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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.

Introduction: Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence. Methods: This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation. Results and discussion: Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus , Rubrobacter , Luteitalea , Nakamurella , and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community. [ABSTRACT FROM AUTHOR]

Litter decomposition has historically been attributed to soil microbial community at local scale, but which fundamental process directly contributes to carbon release from decomposing litter remains not fully understood. Here we used in situ microcosms to assess the temporal changes in soil microbial biomass, taxonomic composition, alpha and beta diversity, network complexity and carbon-degrading functional genes during litter decomposition of a subtropical dominant species (Castanopsis carlesii) in an older (45-years) and a younger (9-years) evergreen broadleaved forests. The soil phospholipid fatty acids, bacterial and fungal community composition, α-diversity indexes and network topological properties were not changed significantly after short-term litter input when litter was decomposed by approximately 70%. However, the absolute abundance of functional genes involved in the decomposition of starch, pectin, hemicellulose, cellulose, chitin and lignin were up-regulated, and these variations were associated with soil α-1.4-glucosidase, β-glucosidase and cellobiohydrolase activities in contributing to litter carbon release during decomposition. These results suggest that the upregulation of functional genes rather than microbial community composition and diversity controls local-scale litter decomposition by encoding and secreting enzymes in these subtropical forests. [ABSTRACT FROM AUTHOR]

Pecans (Carya illinoinensis), one of the most valuable native North American nut crops, are commonly propagated through grafting to preserve the desired characteristics from parent trees. Since successful cultivation of pecan trees relies on the interplay among scion varieties, rootstocks, and soil conditions, this study investigated the microbial change to communities in the soils and roots of southern (87MX5-1.7) and northern (Peruque) rootstocks in a rootstock test orchard. Both grafted with the 'Pawnee' scion cultivar. Bacterial 16S ribosomal RNA and fungal ITS were amplified from both roots and rhizosphere soils of the two 10-yeargrafted trees, then sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The Peruque roots had a higher relative abundance of saprotroph fungi, while 87MX5-1.7 exhibited higher levels of symbiotroph fungi and nitrogen fixation-related bacteria. Among them, the presence of symbiotroph fungi, particularly ectomycorrhizal fungi, notably differed between these two rootstocks, with a significantly higher presence observed in the root of 87MX5-1.7 compared to Peruque. This variation likely leads to divergent pathways of nutrient translocation: Peruque was in favor of multiple fungi (Russula and Inocybe) to gain nutrition, while 87MX5-1.7 preferred a specific domain of fungi (Tuber) and nitrogen fixation-related bacteria (Bradyrhizobia) to form beneficial symbiosis. Moreover, the presence of pathogens suggested a potential risk of Fusarium patch and snow molds in 87MX5-1.7, while canker and black foot disease pose threats in Peruque. The findings of this study suggest that rootstocks from different origins shape rhizosphere microbes differently, potentially affecting nutrient uptake and nut yield. Exploring rootstock-microbe combinations could provide insights into optimizing scion growth and ultimately increasing nut yield. By understanding how different rootstock-microbe interactions influence pecan tree development, growers can strategically select combinations that promote beneficial symbiotic relationships, enhancing nutrient uptake, disease resistance, and overall tree vigor. [ABSTRACT FROM AUTHOR]

Introduction: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China’s largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river– lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu’s outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river–lake systems subjected to different intensities of water flow disturbances. Methods: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and cooccurrence networks between the two regions under varying hydrological regimes. Results and discussion: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river–lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu. [ABSTRACT FROM AUTHOR]

Terrestrial mud volcanoes represent surface features of channels for subsurface methane transport and, therefore, constitute an important source of methane emission from natural environments. How microbial processes regulate methane emissions in terrestrial mud volcanoes has yet to be fully addressed. This study demonstrated the geochemical characteristics and microbial communities of four mud volcano and seep sites in two geological settings of Sicily, Italy. At sites within the accretionary wedge that exhibited higher methane and sulfate concentrations, the communities were dominated by members capable of catalyzing methane and sulfate metabolisms and organic degradation. In particular, both anaerobic and aerobic methanotrophs were abundant and their abundance distribution coincided with the geochemical transition. In contrast, the sites near Mount Etna were characterized by high fluid salinity, CO2, and low methane and sulfate concentrations, with communities consisting of halophilic organic degraders and sulfur metabolizers, along with a minor presence of aerobic methanotrophs. Substantial variations in community composition and geochemistry across spatial and vertical redox gradients suggest that physicochemical contexts imposed by the geology, fluid path, and source characteristics play a vital role in shaping community composition and cycling of methane, sulfur and organic carbon in Sicily mud volcanoes. [ABSTRACT FROM AUTHOR]

