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UNLABELLED: Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. ONE-SENTENCE SUMMARY: This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

AbstractPurple soil is rich in semiconducting minerals, but the impact of these minerals on soil properties and associated microbiome assemblages has received little attention. To better understand the influence of semiconducting minerals in soils, samples were collected from 4 soil classifications, including purple soil, siltstone, farmland, and new formed soil. Goethite was the main semiconducting mineral in purple soil followed by rutile and birnessite, while for siltstone, rutile was the major semiconducting mineral. Proteobacteria (77.77–98.56%) was the most prevalent phylum among all samples, with the second most abundant phylum being Cyanobacteria (purple soil and farmland) and Firmicutes (siltstone and new formed soil). According to the average path length in network analysis, purple soil showed higher species segregation, which suggested purple soil was potentially more susceptible to external interference than the other types. The relationship between microbes may be synergistic due to the positive links between microbial phyla. Rutile affected microbial composition to the greatest extent, accounting for 13.66% of the total variation in microbial assembly, while goethite (r= –0.0947) and birnessite (r = 0.0215) content were also associated with changes in microbial composition. These results demonstrated that semiconducting minerals affected the structure and potential energy utilization of soil microbial communities. [ABSTRACT FROM AUTHOR]

• Earthworms and LAB synergistically enhance TC degradation efficiency. • LAB alleviate the biological stress of TC on earthworms. • Various TC doses significantly affect earthworm body bacterial communities. • High TC doses can elevate pathogenic bacteria dominance. Tetracycline is an antibiotic with extensive veterinary use in the livestock industry. However, their widespread application poses risks to soil health as residue in livestock feces, and their removal is crucial for sustainable soil-ecosystem development. Physical and chemical approaches to extract tetracycline may have adverse effects on soil ecosystems, but no studies have thus far examined the potential for biological methods, such as collective degradation action of soil fauna. Thus, this study aimed to investigate the synergistic effects of lactic acid bacteria (LAB) and earthworms (Eisenia fetida) on biodegradation of tetracycline residues in sheep manure. We assessed earthworm biomass, tetracycline residue, and bacterial communities in both earthworm intestines and vermicompost. Earthworm biomass and tetracycline degradation efficiency increased significantly with LAB addition, with a degradation rate of up to 80.16%. This increase may be attributable to LAB acting as electron donors to spur tetracycline degradation. Additionally, we noted that tetracycline presence significantly influenced bacterial communities in earthworm intestines and vermicompost, elevating the abundance of potential pathogenic bacteria (e.g., Flavobacterium , Gammaproteobacteria , and Enterobacteriaceae). This finding suggests that heightened environmental stress from antibiotics could actually facilitate the growth of less prevalent bacteria, including potential pathogens. In conclusion, our study provides evidence supporting the effectiveness of LAB and earthworms in degrading tetracycline residues. In particular, LAB appears to mitigate stress from tetracycline exposure in earthworms, thus increasing their vermicomposting efficacy. Our work has important implications for soil management, with the potential to enhance pollution clean-up rates while minimizing negative side-effects to soil microbial communities. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Purple Napier grass (PNG), a widely used grass rich in anthocyanin, is commonly employed in the production of silage. However, there is currently limited research on the retention of anthocyanin with or without additives during ensiling. Therefore, this study aimed to investigate the effect of different additives (Lactiplantibacillus plantarum CCZZ1 (LP), glucose, acetic acid, and dried soybean curd residue) on fermentation quality, anthocyanin content, and microbial community structure of PNG silage.Ensiling PNG without additives led to poor fermentation quality and rapid degradation of anthocyanin, resulting in a decline in antioxidant activity and the persistence of harmful microorganisms with high relative abundance. The use of additives, especially LP, effectively increased the relative abundance of L. plantarum, enhancing fermentation quality, the retention of anthocyanin (up to 166% increase rate) and antioxidant activity, while reducing the relative abundance of harmful microorganisms during ensiling for 30 days. Additionally, prolonged ensiling negatively affected the preservation of anthocyanin. Based on both fermentation quality and bioactivity, PNG should be ensiled for 30 days with LP inoculation.The employment of additives, especially LP, improved the fermentation quality, anthocyanin retention, and microbial community structure in PNG silage. To optimize both fermentation quality and bioactivity, it is recommended that PNG be ensiled for 30 days with LP inoculation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Background: Plants that contain brewing microorganisms are used in traditional fermentation starters, which are an essential part of local diet, nutrition, life, and health. Regionally, the plant species used and the microorganisms included in traditional fermentation starters are diverse, endowing local fermented drinks with different flavors and health benefits. However, related traditional knowledge has been scarcely documented or revealed. Methods: An ethnobotanical survey was conducted in five towns of Nayong County in northwestern Guizhou, China. Snowball sampling, semi-structured interviews, free lists, and participatory observation were used to collect information on Jiuqu Plants (JPs) and jiuqu-making techniques. The PacBio platform was used to study the microbial community structure and diversity in the Chuanqing people's jiuqu. Results: In total, 225 informants were interviewed, including 116 who provided plants and technological processes for making Chinese baijiu jiuqu (CBJ) and 139 who provided information about making fermented glutinous rice jiuqu (FGRJ). This study found that older people have more abundant knowledge about CBJ plants. Poaceae was found to be the dominant family used in making CBJ and FGRJ (7 species each). Compared to individual plant parts, the whole plant is most commonly used in two kinds of jiuqu (19.5% in CBJ and 22.6% in FGRJ). The Chuanqing people's jiuqu is used to treat dietary stagnation and indigestion. The highest relative frequency of citation of the CBJ plant was Ficus tikoua Bureau, and the counterpart of the FGRJ plant was Buddleja macrostachya Benth. The dominant bacterial species in jiuqu were Gluconobacter japonicus (YQ1, YQ4) and Pediococcus pentosaceus (YQ2, YQ3), and the dominant fungal species was Rhizopus oryzae. Conclusion: For the first time, this study documents the unique traditional jiuqu knowledge and reveals the microbial mystery behind the FGRJ of the Chuanqing people. Therefore, this study encourages the use of online social media platforms in order to spread Jiuqu culture, the use of the new media wave in order to create multimedia databases, and also suggests that local communities should develop preservation intervention programs, in addition to nurturing the inheritors in order to prevent the disappearance of traditional Jiuqu knowledge. This research contributes to the conservation and demystification of the traditional jiuqu knowledge of the Chuanqing people and lays the foundation for further research on its microbiology, nutrition, and metabolomics. [ABSTRACT FROM AUTHOR]

Mining disturbance has great impacts on soil physicochemical factors, causing notable differences between pre-mining and after-mining conditions, and between coal mining areas and non-mined areas. However, little is known about whether the fissure statuses induced by mining activities affect the edaphic factors and how soil microbial communities respond to these fissure development states. In this study, we systematically investigated the edaphic factors and microbial communities in a mining disturbance area exhibiting the full development status of soil fissures, where the sampling sites were divided into soil fissure development and closure zones. Microbial alpha-and betadiversity, correlation coefficient matrix, non-metric multi-dimensional scaling, principal co-ordinates analysis, mantel test, and microbial co-occurrence network were employed to elucidate variations, correlations, and interactions between edaphic factors and microbial communities under the two different soil fissure states. Results suggested that soil physicochemical properties were significantly affected by fissure states, showing an increasing trend in soil moisture content and soil nutrients. The associations among edaphic factors have weakened during the soil fissure development process. Soil microbial communities showed different compositions and the underlying influential mechanisms between two soil fissure states. Soil moisture content, pH, particle compositions, organic matter, and heavy metals largely affected microbial communities. Rare species were vulnerable to mining disturbance and were keystone taxa that reinforced the overall interconnections of the soil microbial community (e.g., Nordella, Sphingomonas, Massilia, and Rubritepida). Our study revealed the impacts of distinct fissure states on the soil physicochemical properties and microbial communities, and the edaphic conditions showed key contributions to the soil microbial communities, particularly the abundance and ecological roles of rare species. [ABSTRACT FROM AUTHOR]

