect to pH, temperature, and chemical composition of the geothermal features. Results indicated that predominant microbial species varied greatly depending on the physicochemical composition of the geothermal site, with decreases in pH and increases in dissolved heavy metals in the water corresponding to decreases in alpha diversity, especially in the sediment samples. Similarly, sites with acidic pH values had more similar microbial populations (beta diversity) to one another than to relatively neutral or alkaline pH geothermal sites. This study suggests that pH and/or heavy metal concentration is a more important driver for microbial diversity and population profile than the temperature for these sites and is also the first reported microbial diversity study for multiple geothermal sites in Yellowstone National Park, including the relatively new mud volcano Black Dragon’s Caldron, which erupted in 1948. [ABSTRACT FROM AUTHOR]

Background: Fecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients' phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients' phageome composition. Results: Donor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients' phageome toward the donors' composition and increased phageome alpha diversity and variability over time. Conclusions: FMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient's microbiome. Trial registration: The Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174. A4HmAXiKAUhp3nsywzn7_Q Video Abstract [ABSTRACT FROM AUTHOR]

Soil organisms play a key role in carbon and nutrient cycling in forest ecosystems. While soil organisms are strongly influenced by litter chemistry and are highly sensitive to abiotic conditions, little is known about the interactive effects of these two factors. To address this gap in knowledge, we conducted a 10 week microcosm experiment in which we simulated the effects of climate change on soil ecology. More specifically, we studied relationships among litter nutrient concentration, microbial biomass, Collembola demographic parameters, and litter decomposition, exploring the potential impacts of increasing air temperature and decreasing soil moisture. To develop a gradient of nutrient concentrations, we created six tree litter mixtures with materials gathered from Quercus pubescens and its companion species. In contrast to microbes, we observed that Collembola abundance and litter decomposition were interactively affected by soil moisture and air temperature: the negative effect of increasing air temperature on Collembola abundance was amplified by reduced soil moisture, whereas the positive effect of increasing air temperature on litter decomposition disappeared under reduced soil moisture conditions. In contrast to fungi, the response of bacterial biomass and Collembola abundance to litter nutrient concentration was dependent on abiotic conditions. More specifically, the relationships between nutrients, especially calcium and magnesium, and bacterial biomass and Collembola abundance were less robust or disappeared under drier or warmer conditions. In conclusion, our findings underscore that ongoing climate change could affect soil organisms directly as well as indirectly, by altering their responses to litter nutrient concentrations. In addition, we found that nutrient‐rich habitats might be more affected than nutrient‐poor habitats by altered climatic conditions. [ABSTRACT FROM AUTHOR]

Mangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high‐frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0–100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome‐wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045–0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non‐synonymous mutation ratio between 0–20 and 20–100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene‐specific selection, finally resulting in the stratified differentiation occurring between 0–20 and 20–100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems. [ABSTRACT FROM AUTHOR]

BACKGROUND: Bacillus velezensis DQA21 is a functional strain used in the fermentation process of strong‐aroma baijiu; however, its specific role in the process is still unclear. RESULTS: In this study, specific roles of B. velezensis DQA21 in the fermentation process were explored. Bioaugmentation of B. velezensis DQA21 increased the diversity and abundance of the bacterial community during the first 32 days of fermentation and significantly inhibited the diversity and richness of the fungal community during days 12 to 32. According to cluster analysis, changes in the microbial community structure were observed during fermentation, and the fermentation process could be divided into two stages: stage I, days 0–12; and stage II, days 12–45. Additionally, the microbial community structures during the two fermentation stages were significantly different. Co‐occurrence analysis showed that bioaugmentation with Bacillus increased the correlation between microorganisms in jiupei and had a significant impact on the overall network structure of the microbial community. In addition, Bacillus significantly increased the production of flavor substances in jiupei, causing the total esters, total alcohols, and total acids contents to increase by 19.1%, 81.1%, and 25.9% respectively. CONCLUSION: The results suggested that bioaugmentation with B. velezensis DQA21 had a strong impact on the microbial community structure in strong‐aroma baijiu, enhancing the volatile flavor components. Additionally, the work also provides a better understanding on the effect of augmentation on the microbial community in jiupei, which could help better regulation of solid‐state fermentation in strong‐aroma baijiu. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the effects of slightly alkaline electrolyzed water (SAlEW) and slightly acidic electrolyzed water (SAcEW) on the sensory characteristics, chemical composition, and microbiological quality of fresh chilled chicken breast fillets that were submerged for five minutes and stored for 12 days at 4±1°C. The treated samples were contrasted with the untreated (control) samples, which according to the acceptable limits of (ES 1651/2005) had an APC count of 4.97±0.27 and a shelf-life of fewer than five days. The results showed that the chilled chicken fillet treated with SAlEW and SAcEW had a longer shelf life and could be consumed for up to seven and nine days, respectively, where APC was 4.75±0.18 and 4.57±0.02, the E. coli count was 1.82±0.52 and 1.65±0.17, the Staph. aureus count was 1.64±0.07 and 1.53±0.25, and the mold and yeast counts were 3.01±0.05 and 3.28±0.02, log10cfu/g, respectively. The pH values were 6.16±0.02 and 6.21±0.02, TBARS values were 0.84±0.01 and 0.77±0.02, and TVB-N values were 18.78±0.06 and 18.26±0.57, respectively according to the chemical analysis findings. Furthermore, marinating chicken fillet in combination of SAlEW and then SAcEW extended the shelf-life until the 12th day of storage, recorded APC 4.28±0.14, E. coli count 1.53±0.04 and Staph.aureus count 1.42±0.23, mold and yeast count 2.94±0.01 log10cfu/g, with pH value of 6.11±0.05,TBARS value of 0.67±0.03 and TVB-N value was 16.65±0.07. In conclusion, applying SAlEW and then SAcEW had a significantly decontaminating impact on microbial populations and extended the shelf-life of the chicken breast fillets under examination. All treatments worked well to lower the chemical values (pH, TBARS, and TVB-N), however the combination treatment produced the lowest values overall. Using the combination treatment improved the sensory quality of chicken fillets compared to other treated and untreated samples. As electrolyzed water a safe antimicrobial preservative for chilled chicken fillets, it is a potential technique to increase the shelf life and quality of chicken meat without leaving dangerous residues. [ABSTRACT FROM AUTHOR]