The huge amount of urea applied has necessitated best-developed practices to slow down the release of nitrogen (N) fertilizer while minimizing nitrate loss. However, the impact of nitrification inhibitors on mineral-N turnover and the associated microbial mechanisms at different stages remains unknown. A 60- day incubation experiment was conducted with four treatments: no fertilizer (CK), urea (U), urea with copper pyrazole (UC), and urea coated with copper pyrazole (SUC), to evaluate the changes about soil ammonia N (NH4+ -N) and nitrate N ( NO3− -N) levels as well as in soil microbial community throughout the whole incubation period. The results showed that copper pyrazole exhibited significantly higher inhibition rates on urease compared to other metal-pyrazole coordination compounds. The soil NH4+ -N content peaked on the 10th day and was significantly greater in UC compared to U, while the NO3− -N content was significantly greater in U compared to UC on the 60th day. Copper pyrazole mainly decreased the expression of nitrifying (AOB-amoA) and denitrifying (nirK) genes, impacting the soil microbial community. Co-occurrence network suggested that Mycobacterium and Cronobacter sakazakii-driven Cluster 4 community potentially affected the nitrification process in the initial phase, converting NH4+ -N -N to NO3− -N. Fusarium-driven Cluster 3 community likely facilitated the denitrification of NO3− -N and caused N loss to the atmosphere in the late stage. The application of copper pyrazole may influence the process of nitrification and denitrification by regulating soil microbial traits (module community and functional genes). Our research indicates that the addition of copper pyrazole alters the community function driven by keystone taxa, altering mineral-N turnover and supporting the use of nitrification inhibitors in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Metabolite exchange mediates crucial interactions in microbial communities, significantly impacting global carbon and nitrogen cycling. Understanding these chemically-mediated interactions is essential for elucidating natural community functions and developing engineered synthetic communities. This study investigated membrane-separated bioreactors (mBRs) as a novel tool to identify transient metabolites and their producers/consumers in mixed microbial communities. We compared three co-culture methods (direct mixed, 2-chamber mBR, and 3-chamber mBR) to grow a synthetic binary community of the cyanobacterium Synechococcus elongatus PCC 7942 and the fungus Rhodotorula toruloides NBRC 0880, as well as axenic S. elongatus. Despite not being natural lichen constituents, these organisms exhibited interactions resembling those in cyanolichens. S. elongatus fixed CO2 into sugars as the primary shared metabolite, while R. toruloides secreted various biochemicals, predominantly sugar alcohols, mirroring the metabolite exchange observed in natural lichens. The mBR systems successfully captured metabolite gradients and revealed rapidly consumed compounds, including TCA cycle intermediates and amino acids. Our approach demonstrated that the 2-chamber mBR optimally balanced metabolite exchange and growth dynamics. This study provides insights into cross-species metabolic interactions and presents a valuable tool for investigating and engineering synthetic microbial communities with potential applications in biotechnology and environmental science. [ABSTRACT FROM AUTHOR]

Background: Crop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail. Materials and methods: In this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed. Results: The results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems. Conclusions: Different crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems. [ABSTRACT FROM AUTHOR]

In this study, the effects on silage performance and microbial community of sorghum straw treated with the addition of enzymes (cellulase (CE), xylanase (XE)) and extrusion puffing technology, combined with SEM, XRD, and FTIR techniques, were thoroughly investigated. The results showed that the enzyme preparations, especially xylanase, significantly improved the nutritional value and fermentation efficiency of straw and enhanced the silage effect. Extruding significantly changes the surface structure of the straw, increasing the surface area and porosity, and promoting the attachment of microorganisms. This study not only optimized the sorghum straw silage performance but also provided technical support for the efficient use of straw resources, which is of great significance for the sustainable development of animal husbandry and the resource utilization of agricultural waste. [ABSTRACT FROM AUTHOR]