Introduction: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation. Methods: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing. Results and discussion: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10−3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain’s ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq -pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context. [ABSTRACT FROM AUTHOR]

This study investigated the influence of different temperatures (35℃ High temperature and average indoor ambient temperature of 25℃) and lactic acid bacterial additives (Lactiplantibacillus plantarym, Lentilactobacillus buchneri, or a combination of Lactiplantibacillus plantarym and Lentilactobacillus buchneri) on the chemical composition, fermentation quality, and microbial community of alfalfa silage feed. After a 60-day ensiling period, a significant interaction between temperature and additives was observed, affecting the dry matter (DM), crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF) of the silage feed (p < 0.05). Temperature had a highly significant impact on the pH value of the silage feed (p < 0.0001). However, the effect of temperature on lactic acid, acetic acid, propionic acid, and butyric acid was not significant (p > 0.05), while the inoculation of additives had a significant effect on lactic acid, acetic acid, and butyric acid (p > 0.05). As for the dynamic changes of microbial community after silage, the addition of three kinds of bacteria increased the abundance of lactobacillus. Among all treatment groups, the treatment group using complex bacteria had the best fermentation effect, indicating that the effect of complex lactic acid bacteria was better than that of single bacteria in high temperature fermentation. In summary, this study explained the effects of different temperatures and lactic acid bacterial additives on alfalfa fermentation quality and microbial community, and improved our understanding of the mechanism of alfalfa related silage at high temperatures. [ABSTRACT FROM AUTHOR]

Introduction: Microorganisms exhibit intricate interconnections with tea plants; however, despite the well-established role of microorganisms in crop growth and development, research on microbes within the tea plant remains insufficient, particularly regarding endophytic microorganisms. Methods: In this study, we collected samples of leaves and rhizosphere soils from 'Zhuyeqi', 'Baojing Huangjincha#1', 'Baiye#1', and 'Jinxuan' varieties planted. Results: Our analyses revealed significant variations in tea polyphenol contents among tea varieties, particularly with the 'Zhuyeqi' variety exhibiting higher levels of tea polyphenols (>20% contents). Microbiome studies have revealed that endophytic microbial community in tea plants exhibited higher host specificity compared to rhizospheric microbial community. Analyses of across-ecological niches of the microbial community associated with tea plants revealed that soil bacteria serve as a significant reservoir for endophytic bacteria in tea plants, Bacillus may play a crucial role in shaping the bacterial community acrossecological niche within the tea plants with higher tea polyphenol levels. In the aforementioned analyses, the microbial community of 'Zhuyeqi' exhibited a higher degree of host specificity for leaf endophytic microorganisms, the topological structure of the co-occurrence network is also more intricate, harboring a greater number of potential core microorganisms within its nodes. A closer examination was conducted on the microbial community of 'Zhuyeqi', further analyses of its endophytic bacteria indicated that its endophytic microbial community harbored a greater abundance of biomarkers, particularly among bacteria, and the enriched Methylobacterium and Sphingomonas in 'Zhuyeqi' may play distinct roles in disease resistance and drought resilience in tea plants. Conclusion: In summary, this study has shed light on the intricate relationships of tea plant varieties with their associated microbial communities, unveiling the importance of microorganisms and tea varieties with higher tea polyphenols, and offering valuable insights to the study of microorganisms and tea plants. [ABSTRACT FROM AUTHOR]

Capsaicinoids are produced uniquely in pepper fruits, and its level determines the commercial quality and health-promoting properties of pepper. So, it is particularly important to increase capsaicinoids content in pepper. Rhizosphere microbiota is critical to plant growth and performance, and affected by plant varieties. However, the impact of pepper varieties with different capsaicinoids yields on the rhizosphere microbiota is poorly understood. Using high-throughput sequencing of the 16S rRNA and internal transcribed spacer (ITS) region, we investigated the rhizosphere microbial community among five pepper varieties containing different capsaicinoids. Our results demonstrated that pepper variety significantly influenced the diversity and structure of rhizosphere microbial community. Bacterial diversity in varieties with high capsaicinoids content was significantly higher than in varieties with low capsaicinoids content, while fungal diversity was opposite to bacterial diversity. The correlation analysis revealed that 19 dominant bacterial genera (e.g., Chujaibacter, Rhodanobacter, and Gemmatimonas) were significantly correlated with capsaicinoids content, and nine of them were also significantly associated with soil nutrients, whereas only one fungal genus (Podospora) was significantly correlated with capsaicinoids content. Additionally, almost all genera which significantly correlated to capsaicinoids content were biomarkers of the five pepper varieties and the correlation was well corresponding to the capsaicinoids content. Overall, our results confirmed that the variety of pepper significantly affected the rhizosphere microbial community in the fields, and bacteria and fungi responded differently to capsaicinoids, which may affect the biosynthesis of capsaicinoids and contribute to further improvement of capsaicinoids production in pepper fruits. [ABSTRACT FROM AUTHOR]

Introduction: Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood. Methods: This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm). Results and Discussion: It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2. [ABSTRACT FROM AUTHOR]

Microbial communities play a crucial role in the physiology of animal hosts; however, little is known about bacterial symbionts with the group cephalopods, specifically octopuses, and the function of these symbionts. The goal of this study was to determine if octopuses have a unique skin microbiome. The skin microbiome of two sympatric octopuses (Octopus vulgaris and Macrotritopus defilippi) was compared with the surrounding environment, sediment and seawater, to determine if octopus have a unique skin microbiome. High throughput sequencing of the bacterial 16S rRNA gene (V3-V4 region) amplicons was performed using an Illumina MiSeq. Sediment showed the greatest alpha diversity followed by octopus then seawater. Beta diversity revealed a difference in microbial composition between the octopus skin microbiome and sediment and seawater. While phylum Bacteroidetes appeared rare in environmental samples, it was most abundant for the octopus skin microbiome with the majority of the bacteria comprising the family Flavobacteriaceae. Proteobacteria, the largest group of bacteria, also constituted the octopus skin microbiome. Many of these groups occur on both octopus species; however, certain taxa differed in relative abundance between octopus species and may show species-specific host selection. Several bacteria that were identified for the octopus skin microbiome have been isolated from other marine animal hosts, identified as biodegraders and/ or produce pigments and squalene, or act as predators of other bacteria. These groups may play a role in defense against environmental stressors or pathogenic bacteria. This is the first study to characterize the skin microbiome in two wild sympatric octopuses. Due to the importance of bacterial symbionts, this can provide insight to the physiology, behavior, ecology, and ultimately the health of these important animals in marine environments as well as care in captive or laboratory settings. [ABSTRACT FROM AUTHOR]

Roasted-rice leachate fermentation, a distinctive local tobacco fermentation method in Sichuan, imparts a mellow flavor and glossy texture to tobacco leaves, along with a roasted rice aroma. In order to find out the impact of roasted-rice leachate on cigar tobacco leaves, the physicochemical properties, volatile flavor profile, and microbial community were investigated. The content of protein significantly decreased after fermentation. The volatile flavor compounds increased following roasted-rice leachate fermentation, including aldehydes, alcohols, acids, and esters. High-throughput sequencing identified Staphylococcus, Pseudomonas, Pantoea, Oceanobacillus, Delftia, Corynebacterium, Sphingomonas, Aspergillus, Weissella, and Debaryomyces as the primary genera. Network and correlation analysis showed Debaryomyces played a crucial role in roasted-rice leachate fermentation, due to its numerous connections with other microbes and positive relationships with linoelaidic acid, aromandendrene, and benzaldehyde. This study is useful for gaining insight into the relationship between flavor compounds and microorganisms and provides references regarding the effect of extra nutrients on traditional fermentation products. Key points: • Volatile flavor compounds increased following roasted-rice leachate fermentation • Staphylococcus was the primary genera in fermented cigar • Debaryomyces may improve the quality of tobacco leaves [ABSTRACT FROM AUTHOR]