Plastics are synthetic organic compounds whose widespread use generates enormous waste. Different processes, such as mechanical abrasion, microbiological activity, and UVB irradiation, can fragment the plastic material and generate microplastics (MPs). MPs are ubiquitous, and various organisms, including humans, can ingest or inhale them, with potential adverse health effects. The differences between UV-aged and virgin particles were studied to evaluate the genotoxic damage and oxidative stress induced by polystyrene MPs with 1 and 5 µm sizes on the monocyte-like cell line (THP-1). Fourier transform infrared spectroscopy and Ζ-potential measurements were used to characterise MP particles after UVB exposure. Cells exposed to MPs show a widespread change in the cellular environment with the generation of reactive oxidative species (ROS), as indicated by the increased malondialdehyde level. The occurrence of genotoxic damage is correlated to the smaller size and ageing state of the MPs. The biochemical and genomic alterations observed in this in vitro study suggest that MPs, ubiquitous pollutants, following natural degradation and oxidation processes can cause various adverse effects on the health of the exposed population, making it necessary to carry out further studies to better define the real risk. [ABSTRACT FROM AUTHOR]

This work presents a low-cost, open-source turbidimeter, the 'Erlenmeter', designed to monitor the growth of microorganisms in batch cultures. It is easy to build, based exclusively on inexpensive off-the-shelf electronic components and 3D-printed parts. The Erlenmeter allows measuring the optical density of cultures on standard Erlenmeyer flasks without the need to open the flasks to collect aliquots, ensuring speed, minimal use of consumables, and elimination of the risk of contamination. These features make it particularly well-suited not just for routine research assays but also for experimental teaching. Here we illustrate the use of the Erlenmeter turbidimeter to record the growth of the microalga Phaeodactylum tricornutum, of the bacterium Escherichia coli, and of the yeast Saccharomyces cerevisiae, model organisms that are widely used in research and teaching. The Erlenmeter allows a detailed characterization of the growth curves of all organisms, confirming its usefulness for studying microbial populations dynamics both for research purposes and in classroom settings. [ABSTRACT FROM AUTHOR]

This study aimed to assess the effects of Chinese Baijiu with different flavors as supplementary material on microbial communities and flavor formation during inoculated fermentation of Chinese Dongbei Suancai. The results showed that the addition of Fen flavor Baijiu significantly increased the relative abundance of Candida, Luzhou flavor Baijiu increased the relative abundance of Pedobacter and Hannaella, while Maotai flavor Baijiu increased the Chryseobacterium and Kazachstania. A total of 226 volatile metabolites were detected in Suancai fermented when adding different flavors of Baijiu. Furthermore, the significantly upregulated metabolites (p < 0.01) of Suancai after adding Baijiu increased by 328.57%, whereas the significantly downregulated metabolites decreased by 74.60%. Simultaneously, the addition of Baijiu promoted the synthesis and decomposition of amino acids and short-chain fatty acids in the early and middle stages of fermentation. Further, Maotai flavor Baijiu improved the diversification of metabolic pathways in the late stage of Suancai fermentation. The E-nose response showed that sulfur-organic, broad-alcohol, sulfur-chlor was the principal differential flavor in Suancai caused by adding Baijiu with different flavors. Simultaneously, Fen flavor Baijiu and Luzhou flavor Baijiu accelerated the formation of the Suancai flavor. These results indicated that Baijiu with different flavors had significant effects on the flavor formation of inoculated fermented Suancai. [ABSTRACT FROM AUTHOR]