The magnitude of plant–soil feedback (PSF) can depend on the time of conditioning as well as the length of feedback. Understanding the temporal variation in PSF requires insight in the response of both soil characteristics and the plant. We examined how conspecific PSF varies with the length of conditioning and the size of the response plant using Jacobaea vulgaris, a species known to experience negative conspecific PSF. Together with reanalysis of an existing microbial sequence dataset, we tested whether the temporal variation in PSF is due to size‐dependent plant sensitivity to conditioned soil or due to compositional changes in microbial communities of conditioned soil. Further, by reanalysing another existing dataset, we examined temporal dynamics of the relative growth rates (RGR) of J. vulgaris during the feedback phase. Testing varying conditioning lengths, uncovered that J. vulgaris exhibited the strongest negative PSF at 5 weeks of conditioning, after which PSF gradually attenuated. Plant sensitivity to conditioned soil decreased with increasing plant age/size of the response plant. In the feedback phase, the RGR of J. vulgaris was first higher, then lower and at the end similar in ‘away’ soil compared to ‘home’ soil. The dissimilarity in bacterial and fungal communities in ‘home’ and ‘away’ soil significantly decreased during the feedback phase. When J. vulgaris grew in ‘away’ soil, the relative abundance of 10 (out of 80) bacterial OTUs that positively correlated with plant growth decreased over time, while 5 (out of 86) OTUs that negatively correlated with plant growth the relative abundance increased over time. Additionally, only one (out of 10) fungal OTU that negatively associated with plant growth increased over time in ‘away’ soil. Synthesis. Our findings illustrate that PSF varies with the duration of soil conditioning and of the feedback phase. During the feedback phase, changes in PSF can be attributed to both the size‐dependent plant sensitivity to conditioned soil and temporal changes in the microbial community of conditioned soil. This highlights the importance of considering the reconditioning of soil microbial communities by the test plants during the feedback phase for understanding temporal variation in PSF. [ABSTRACT FROM AUTHOR]

Grazing has been shown to impact the soil environment and microbial necromass carbon (MNC), which in turn regulates soil organic carbon (SOC). However, the carbon sequestration potential of fungi and bacteria under different stocking rates remains unclear, limiting our understanding of soil carbon sequestration in grazing management. In 2004, we established grazing experiments in the desert steppe of northern China with four stocking rates. Our findings indicate that MNC decreased under moderate and heavy grazing, while light grazing did not significantly differ from no grazing. Notably, the reduction in fungal necromass carbon, rather than bacterial necromass carbon, was primarily responsible for the decreased contribution of MNC to SOC. This difference is attributed to the varying effects of sheep grazing on fungal and bacterial community characteristics, including richness, diversity, and composition. Thus, to accurately predict carbon dynamics in grassland ecosystems, it is essential to consider that the ecological impacts and carbon sequestration potential of microbial communities may vary with different grazing management practices. [ABSTRACT FROM AUTHOR]

Introduction: Microorganisms as a component of scalp ecosystem play a vital role in human scalp health. Soapberry pericarp is employed in improving scalp health, and its content of active ingredients could be enhanced resulted in fermentation. This study aims to investigate the effect of the fermentation filtrate from soapberry pericarp on the diversity of scalp microorganisms. Methods: The components in fermentation filtrate from soapberry pericarp were analyzed by HPLC-Q-Orbitrap HRMS, and 16S and ITS sequences of 198 samples from three different used stages (Day 0, Day 7, Day 28) were sequenced using the Illumina Novaseq platform. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (weighted unifrac and unweighted unifrac). Principal coordinate analysis (PCoA) and linear discriminant analysis (LDA) effect size analysis (LEfSe) were used to visualize microbial variation among different stages. Results: There were 22 components were identified in the fermentation filtrate from soapberry pericarp by HPLC-Q-Orbitrap HRMS. The alpha-diversity and beta-diversity analyses showed that scalp microbial diversity and composition were influenced by the fermentation filtrate of soapberry pericarp. Based on functional analysis, this study found an enrichment of healthy scalp-related bacterial pathways, such as amino acid, nucleoside, and nucleotide biosynthesis, while a decrease in fungal pathogenesis pathways, specifically saprotroph and symbiotroph pathways, was observed. Discussion: The study described about the complex community dynamics of human scalp microorganisms during the stages of using the fermentation filtrate from soapberry pericarp. This result will help rationally utilize the fermentation filtrate from soapberry pericarp to keep or improve human scalp health. [ABSTRACT FROM AUTHOR]