Background: Thinning practices are useful measures in forest management and play an essential role in maintaining ecological stability. However, the effects of thinning on the soil properties and microbial community in large Chinese fir timber plantations remain unknown. The purpose of this study was to investigate the changes in soil physicochemical properties and microbial community composition in topsoil (0–20 cm) under six different intensities (i.e., 300 (R300), 450 (R450), 600 (R600), 750 (R750) and 900 (R900) trees per hectare and 1650 (R1650) as a control) in a large Chinese fir timber plantation. Results: Compared with the CK treatment, thinning significantly altered the contents of soil organic carbon (SOC) and its fractions but not in a linear fashion; these indicators were highest in R900. In addition, thinning did not significantly affect the soil microbial community diversity indices but significantly affected the relative abundance of the core microbial community. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial phyla; the relative abundances of Proteobacteria and Acidobacteria were highest in R900, and that of Actinobacteria was lowest in R900. The dominant fungal phyla were Ascomycota, Basidiomycota and Mucoromycota; the relative abundance of Ascomycota was lowest in R900, and that of Mucoromycota was highest in R900. The fungal microbial community composition was more sensitive than the bacterial community composition. The activity of the carbon-cycling genes was not linearly correlated with thinning, and the abundance of C-cycle genes was highest in R900. Conclusions: These findings are important because they show that SOC and its fractions and the abundance of the soil microorganism community in large Chinese fir timber plantations can be significantly altered by thinning, thus affecting the capacity for carbon storage. These results may advance our understanding of how the density of large timber plantations could be modified to promote soil carbon storage. [ABSTRACT FROM AUTHOR]

Introduction: Clubroot disease is a devastating soil borne disease caused by infection with Plasmodiophora brassicae, which primarily affects cruciferous plants. The microbial diversity of the soil is an essential indicator of its quality. Methods: This study measured the physicochemical properties of the soil to study the effect of its microbial diversity on the infection of oilseed rape with P. brassicae. High-throughput sequences of the soil bacteria and fungi in the interroot soils of P. brassicae were analyzed under different treatment conditions. Results: In the study, it was found that the efficiency of strain X216 in preventing and controlling the root disease of rapeseed was positively correlated with the amount of solution used to irrigate the root system. The results of the greenhouse and field trials showed that the efficiency of strain X216 against the root disease of rapeseed was 43.16% in the field and 62.14% in the greenhouse. Proteobacteria, Chloroflexi, Rozellomycota, and Basidiomycota are critical phylum in the development of clubroot disease. The application of biocontrol increased the relative abundance of Actinobacteria, Bacillus, Mesorhizobium, Mycobacterium, Streptomyces and Filobasidium, which affected the structure and abundance of microbial communities. A principal coordinate analysis showed that the microbial structure in the soil varied substantially in the bacterial community, and there was no significant difference in soil structure in the fungal community. Discussion: The occurrence of clubroot disease affected the structure of interroot microbial community composition in the soil, which resulted in a decrease in its community diversity. The application of the biocontrol bacterium X216 increased the soil microbial diversity. It effectively reduced the occurrence of P. brassicae, and this study provides a basis to study the microbial diversity in cruciferous crops. [ABSTRACT FROM AUTHOR]

Sweet sorghum can be used to produce a substantial quantity of biofuel due to its high biological yield and high carbohydrate content. In this study, we investigated the dynamic changes in fermentation characteristics, carbohydrate components, and the bacterial community during the ensiling of wilted and unwilted sweet sorghum. The results revealed a rapid fermentation pattern and high-quality fermentation quality in wilted and unwilted sweet sorghum, wherein lactic acid, and acetic acid accumulated and stabilized during the initial 9 days of ensiling, with the pH values less than 4.2, until 60 days of ensiling. We found that the ensiling of sweet sorghum involved the degradation (5% ~ 10%) of neutral detergent fiber (NDF) and hemicellulose and that the degradation of NDF fit a first-order exponential decay model. A shift in dominance from Lactococcus to Lactobacillus occurred before the first 9 days of ensiling, and the abundance of Lactobacillus (r = -0.68, p < 0.001) was negatively correlated with the NDF content. The relative abundances of Lactobacillus in wilted and unwilted sweet sorghum after ensiling for 60 days were 76.30 and 93.49%, respectively, and relatively high fermentation quality was obtained. In summary, ensiling is proposed as a biological pretreatment for sweet sorghum for subsequent biofuel production, and unlike other materials, sweet sorghum quickly achieves good fermentation quality and has great potential for bioresource production. [ABSTRACT FROM AUTHOR]

This study explores the potential of food waste-recycling wastewater (FRW) for biogas production, emphasizing oil–water separation before anaerobic digestion. Three FRW samples were analyzed: non-treated (FRW), water–oil separated (FRW_sep), and mixed with domestic sewage (FRW_mix). Physicochemical characterization showed a 26% reduction in crude lipid content after oil–water separation. The biochemical methane potential (BMP) tests revealed similar methane yields for FRW_sep and FRW_mix compared to non-treated FRW. Microbial analysis identified Firmicutes and Methanoculleus as active populations. Energy balance suggests that combining biodiesel and biogas production can enhance net energy recovery. This research indicates that oil–water separation in FRW treatment can optimize anaerobic digestion, contributing to sustainable waste management and renewable energy generation. [ABSTRACT FROM AUTHOR]

Simple Summary: Dietary energy level impacts rumen function and the microflora in ruminants, which are closely related to their growth and well-being. This study explored how dietary energy levels affect sheep's growth performance, nutrient digestibility, rumen fermentation, barrier function, and microflora. Our findings indicated that the average daily weight gain and nutrient digestibility improve with the increase of dietary energy. Meanwhile, the concentration of total volatile fatty acids and propionate in rumen increased, which indicated the enhancement of rumen fermentation. The content and expression of tight junction proteins, which represents rumen barrier function, increased with the increase of dietary energy. In addition, the bacterial diversity in rumen decreased, and the relative abundance of some bacteria like Prevotellaceae, Muribaculaceae, Saccharofermentans, Prevotella and Succiniclasticum changed at the family and genus levels. Ultimately, the growth performance, fermentation characteristics and barrier function were the best when the daily dietary metabolizable energy was 9.8–10.4 MJ/kg. This study revealed the complex interaction between diet, microbiota, and rumen health, ultimately guiding the development of more effective and scientifically informed animal feeding strategies. Dietary energy is crucial for ruminants' performance and health. To determine optimal dietary energy levels for growing sheep, we evaluated their growth performance, nutrient digestibility, rumen fermentation, barrier function, and microbiota under varying metabolic energy (ME) diets. Forty-five growing Yunnan semi-fine wool sheep, aged 10 months and weighing 30.8 ± 1.9 kg, were randomly allocated to five treatments, each receiving diets with ME levels of 8.0, 8.6, 9.2, 9.8 or 10.4 MJ/kg. The results showed that with increasing dietary energy, the average daily gain (ADG) as well as the digestibility of dry matter (DM) and organic matter (OM) increased (p < 0.05), while the feed conversion ratio (FCR) decreased linearly (p = 0.01). The concentration of total VFA (p = 0.03) and propionate (p = 0.01) in the rumen increased linearly, while rumen pH (p < 0.01) and the acetate–propionate ratio (p = 0.01) decreased linearly. Meanwhile, the protein contents of Claudin-4, Claudin-7, Occludin and ZO-1 as well as the relative mRNA expression of Claudin-4 and Occludin also increased (p < 0.05). In addition, rumen bacterial diversity decreased with the increase of dietary energy, and the relative abundance of some bacteria (like Saccharofermentans, Prevotella and Succiniclasticum) changed. In conclusion, increasing dietary energy levels enhanced growth performance, nutrient digestibility, rumen fermentation, and barrier function, and altered the rumen bacterial community distribution. The optimal dietary ME for these parameters in sheep at this growth stage was between 9.8 and 10.4 MJ/kg. [ABSTRACT FROM AUTHOR]