In a 42-day study, 195 [(Landrace × Yorkshire) × Duroc)] piglets, weighing 6.52 ± 0.59 kg, were randomly assigned to three treatment groups with 13 replicates and 5 pigs (3 barrows and 2 gilts) per pen, and used to evaluate the impact of weaning pig diets containing almond hulls (AHs) on growth performance, nutrient utilization, faecal microbiome, noxious gas emissions, and faecal score. The following dietary treatment groups were applied: basal diet as control, basal diet + 3% AH as TRT1; basal diet + 6% AH as TRT2. At the end of the experiment, the average daily gain and gain-to-feed ratio showed an increasing trend. However, despite these changes, the average daily feed intake remained constant, as did nutrient digestibility, faecal microbiome (Salmonella, Escherichia coli, and Lactobacillus), and faecal score. Among the noxious gases, only NH3 tended to decrease, while other gases (CO2, H2S, methyl mercaptans, acetic acid) remained stable. These findings indicated that the inclusion of AHs in the diet could improve growth performance and reduce NH3 gas production without negative impact on nutrient absorption, microbial populations, and faecal score in weaned piglets. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the effects of the level and type of essential oils (EOs) derived from oregano (ORO), thyme (THO), clove (CLO), and cinnamon (CIO), when used as feed additives, on in vitro rumen fermentation and methanogenesis. This was achieved by conducting a metaanalysis that integrated data from relevant studies. A total of 17 articles were included comprising 154 data points. The collected data were subsequently analysed using a mixed model methodology implemented in a SAS software version 9.4. The findings showed that the level of EOs exerted a significant (P < 0.01) linear effect, resulting in increased pH, decreased volume of total gas, CH4, and NH3, reduced total volatile fatty acids (VFA) levels, dry matter digestibility (DMD), organic matter digestibility (OMD), and bacterial population. A quadratic effect was also observed with respect to reduced (P < 0.01) CO2 and propionate (C3 ) levels. Additionally, the protozoan population demonstrated a linear decrease (P < 0.05), while butyrate (C4) concentration exhibited a quadratic increase (P < 0.05). However, increasing levels of EOs did not affect the acetate (C2)- and methanogen-producing bacterial populations. With respect to different EO types, ORO and THO significantly reduced (P < 0.05) total gas (30–41%) and CH4 production (38–39%) compared to the control. ORO and CLO in turn significantly decreased (P < 0.05) C3 generation (5–7%), while ORO increased C4 levels (14%) compared to the control. Moreover, CLO, CIO, and THY administration led to a decrease in OMD (8–23%). Due to the limited dataset on microbial population, the diverse types of EOs showed no significant impact on bacterial, protozoan, or methanogen populations. In conclusion, while specific doses of EOs can suppress ruminal methane emissions, they can also inhibit rumen fermentation processes. Among the EOs examined, ORO demonstrated the most potent antimicrobial ability against methanogenesis. [ABSTRACT FROM AUTHOR]

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The deteriorating soil health under continuous monoculture is commonly found across various cropping systems. This study evaluated the effects of different tillage practices (conventional tillage and no till) and species mixtures (legumes and grasses) on arbuscular mycorrhizal fungi (AMF) community properties, soil nutrients, and enzyme activity in a 3-year experiment. Compared with traditional tillage, the number of AMF species under no-till conditions was increased, with the Glomus group being dominant. Under different tillage conditions, TN (total N) and AN (available N) contents under no till were significantly higher than those under conventional tillage, while no significant differences among other nutrients were found. The activities of soil acid phosphatase (S-ACP), soil dehydrogenase (S-DHA), and soil sucrose (S-SC) under conventional tillage were significantly higher than those under no till, and the cover crop mixtures also had an exclusive advantage in yield. Soil organic matter (SOM) indicated a significant negative correlation with glomalin-related soil protein (GRSP). The increase in diversity associated with the AMF species community was strongly correlated with the increase in three enzyme activities, and AN was negatively correlated with all species. Tillage did not significantly change soil chemistry, except for AN, and the high concentration of AN led to a decrease in AMF species. The results of this study showed that no till was an effective measure for enriching soil micro-organism population. Additionally, soil AMF diversity was improved by cover crop mixtures, and microbial diversity was higher than that under monoculture cover crops. Different AMF groups responded differently to tillage and cover crop mixtures. Across all mixtures, the combination of hairy vetch (Vicia villosa R.) and ryegrass (Lolium perenne L.) performed the best. [ABSTRACT FROM AUTHOR]

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the "gateway microbiomes". Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness. [ABSTRACT FROM AUTHOR]