Background: Microbial communities significantly influence the vector capacity of ticks, which, along with tick-borne diseases, pose an increasing global threat. Due to the substantial individual variability caused by various factors, it is essential to assess tick microbial communities and vectorial capacities under different environmental conditions. However, there is a relative scarcity of research on the microbial communities and pathogen transmission of ticks in different physiological states and environmental conditions, especially in Hainan Island, southern China. Methods: From 2021 to 2022, we collected 4,167 tick samples, grouping them by blood meal status, developmental stage, sex, time, geographical location, and tick species. We selected 128 samples for full-length 16S rRNA sequencing to describe microbial community characteristics and identify potential biomarkers. Seven hundred seventy-two samples were tested for seven tick-borne pathogens (Rickettsia, Borrelia burgdorferi, Ehrlichia, Anaplasma, Theileria, Babesia, and Hepatozoon), and sera from 208 residents of Hainan Island were tested for IgG antibodies against Rickettsia and B. burgdorferi. Results: Blood meal status, developmental stage, sex, time, geographical location, and tick species significantly influenced the microbial communities of ticks. We observed distinct microbial community characteristics across different states. We noted the non-random replacement of stable and transient species, with functional differences between parasitic and engorged ticks mainly driven by transient species. Functionally, we observed three distinct response patterns: driven by stable species, transient species, and both together in response to the six factors. We identified 273 potential biomarkers (200 robust core species and 73 robust differential species). Six genera and eight species of pathogens were detected in ticks, with an overall positivity rate of 12.44% (96/772). Among humans, 18.27% (38/208) of serum samples were positive for at least one tick-borne pathogen IgG. Conclusion: Our findings indicate that these six factors significantly influence both tick microbial communities and vectorial capacity, with varying effects on vector competence for different pathogens and inconsistent impacts on microbial communities under different conditions. This study supplemented the understanding of tick microbial communities on Hainan Island, assessed the relatively high risk of tick-borne pathogens in the region, and evaluated the impact of these factors on both microbial communities and vectorial capacity. [ABSTRACT FROM AUTHOR]

Zizhong Dongjian (ZZDJ) is one of the most famous and popular fermented vegetables in China. The aim of this study was to explore the microbial communities and volatile flavor compounds of ZZDJ during different fermentation periods, as well as to reveal the potential correlation between microbiota and flavor. A total of 84 volatile flavor compounds were detected in 0‐year to 3‐year ZZDJ samples. Hydrocarbons were the most abundant flavor compounds in 0‐year and 1‐year samples, while esters became the predominant flavor components in 2‐year and 3‐year samples. Furthermore, Loigolactobacillus, Pseudomonas, and Virgibacillus were most predominant bacteria during the fermentation process of ZZDJ. Interestingly, all the fungi identified were yeasts. Among them, Zygosaccharomyces and Symmetrospora dominated alternatively throughout the fermentation process of ZZDJ. Through analysis of relativity between flavor compounds and microorganism of ZZDJ, we found that Uncultured Pseudomonas sp., Virgibacillus sediminis, Zygosaccharomyces rouxii, and Symmetrospora marina might play important roles in flavor information of ZZDJ. [ABSTRACT FROM AUTHOR]

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology. [ABSTRACT FROM AUTHOR]