To solve the bottleneck of low degradation rate and low biogas yield in anaerobic digestion of food waste, the addition of anionic surfactant sodium N-lauroylsarcosinate (SN) and nonionic surfactant primary alcohol ethoxylate (AEO) were proposed. The results showed that both surfactants could promote the methane production and facilitate the degradation of food waste. The highest methane yield per mass of volatile solid was obtained in 0.1 g/L AEO (497.14 mL) and 1 g/L SN (445.51 mL), which was improved by 92% and 72% compared with the control group. While with the increase of surfactant concentration, methane yield was decreased due to negative effect caused by the surfactant. This corresponded with the variation of pH, total volatile fatty acids (TVFAs), and soluble chemical oxygen demand (SCOD). The microbial community analysis showed that the relative abundance of methanobacterium increased while the relative abundance of methanosaeta decreased after the addition of surfactant. Meanwhile, the methane production pathway was shifted from codominance of hydrogenotrophic and aceticlastic methanogens to predominance by hydrogenotrophic methanogens in the groups with low concentration of AEO and SN. [ABSTRACT FROM AUTHOR]

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future. Novelty statement: To date, little is known about the bacterial communities in the rhizosphere of moso bamboo under Cd and Pb multiple stresses. This study investigated the assembly patterns and key taxa of rhizospheric bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils. It was found that the bacterial community structure in bamboo rhizosphere is easily influenced by soil chemical environment, such as fertilities and heavy metals. The key bacterial taxa identified here could be target microbe in future microbe-assistant phytoremediation. [ABSTRACT FROM AUTHOR]

The purification of biogas as a product of anaerobic digestion has gradually become a research focus. In situ hydrogen-assisted biogas purification is an effective way to enhance the reaction rate, but the solubility and mass transfer efficiency of hydrogen are the difficulties that constrain the technology. Thus, four continuous hydrogen injection modes M1: 1 mL/min, M2: 2 mL/min, M3: 5 mL/min, and M4: 10 mL/min and two intermittent hydrogen injection modes A: 4 mL/min (interval 20 min) and B: 6 mL/min (interval 40 min) were designed to explore the effect of different hydrogen injection modes on in situ biogas upgrading of upflow anaerobic sludge bed (UASB) in the research. The results showed that the methane production showed a trend of increasing first and then decreasing in continuous hydrogenation experiment. The CH4 production reached its peak at 86.2% in the M2 stage. In the two batch hydrogenation tests, group A showed better hydrogenation effect with a CH4 production of about 92%, which was 4% higher than that of group B. The hydrogenotrophic methanogens (HMs) in group A archaea community were more effectively enriched, with an abundance of 52.83% of Methanobacterium. The results illustrate that proper hydrogen injection can enhance anaerobic digestion and promote biogas purification, and the effect of short-term intermittent hydrogen injection is more significant. [ABSTRACT FROM AUTHOR]

BACKGROUND: The development of agricultural practices requires an understanding of the improvement of salt tolerance and crop growth in agricultural systems through magnetized‐ionized water irrigation. METHOD: This study examined the impacts of fresh water (F), brackish water (B), magnetized‐ionized fresh water (MIF), and magnetized‐ionized brackish water (MIB) on soil properties and the growth of cotton seedlings through microbial analysis during the cotton seedling period. RESULTS: The results revealed that magnetized‐ionized water irrigation improved soil water retention and promoted salt leaching. In comparison with F irrigation, plant height, leaf area index (LAI), dry matter accumulation (DM), and chlorophyll content (SPAD) levels increased by 3.61%, 4.07%, 5.76%, and 1.33%, respectively, under MIF irrigation. Similarly, when compared with B irrigation, LAI, DM, and SPAD increased by 5.13%, 6.12%, and 3.12% under MIB irrigation. Magnetized‐ionized water irrigation also led to a notable rise in the relative abundance of beneficial soil bacterial communities, particularly Pseudomonas and Azoarcus, as well as fungal communities like Trichoderma, while reducing the prevalence of pathogenic fungi, such as Lasionectria, Gibberella, and Alternaria. Notably, this irrigation approach induced alterations in soil properties, and partial least squares path modeling revealed significant links between soil properties and both cotton growth and fungal community structure (with path coefficients of −0.884 and 0.693, respectively). CONCLUSION: This study elucidated the distinct effects of soil properties and growth indices on cotton yield during the seedling period, providing a crucial scientific foundation for enhancing future agricultural production through the use of magnetized‐ionized water irrigation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Lakes offer a primary setting for the collection and spread of antibiotic resistance genes (ARGs) within natural habitats, so it is of great importance and urgency to investigate the characteristics of ARGs in such aquatic ecosystems. Herein, the occurrence and distribution of microbial populations, ARGs, and mobile genetic elements (MGEs) in Poyang Lake, the largest freshwater lake in China, were analyzed in-depth through metagenomic sequencing. Surface water and sediment samples were examined simultaneously at 10 sampling sites covering the inlets of five tributaries and central lake areas. Results showed that the antibiotic concentration was at a low level in both surface water and sediment. Proteobacteria and Actinobacteria were the two most prevalent phyla across all sampling sites. The surface water displayed a greater relative abundance of ARGs than the sediment. Multidrug resistance genes were the most abundant and diverse ARGs. Gene uppP was the most abundant ARG in both the surface water and sediment samples. ARGs in the sediment showed a decreasing trend from inlet to outlet of Poyang Lake, while in the water, the relative abundance of ARGs increased first and then decreased from inlet to outlet. ARG levels in Poyang Lake are thought to be closely related to human activity. A broad spectrum of MGEs series was recognized in both surface water and sediment samples; the abundance of MGEs was consistent with ARGs' abundance. Additionally, the makeup of the microbial community significantly influenced the resistome, suggesting that the composition of ARGs was largely affected by the microbial community. These findings indicate that lake water can act as a significant medium for ARGs dispersion, and the clustering and spread of ARGs are prone to the effects of human activities in aquatic habitats. [ABSTRACT FROM AUTHOR]

Polycyclic aromatic hydrocarbons (PAHs) are persistent environmental pollutants commonly found in water and sediments, posing significant health risks due to their toxicity, carcinogenicity, and mutagenicity. The stable and sustainable degradation of PAHs has garnered significant attention from researchers. Biological electrochemical systems (BESs) offer a promising approach with advantages in energy efficiency, safety, environmental protection, and long-term operation. This review examines the degradation performance and microbial community dynamics of BESs in the treatment of PAH-contaminated water and sediments. Additionally, the metabolites formed during the degradation process were also summarized. This review summarizes the degradation characteristics of PAH-contaminated water and sediments and aims to guide future research and optimize BESs for effective remediation of PAHs in various environmental settings. [ABSTRACT FROM AUTHOR]

When using runoff infiltration devices to remove nitrogen and phosphorus pollutants from urban runoff, the quality of the effluent is affected by the length of dry spells between rain events. This study presents a novel analysis of how these dry periods impact the device's effectiveness in removing pollutants and the resulting biological succession within the filter. Our analysis examines nitrogen and phosphorus removal in a rainwater filtration context, providing new insights into how dry period duration influences infiltration system performance. The results indicate that biological processes have a significant impact on reducing total nitrogen (TN) and total phosphorus (TP) contents under different drying periods. A 3-day drying period is most effective for reducing TN through biological processes, while a 7-day period is best for TP reduction. This suggests that moderately extending the drying period improves TP removal efficiency but does not enhance TN removal. The dominant bacterial phylum responsible for denitrification and phosphorus removal is Proteobacteria, with Pseudomonas and Acinetobacter as the leading genera. As the drying period lengthens, the dominant genera shift from Pseudomonas to Massilia. At a 3-day drying period, denitrification primarily occurs through Pseudomonas on the surfaces of maifanite and zeolite. At a 7-day dry-out period, Acinetobacter is mainly responsible for phosphate removal on maifanite surfaces. However, after a 14-day dry-out period, both biomass and bioactivity of Pseudomonas and Acinetobacter decrease, leading to reduced efficiency in removing nitrogen and phosphorus pollutants from runoff infiltration devices. These results aid in developing runoff infiltration devices for specific scenarios and offer crucial guidance for regulating runoff pollution control technologies. [ABSTRACT FROM AUTHOR]

An integrated constructed wetland-microbial electrolysis cell (ICW-MEC) system was investigated for nitrogen removal under different pollution loads, hydraulic loads (HLRs), and aeration conditions. The treatment performance of each unit and the microbial community characteristics for nitrogen removal were elucidated. The results showed that, on average, 80% of NH4+-N, around 70% of nitrate nitrogen (NO3−-N), and 70% of total nitrogen (TN) were removed by the system under three pollution loads, with less influence by pollution loads. The high removal efficiencies of NH4+-N (81.8%), NO3−-N (71.4%), and TN (72.8%) indicated tolerable to high HLRs. The intermittent aeration negatively affected NH4+-N removal, while increasing NO3−-N and TN removals by 3.2–13.0% and 3.7–16.7%. The contribution efficiencies of the secondary unit to the removal of NH4+-N, NO3−-N, TN, and total organic carbon (TOC) reached 47.4%, 55.0%, 45.9%, and 38.8%, respectively. The distinct microbial communities existed in various units of the ICW-MEC system, which were strongly affected by environmental factors and shaped by diverse fillers and structures of the system. The dominant bacteria contributed to the efficient nitrogen removal performance of the ICW-MEC system. The three units exerted their advantages to ensure efficient and stable system operation. [ABSTRACT FROM AUTHOR]

Spartina alterniflora is recognized as one of the most detrimental invasive species along China's coastlines, highlighting the need for effective and environmentally safe management strategies to preserve intertidal zones. This study assessed the effectiveness of combining plant growth regulators (PRGs) with physical cutting to manage S. alterniflora, using 16S rRNA and 18S rRNA gene sequencing to evaluate the impacts on the plant and associated soil micro-organisms. The results showed that compared to the control (CK), the regeneration numbers for treatments with abscisic acid (ABA), gibberellin (GA), paclobutrazol (PP333), garcinol (GC), and glyphosate (GP) decreased by 29.75%, 23.25%, 15.75%, 94.50%, and 40.50%, respectively. Comparative analysis revealed no statistically significant variation in the inhibitory effects of ABA and GP on the germination of S. alterniflora (p > 0.05). Additionally, applying PRGs and herbicides increased the diversity indices of soil bacteria and fungi. Principal Coordinates Analysis (PCoA) showed that the impact of PRGs on the fungal community was less pronounced than that of herbicides. Significant differences were also noted in the abundance of microbial functional genes related to methanotrophy, hydrocarbon degradation, and denitrification compared to the control (p < 0.05). This study aimed to assess the potential of PRGs in controlling the invasion of S. alterniflora and to elucidate their impacts on soil microbial communities and functional gene expression. [ABSTRACT FROM AUTHOR]

The distributional characteristics of microorganisms in karst cave ecosystems have been widely studied. However, in such a dark, humid, and oligotrophic habitat, studies on the differences in carbon-sequestering bacteria in multiple habitats are limited. Therefore, to learn the distribution characteristics of carbon-sequestering colonies in cave habitats and their correlation with habitat factors (e.g., pH, Ca2+, Mg2+, etc.), samples from five cave habitats (weathered rock walls, underground river water, drips, sediments, and air) were collected from the twilight and dark zones of Shiziyan Cave (CO2 concentration 5385 ppm). The results of high-throughput sequencing and statistical analyses showed that there were significant differences in the distribution of communities in different habitats, with higher abundance in sediments habitat and underground river water habitat, and the dominant phyla of Pseudomonadota (30.53%) and Cyanobacteria (75.11%) in these two habitats. The microbial diversity of the carbon-sequestering microbial community was higher in sediments than in underground river water. The pH, and Ca2+, SO 4 2 − , and NO 3 − concentrations can alter the diversity of carbon-sequestering microbes, thereby affecting carbon cycling in caves. Carbon metabolism analyses suggest that microbes in the habitat can cooperate and coexist by participating in different carbon metabolic pathways. These results expanded our understanding of carbon-sequestering microbial communities in cave systems and their responses to the environment. [ABSTRACT FROM AUTHOR]

Groundwater near a sulfuric acid plant in Xingyang, Henan, China was sampled from seven distinct sites to explore the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Results showed that genes aadA, blaCTX-M, tetA, qnrA, and sul1 were detected with 100% frequency followed by aac(6')-Ib (85.71%), ermB (85.71%), and tetX (71.42%). Most abundant ARGs were sul1 in LSA2 (1.15 × 1011 copies/mL), tetA in LSA6 (4.95 × 1010 copies/mL), aadA in LSA2 (4.56 × 109 copies/mL), blaCTX-M in LSA4 (1.19 × 109 copies/mL), and ermB in LSA5 (1.07 × 109 copies/mL). Moreover, in LSA2, intl1 as a marker of class 1 integron emerged as the most abundant gene as part of MGE (2.25 × 1011 copies/mL), trailed by ISCR1 (1.57 × 109 copies/mL). Environmental factors explained 81.34% of ARG variations, with a strong positive correlation between the intl2 and blaCTX-M genes, as well as the ISCR1 gene and qnrA, tetA, intl2, and blaCTX-M. Furthermore, the intI1 gene had a strong positive connection with the aadA, tetA, and sul1 genes. Moreover, the aac(6')-Ib gene was associated with As, Pb, Mg, Ca, and HCO3-. The intl2 gene was also shown to be strongly associated with Cd. Notably, network analysis highlighted blaCTX-M as the most frequently appearing gene across networks of at least five genera. Particularly, Lactobacillus, Plesiomonas, and Ligilactobacillus demonstrated correlations with aadA, qnrA, blaCTX-M, intI2, and ISCR1. Based on 16S rRNA sequencing, the dominant phyla were Proteobacteria, Firmicutes, Bacteroidota, Acidobacteriota, and Actinobacteriota, with dominant genera including Pseudomonas, Ligilactobacillus, Azoarcus, Vogesella, Streptococcus, Plesiomonas, and Ferritrophicum. These findings enhance our understanding of ARG distribution in groundwater, signaling substantial contamination by ARGs and potential risks to public health. [ABSTRACT FROM AUTHOR]

Meju is a traditional Korean soybean brick characterized by diverse microbial communities. The microbial communities in Meju were identified at the phylum and genus levels using high-throughput sequencing. During Meju fermentation, diverse factors such as total bacterial cell numbers, moisture content, salinity, pH, enzyme activities, and free amino acids were monitored. After 30 days of fermentation, microbial adaptation and increased protease activity resulted in significant changes, including an increase in pH and alterations in free amino acid content by day 70. Bacterial community analysis revealed significant changes in Bacillus, Lactococcus, and Enterococcus levels as fermentation progressed. The decrease in pH during fermentation was influenced by lactic acid bacteria, which affected bacterial dynamics. At the end of fermentation, the fungal community was dominated by Monascus, Aspergillus, and Scopulariopsis, which affected the free amino acid levels. These results indicate that pH and moisture content may be significant factors in determining microbial communities. [ABSTRACT FROM AUTHOR]