Environmental gradients can influence morpho-physiological and life-history differences in natural populations. It is unclear, however, to what extent such gradients can also modulate phenotypic differences in other organismal characteristics such as the structure and function of host-associated microbial communities. In this work, we addressed this question by assessing intra-specific variation in the diversity, structure and function of environmental-associated (sediment and water) and animal-associated (skin and gut) microbiota along an environmental gradient of pollution in one of the most urbanized coastal areas in the world. Using the tropical sea cucumber Holothuria leucospilota, we tested the interplay between deterministic (e.g., environmental/host filtering) and stochastic (e.g., random microbial dispersal) processes underpinning host-microbiome interactions and microbial assemblages. Overall, our results indicate that microbial communities are complex and vary in structure and function between the environment and the animal hosts. However, these differences are modulated by the level of pollution across the gradient with marked clines in alpha and beta diversity. Yet, such clines and overall differences showed opposite directions when comparing environmental- and animal-associated microbial communities. In the sea cucumbers, intrinsic characteristics (e.g., body compartments, biochemistry composition, immune systems), may underpin the observed intra-individual differences in the associated microbiomes, and their divergence from the environmental source. Such regulation favours specific microbial functional pathways that may play an important role in the survival and physiology of the animal host, particularly in high polluted areas. These findings suggest that the interplay between both, environmental and host filtering underpins microbial community assembly in H. leucospilota along the pollution gradient in Hong Kong. [ABSTRACT FROM AUTHOR]

Fermentation is an effective method for ameliorating the gelation properties of freshwater fish surimi, but the formation of biogenic amines (BAs) during fermentation should also be controlled. In this study, the BAs in fermented tilapia surimi were inhibited by the collaborative fermentation of Latilactobacillus sakei and Pediococcus acidilactici, followed by the revelation of the BA inhibition mechanism. Most of the BAs, and the total BA, as well as their precusor free amino acids (FAAs), were significantly reduced, while the umami FAAs, including glutamic acid and aspartic acid, were significantly enhanced after cooperative fermentation with starters. The high-throughput sequencing found that the spoilage microorganisms such as Acinetobacter, Micrococcus, and Streptococcus as well as Pediococcus were significantly inhibited, while Latilactobacillus rapidly became the dominant genus after cooperative fermentation, suggesting the better environment adaptability of L. sakei than P. acidilactici. The group-dimension correlation analysis suggested that Lactiplantibacillus had the greatest influence on the decrease in BAss. The quick acidification of starters, especially L. sakei, could inhibit the growth and metabolism of spoilage microorganisms to reduce BAs. L. sakei and P. acidilactici can be developed as the special starters to control the BA production in the fermented tilapia surimi through collaborative fermentation. [ABSTRACT FROM AUTHOR]

The aim of this study was to examine the biological activity and probiotic properties of lactic acid bacteria (LAB) isolated from sweet potato stalk kimchi (SPK). Various LAB and Bacillus spp. are active in the early stages of the fermentation of kimchi made from sweet potato stalk. Four strains of LAB were identified, including SPK2 (Levilactobacillus brevis ATCC 14869), SPK3 (Latilactobacillus sakei NBRC 15893), SPK8 and SPK9 (Leuconostoc mesenteroides subsp. dextranicum NCFB 529). SPK2, SPK3, SPK8, and SPK9 showed 64.64–94.23% bile acid resistance and 78.66–82.61% pH resistance. We identified over 106 CFU/mL after heat treatment at 75 °C. Four strains showed high antimicrobial activity to Escherichia coli and Salmonella Typhimurium with a clear zone of >11 mm. SPK2 had the highest antioxidative potentials, higher than the other three bacteria, with 44.96 μg of gallic acid equivalent/mg and 63.57% DPPH scavenging activity. These results demonstrate that the four strains isolated from sweet potato kimchi stalk show potential as probiotics with excellent antibacterial effects and may be useful in developing health-promoting products. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this experiment was to explore the effect of adding cellulase and laccase on fermentation quality and microbial community in mixed silage of corn stover and wet brewer’s grains. Try to a new approach for the proper preservation and utilization of the agro-industrial by-products (corn stover and wet brewer’s grains). Methods: The experiment was divided into four groups: CK (control), C (cellulase, 120 U/g fresh matter [FM]), L (laccase, 50 U/g FM), CL (cellulase 120 U/g FW and laccase 50 U/g FM), and the chemical composition, fermentation quality, microbial population and microbial community in mixed silage of corn stover and wet brewer’s grains after 30 day’s fermentation were determined. Results: Compared to control, the addition of cellulase significantly increased crude protein (CP), water-soluble carbohydrate (WSC), lactic acid bacteria (LAB) counts, while significantly decreased the neutral detergent fiber (NDF), acid detergent fiber (ADF) content (P < 0.05). Adding laccase significantly decreased the acid detergent lignin (ADL) content (P < 0.05). Combined application of cellulase and laccase significantly increased the CP, WSC content and LAB counts, while significantly decreased pH value, NDF, ADF and ADL content (P < 0.05), thereby improving fermentation quality. In addition, the application of cellulase and laccase increased the abundance of Firmicutes and LAB genera, and decreased microbial diversity level of the sample. Conclusion: The combined application of cellulase and laccase further improved fermentation quality and microbial community in mixed silage of corn stover and wet brewer’s grains. [ABSTRACT FROM AUTHOR]