BACKGROUND: The microbial community plays a crucial role in Chinese strong‐flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing. RESULTS: The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate. CONCLUSION: These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality‐control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Bean paste is a traditional Chinese fermented condiment, which is loved by consumers for its pleasant flavor and nutritional properties. However, the microbial communities and related flavor compounds in bean paste remain unclear. We studied the correlation between the core functional microorganisms and flavor compounds in bean paste samples at different fermentation stages. Bacterial and fungal communities changed significantly during fermentation. The results indicated that the dominant bacterial genera were Staphylococcus, Lactococcus, and Bacillus. The dominant fungi were Aspergillus and Lichtheimia. During the early and late stages of bean paste fermentation, alcohols, hydrocarbons, esters, and phenols were the main flavor compounds detected. The types and proportions of alcohols and esters in the bean pastes fermented for different durations were similar, whereas the relative contents of phenols and hydrocarbons were higher in the later stages of fermentation. Correlation analysis revealed that core functional microorganisms played a key role in the fermentation process, and the potential correlation between bacterial genera and flavors was stronger than that of fungal genera. Staphylococcus abundance was significantly correlated with the flavor levels of ethyl oleate, ç‐pinene, diallyl disulfide, á‐myrcene, D‐limonene, and tetradecanoic acid, ethyl ester. The abundance of Aspergillus and Lichtheimia was significantly correlated with the flavor levels of á‐myrcene, ç‐pinene, and DL‐3‐phenyllactic acid. This study explored the relationship between microorganisms and flavor compounds in bean paste to deepen our understanding of the mechanism of flavor formation for bean paste. [ABSTRACT FROM AUTHOR]

Pyrazines are important flavor components and healthy active components in Baijiu, which including tetramethylpyrazine (TTMP). During the brewing process, the traceability of microbial communities and the content distribution characteristics of TTMP are important for improving the quality and style characteristics of compound-flavored Baijiu (CFB). However, the traceability analysis of microorganisms in fermented grains (FG)--used in the production of CFB--lacks quantitative and systematic evaluation. In this study, the microbial communities and TTMP content of Jiuqu (JQ), Liangpei (LP), FG, and pitmud (CP) used in CFB production were characterized; further, coordinate and discriminant analyses were employed to determine differences in microbial communities. Additionally, traceability and correlation analyses were performed to reveal the origin of microbial communities in FG. The source, content, and distribution characteristics of TTMP based on the brewing process have also been discussed. The results showed thatmost of the bacterial and fungal communities at different levels of FG came fromother sources, and themicroorganisms of Cladosporium, Acetobacter, Aspergillus, Methanosarcina, and Bacillus were considered have a osculating correlations with TTMP content of FG. Taken together, this study provides insights into the origin of microbial communities in FG and the distribution characteristics of TTMP based on the CFB brewing process. The current findings are conducive for optimizing the fermentation process and improving the quality and style characteristics of CFB. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study was to investigate the effects of Lactiplantibacillus plantarum (L. plantarum) and propionic acid (PA) on fermentation characteristics and microbial community of amaranth (Amaranthus hypochondriaus) silage with different moisture contents. Methods: Amaranth was harvested at maturity stage and prepared for ensiling. There were two moisture content gradients (80%: AhG, 70%: AhS; fresh material: FM) and three treatments (control: CK, L. plantarum: LP, propionic acid: PA) set up, and silages were opened after 60 d of ensiling. Results: The results showed that the addition of L. plantarum and PA increased lactic acid (LA) content and decreased pH of amaranth after fermentation. In particular, the addition of PA significantly increased crude protein content (p < 0.05). LA content was higher in wilted silage than in high-moisture silage, and it was higher with the addition of L. plantarum and PA (p < 0.05). The dominant species of AhGLP, AhSCK, AhSLP and AhSPA were mainly L. plantarum, Lentilactobacillus buchneri and Levilactobacillus brevis. The dominant species in AhGCK include Enterobacter cloacae, and Xanthomonas oryzae was dominated in AhGPA, which affected fermentation quality. L. plantarum and PA acted synergistically after ensiling to accelerate the succession of dominant species from gram-negative to gram-positive bacteria, forming a symbiotic microbial network centred on lactic acid bacteria. Both wilting and additive silage preparation methods increased the degree of dominance of global and overview maps and carbohydrate metabolism, and decreased the degree of dominance of amino acid metabolism categories. Conclusion: In conclusion, the addition of L. plantarum to silage can effectively improve the fermentation characteristics of amaranth, increase the diversity of bacterial communities, and regulate the microbial community and its functional metabolic pathways to achieve the desired fermentation effect. [ABSTRACT FROM AUTHOR]

Heat stress (HS) causes severe economic losses in sheep industry worldwide. The objective of the present study was to investigate the effects of a herbal formula (HF) supplement on growth, digestibility, antioxidant capacity, and rumen microbes in fattening lambs under HS. The HF composed of four herbs was prepared based on the theory of compatibility of Chinese medicine "Jun-Chen-Zuo-Shi". Two-hundred forty 3-month weaned lambs (initial weight 36.61 ± 0.73 kg) were randomly allocated into four groups, supplemented 0% (Control), 0.5%, 1.0%, and 1.5% HF in diets. All lambs were exposed to HS conditions with 79.7 of average temperature–humidity index throughout an experimental period of 35 days. Growth performance, apparent digestibility, and antioxidant activities, involving antioxidant enzymes and heat shock proteins (HSPs), were measured at the end of trial, as well as microbial communities in bacteria and archaea. Results showed that 0.5% HF increased (P = 0.02) average daily gain by 13.80% and decreased feed-to-gain ratio (P = 0.03) by 14.68%, compared to control. With increasing HF doses, the digestibility of ether extract and acid detergent fiber demonstrated a cubical (P < 0.01) and quadratic (P = 0.03) relation, respectively; moreover, glutathione peroxidase and catalase activities demonstrated a quadratic increase (P < 0.01). Serum levels of HSP60, HSP70, and HSP90 for 0.5% HF were lower than that in control (P < 0.05). On the other hand, total volatile fatty acid, acetic acid, butyric acid, valeric acid, and isovaleric acid levels exhibited quadratic increases (P ≤ 0.01) with HF doses. From rumen microbes, the abundance and diversity of bacterial community were improved by HF supplements. Particularly for 0.5% HF group, the operational taxonomic units were the greatest among all groups. Compared to control, Prevotella abundance for HF supplements from 0.5 to 1.5% increased by 35.57 to 60.15%, and Succiniclasticum abundance demonstrated a quadratic pattern (P = 0.02) with doses. Additionally, Methanosphaera abundance in archaeal community raised by 0.2 to 3.3-folds when lambs were fed the HF additions of 0.5 to 1.5%. In summary, dietary HF supplements would contribute to alleviating HS in lambs, and our results suggest the optimal dose of 0.5% HF supplement in diet. [ABSTRACT FROM AUTHOR]

Background: Compost-bedded pack barns (CBP) are getting huge attention as an alternative housing system for dairy cows due to their beneficial impact on animal welfare. Effective microorganisms (EM) inoculums are believed to enhance compost quality, improve soil structure and benefit the environment. However, little information is available on the impact of incubation with external EM combinations on the barn environment, compost quality and microbial diversity in CBP. This experiment was carried out to investigate the effect of inoculating different combinations of EM [Lactobacillus plantarum (L), Compound Bacillus (B) and Saccharomyces cerevisiae (S)] on compost quality and microbial communities of CBP products, as well as the relationship with the heifers' barn environment. CBP barns were subjected to the following four treatments: CON with no EM inoculum, LB/LS/LBS were Incubated with weight ratios of 1:2 (L: B), 1:2 (L: S), 1:1:1 (L: B: S), respectively. Results: The EM inoculation (LB, LS, LBS) reduced the concentration of respirable particulate matter (PM10 and PM2.5) in the CBP, and decreased the serum total protein and total cholesterol levels in heifers. Notably, LBS achieved the highest content of high-density lipoprotein compared to other treatments. Microbiome results revealed that EM inoculation reduced the bacterial abundance (Chao1 index) and fungal diversity (Shannon & Simpson indexes), while increasing the relative abundance of various bacterial genera (Pseudomonas, Paracoccus, Aequorivita) and fungi (Pestalotiopsis), which are associated with cellulose decomposition that ultimately resulted in accelerating organic matter degradation and humification. Furthermore, high nutrient elements (TK&TP) and low mycotoxin content were obtained with EM inoculation, with LBS showing a particularly pronounced effect. Meanwhile, LBS contributed to a decline in the proportion of fungal pathogen categories but also led to an increase in fungal saprotroph categories. Conclusion: Generally, EM inoculation positively impacted compost product quality as organic fertilizer and barn environment by modifying the abundance of cellulolytic bacteria and fungi, while inhibiting the reproduction of pathogenic microbes, especially co-supplementing with L, B and S achieved an amplifying effect. [ABSTRACT FROM AUTHOR]

Background: Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed. Results: The results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting. Conclusions: In conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum. [ABSTRACT FROM AUTHOR]

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Soil provides essential nutrients for plant growth, but excess salts hinder development, making crops more vulnerable under climate change conditions. Soil microorganisms play a significant role in nutrient cycling. However, limited information is available on microbial behavior/community changes, and functional diversity in different soil types (normal, sodic, and highly sodic) and cropping systems [rice-wheat (RW); rice-wheat-mungbean (RWMb); maizewheat-mungbean (MWMb)] and management practices in the north-western Indo-Gangetic Plains of India. We investigated the influence of different soil types on physical and chemical properties at the surface level (0-15 cm) in relation to soil microbial population, activities, and functional diversity, focusing on community-level physiological profiling (CLPP) under different agriculture systems. Seven treatment combinations of soil types, cropping systems, and management practices were evaluated. Soil pHs were found to be lower in zerotill (ZT)-based sodic soil than in conventional-till (CT) sodic soil. Soil organic carbon (SOC) (0.91 and 0.90%) content and available N (154.46 and 132.74 kg ha-1) were higher with the ZT-based system under normal (N) soils (ZT-RWMb-N and ZT-MWMb-N) than in CT-based normal soil (0.67 and 121.04 kg ha-1). Similarly, higher SOC and N (0.85 and 76.11 kg ha-1) were found under ZT management in sodic soils (S) than under CT management (0.73% and 121.05 kg ha-1). Substrate utilization (amino acids, amines, carbohydrates, carboxylic acids, phenolic compounds, and polymers) increased with the incubation period. During 0-120 h of incubation, the highest utilization of amino acids, amines, carboxylic acids, phenolic compounds, and polymers was observed for ZT-MWMb-S soils, while the lowest was recorded for ZT-MWMb-N soils. Under high salt conditions, soil enzymatic activities (dehydrogenase, acid phosphatase, alkaline phosphatase, etc.) declined significantly compared to normal soils, affecting soil chemical and physical conditions. Microbial population and enzyme activities decreased with increasing salt stress across all cropping systems. These findings suggest that adopting efficient crop management practices can help mitigate the adverse effects of soil salinity on microbial diversity and soil health, thereby enhancing sustainable agricultural productivity in salt-affected regions. [ABSTRACT FROM AUTHOR]

This study was undertaken in order to explore the correlation between the quality changes and microbial community in sauced duck necks during cold storage. Commercial sauced duck necks in modified atmosphere packaging were stored at 4 °C for 1, 4, 7, 10, and 13 days, and the changes in pH, thiobarbituric acid reactive substances (TBARS) value, color, texture, total bacterial count, total volatile base nitrogen (TVB-N) content, and microbial community were analyzed. The results showed that the pH initially decreased and then increased with storage time, while brightness (L*), redness (a*), yellowness (b*) and hardness exhibited a decreasing trend, and elasticity, chewiness, cohesiveness and adhesiveness showed an initial increase followed by a decrease. The total bacterial count, TVB-N and TBARS values all gradually increased during storage, with the total bacterial count and TVB-N exceeding the acceptable limits on the 10th day. Microbial diversity diminished gradually with storage time. At the initial stage of storage, the dominant bacteria were Rhodococcus, Acinetobacter, Ureibacillus and Symbiobacterium, while those in the late storage period were Rhodococcus, Acinetobacter, Leuconostoc and Lactobacillus. Principal co-ordinate analysis indicated the two principal coordinates explained 74.03% of the variation, and differences in microbial community composition occurred after 4 days of storage. Correlation analysis showed that Leuconostoc was positively correlated with pH, total bacterial count, TVB-N content and TBARS value during cold storage of sauced duck necks, indicating that Leuconostoc was the primary spoilage bacteria during storage. [ABSTRACT FROM AUTHOR]

Anaerobic ammonia oxidation process has the advantages of energy and cost reduction, therefore, it has been considered as one of the main alternatives to conventional biological denitrification process in recent years. Biochar has been applied in the anammox process for nitrogen removal efficiency. But, due to its extracellular electron transfer capacity and abundance of redox-specific functional groups, which served as extracellular electron acceptor to anaerobically oxidize NH4+ is still controversy. In this study, the anaerobic ammonia oxidation was investigated when biochar was used as electron acceptor in the wastewater. According to the optimal process variables determined in the batch tests, when the influent NH4+-N concentration in the anaerobic ammonia oxidation reaction was 30–50 mg/L and the biochar dosing was at 10 g/L, it showed some promotion in the long-term experiments. The anaerobic ammonia oxidation process with biochar as the electron acceptor reached more than 60% NH4+-N removal efficiency in the system, and the ΔNO3--N/ΔNH4+-N ratio reached 0.19 which tended to the theoretical value. After 20 days, the voltage in the system keeps fluctuating about 4 mV, indicated that the functional bacteria using biochar as the electron acceptor gradually dominated the system. In addition, the abundance of norank_f__norank_o__SBR1031 in the Chloroflexi phylum has increased significantly at 29.92%, while the abundance of the major genus Candidatus_Kuenenia in AnAOB has decreased slightly at 11.47%. [ABSTRACT FROM AUTHOR]

Light-flavor Baijiu (LFB) fermentation is a representative spontaneous mixedculture solid-state fermentation process in which sorghum is used as the raw material. Raw materials and microorganisms are crucial to the flavor formation and quality of LFB. However, the microbial and physicochemical dynamics of different sorghum varieties during LFB fermentation, as well as their impact on flavor compounds are still largely unknown. Herein, PacBio single-molecule real-time (SMRT) sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) were applied to investigate microbial community succession and volatile flavor formation in glutinous/non-glutinous sorghum-based fermented grains during LFB fermentation. Fermented grains made of glutinous sorghum Liangnuo No. 1 (GLN) had higher bacterial α-diversity and lower fungal α-diversity than those with fermented grains prepared with non-glutinous red sorghum (NRS) (p < 0.05). The dominant microbial species were Saccharomyces cerevisiae, Acetobacter pasteurinus, and Lactobacillus helveticus, the latter two of which were the predominant bacteria observed at the end of fermentation in GLN and NRS, respectively. Moisture content and reducing sugar had a more significant impact on the microorganisms in GLN, while amino acid nitrogen, total free amino acids, and residual starch were the main driving factors driving the microbial community in NRS. The correlation network and discriminant analysis indicated that a relatively high content of 4-vinylguaiacol showed a significant positive association with significant differential microbial species in GLN. These results provided valuable insights for improving the quality of LFB. [ABSTRACT FROM AUTHOR]

If dihydrogen (H2) becomes a major part of the energy mix, massive storage in underground gas storage (UGS), such as in deep aquifers, will be needed. The development of H2 requires a growing share of H2 in natural gas (and its current infrastructure), which is expected to reach approximately 2% in Europe. The impact of H2 in aquifers is uncertain, mainly because its behavior is site dependent. The main concern is the consequences of its consumption by autochthonous microorganisms, which, in addition to energy loss, could lead to reservoir souring and alter the petrological properties of the aquifer. In this work, the coinjection of 2% H2 in a natural gas blend in a low-salinity deep aquifer was simulated in a three-phase (aquifer rock, formation water, and natural gas/H2 mix) high-pressure reactor for 3 months with autochthonous microorganisms using a protocol described in a previous study. This protocol was improved by the addition of protocol coupling experimental measures and modeling to calculate the pH and redox potential of the reactor. Modeling was performed to better analyze the experimental data. As in previous experiments, sulfate reduction was the first reaction to occur, and sulfate was quickly consumed. Then, formate production, acetogenesis, and methanogenesis occurred. Overall, H2 consumption was mainly caused by methanogenesis. Contrary to previous experiments simulating H2 injection in aquifers of higher salinity using the same protocol, microbial H2 consumption remained limited, probably because of nutrient depletion. Although calcite dissolution and iron sulfide mineral precipitation likely occurred, no notable evolution of the rock phase was observed after the experiment. Overall, our results suggested that H2 can be stable in this aquifer after an initial loss. More generally, aquifers with low salinity and especially low electron acceptor availability should be favored for H2 costorage with natural gas. [ABSTRACT FROM AUTHOR]

Secondary microbial methane could provide a valuable energy source if it were better understood. Although coal seam is an ideal environment for investigating secondary microbial methane, there are few studies to trace the secondary microbial methane of high-rank coals. Here, we collected co-produced water samples from coalbeds in the Qinshui Basin (China) and analyzed the microbial community structure by 16S ribosomal RNA (16S rRNA) amplicon sequencing analysis. 16S rRNA sequencing demonstrated abundant methanogens in coalbeds including 6 orders (Methanobacteriales, Methanococcales, Methanofastidiosales, Methanomassiliicoccale, Methanomicrobiales, and Methanosarciniales) and 22 genera of methanogens. Superheavy DIC (δ13CDIC ranging from -4.2‰ to 34.8‰) and abundance of methanogenic microbes in co-produced water revealed the generation of secondary biogenic methane in high-rank coal seams in the Qingshui Basin. Hydrogenotrophic methanogenesis is the main pathway for secondary biogenic methane production. In deeply buried coal seams, biogenic methane is dominated by CO2 and H2 reduction methanogenesis, and in shallow buried coal seams, it may be produced synergistically by hydrocarbon degradation and hydrogenotrophic methanogenic microbes. The study discussed here is important for a better understanding of the generation of secondary microbial methane in high-rank coal. [ABSTRACT FROM AUTHOR]

This article is an editorial that discusses the development and ecological functions of biological soil crusts (biocrusts). Biocrusts are composed of microorganisms and play important roles in soil stabilization, microbial diversity, and ecosystem development. The editorial emphasizes the need for further research on biocrust communities and their impact on landscape-scale outcomes. It also highlights the ecological functions of biocrusts, such as reducing erosion and influencing biogeochemical cycles. The article concludes by discussing the importance of understanding biocrusts for ecological restoration and land management strategies. Another document provides a list of references for articles related to biological soil crusts, covering topics such as land degradation neutrality, ecological restoration, and the impact of biocrusts on microbial communities. The articles also explore the composition and response of biocrusts to climate change and physical disturbance, as well as their effects on soil properties and metabolic response to hydration. [Extracted from the article]

Background: Douzhi, a traditional Chinese fermented beverage, features microbial communities primarily composed of lactic acid bacteria (LAB). As fermented foods continue to gain recognition and popularity, douzhi is attracting growing interest. However, investigation of the critical aspects of douzhi's fermentation processes, including fermentation characteristics and microbial community dynamics, remains vital for enhancing food safety and quality for douzhi, as well as for similar fermented food products. Method: In this study, we collected douzhi microbial communities from four chain stores, using them as fermentation starter cultures. The microbial dynamics of the fermentation were analyzed, focusing on the inoculation of LAB strains and the transition from a mung bean-based matrix to skimmed milk. The metabolomic profiles of the fermented mung bean matrices were also studied. Results: Douzhi samples obtained from representative chain stores were found to be overwhelmingly dominated by LAB. When inoculated along with the douzhi community, both LAB strains exhibited notable and substantial reductions in the pH value of the designated mung bean matrices compared to those inoculated indigenous microbiota. Specifically, Lactiplantibacillus plantarum CGMCC 1.1856 retained its population, whereas Pediococcus pentosaceus CGMCC 1.2695 exhibited a decrease in relative abundance. Using skimmed milk as a fermentation substrate instead of the mung bean matrix resulted in significant shifts in microbial communities, particularly leading to an increase in Escherichia sp. The metagenomic analyses and functional predictions illustrated that various metabolic functions were enhanced during the fermentation process due to LAB inoculation. The liquid chromatography-mass spectrometry based metabolomic analysis revealed that the inoculation of Lactiplantibacillus plantarum and Pediococcus pentosaceus in mung bean matrix did not introduce new metabolites but significantly altered the concentration and profile of existing metabolites, especially increased low molecular carbohydrates, which may enhance the nutritional potential of the fermented product. Discussion: This study examines the microbial dynamics of douzhi microbiota fermentation, emphasizing the role of lactic acid bacteria in enhancing fermentation activity and metabolite profiles. These insights contribute to improving manufacturing processes and ensuring the safety and quality of douzhi and similar fermented foods. [ABSTRACT FROM AUTHOR]

The normal operation of the Three Gorges Reservoir, which involves periodic water storage and discharge, has led to strong disturbances in environmental conditions that alter soil microbial habitats in the riparian zones. Riparian zones are an important part of controlling pollution in the Three Gorges Reservoir area, since they act as a final ecological barrier that intercepts pollutants. Meanwhile, monitoring the health of microbial communities in the riparian zone is crucial for maintaining the ecological security of the reservoir area. We specifically investigate the Daning River, which are tributaries of the Three Gorges Reservoir and have typical riparian zones. Soil samples from these areas were subjected to high-throughput sequencing of 16S rRNA genes and 18S rRNA genes, in order to obtain the characteristics of the present microbial communities under strong disturbances in the riparian zones. We studied the characteristics and distribution patterns of microbial communities and their relationship with soil physicochemical properties. The study results indicate that microbial communities exhibit high diversity and evenness, and spatial heterogeneity is present. The ASV dataset contains many sequences not assigned to known genera, suggesting the presence of new fungal genera in the riparian zone. Redundancy analysis (RDA) revealed that pH and NH 4 + -N were the primary environmental factors driving bacterial community variation in the riparian zone, while pH, total carbon (TC) content, and NO 3 - -N were identified as the main drivers of soil archaeal community variation. [ABSTRACT FROM AUTHOR]

Introduction: Cultured fish species are increasingly exposed to fungi and bacteria in the rearing environment, often causing disease and mortality causing aquaculture producers to rely on the use of chemical therapeutants which may have negative consequences for both human and environmental health. This study investigated the effect of humic acid as a treatment to reduce fungal and bacterial infections to increase survival during the incubation of rainbow trout (Oncorhynchus mykiss) eggs. Methods: Humic acid, an aqueous extract of oxidized lignite was added to water entering both stacked tray and jar type incubators at a dosage rate of 5 mg/L from fertilization until hatching. Results: The water treatment eliminated observable fungus and significantly improved survival until hatching in the treated incubator trays (77.2%) compared to the untreated controls (55.5%) (p = 0.001). Egg survival was not improved in the incubator jars. The humic acid reduced bacterial diversity, but only in the stacked tray incubators and altered bacterial composition of the water after 20 days of treatment. Discussion: The treatment increased the bacterial abundance of Burkholderiales, positively associated with healthy fish eggs and decreased the abundance of Flavobacterium and Aeromonas, known fish pathogens. These findings support the topical treatment of humic acid as a potential alternative treatment to prevent fungal infections and reduce mortality during incubation of rainbow trout eggs. [ABSTRACT FROM AUTHOR]

Introduction: Currently, straw biodegradation and soil improvement in rice)mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession. Methods: In this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms. Results: The results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity. Discussion: Overall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems. [ABSTRACT FROM AUTHOR]