Background: The root-associated microbiomes are crucial in promoting plant growth and development through symbiotic interactions with their hosts. Plants may shape their microbiomes by secreting specific root exudates. However, the potential mechanisms how plant species determine root exudates and drive microbiome assembly have been little studied. In this study, three wild tobaccos and one cultivated tobacco were used to investigate the commonalities and differences of both root-associated microbiomes and root exudates. Results: Amplicon sequencing results suggested that tobacco species significantly affected microbial communities in both the rhizosphere and root endosphere, with the strongest impact on the fungal community in the root endosphere. The microbial networks of wild tobacco species were more stable than that of the cultivated tobacco, and fungal members played a more important role in the networks of wild tobacco species, while bacterial members did so in the cultivated tobacco. The rhizosphere bacteria of wild tobacco species showed a higher functional diversity than that of the cultivated tobacco, while the bacteria in the root endosphere presented a contrary pattern. Metabolomics analysis showed significant differences in the composition and abundance of root exudates among the four tobacco species, and the greatest difference was found between the three wild species and the cultivated one. Correlation analysis showed the strongest correlation between metabolites and rhizosphere bacteria, in which O-benzoic acid (2-methoxybenzoic acid) had the most positive correlations with rhizosphere bacteria, while β-ureidoisobutenoic acid had the most negative correlations with rhizosphere bacteria. The rhizosphere bacteria Streptomyces, Hydrophilus and Roseobacter had the strongest positive correlations with metabolites, and the rhizosphere bacterium Nitrobacter had the most negative correlations with metabolites. Conclusion: This study revealed the differences of microbial communities and root exudates in the rhizosphere and root endosphere of four tobacco species, which can further improve our understanding of plant–microbiome interactions during crop domestication. [ABSTRACT FROM AUTHOR]

To develop a unique flavor of rice wine, coffee flowers (by-products of the coffee industry) were added because of their biologically active compounds that are conducive to health, and the fermentation parameters were optimized. In addition, the dynamic changes of microbial communities and volatile flavor compounds (VFCs) during the different fermentation stages were investigated. After the optimization of the fermentation parameters, a novel product, i.e., the coffee flower rice wine (CFRW), was obtained with a bright yellow transparent, fragrant, and harmonious aroma and mellow and refreshing taste by sensory evaluation, when 4.62% of the coffee flowers and 1.93% koji were added and fermented at 24.10°C for 3.88 days. The results showed that Lactococcus was the dominant bacteria, accounting for 87.0-95.7%, while Rhizopus and Cladosporium were the main fungi, accounting for 68.2% and 11.3% on average, respectively, in the fermentation process of the CFRW. Meanwhile, twenty-three VFCs were detected in the CFRW, which included three alcohols, six terpenes, ten esters, three aromatics, and one furan. The correlation analysis revealed that there were 16 significant positive correlations and 23 significant negative correlations between the bacterium and VFCs (|ρ| > 0.6, p < 0.05), while there were 12 significant positive correlations and one significant negative correlation between the fungi and VFCs (|ρ| > 0.6, p < 0.05). Furthermore, five VFCs, including linalool, geraniol, ethyl acetate, 1-hexanol, and 3-methyl-1-butanol, contributed vital flavors to the CFRW, and they were all significantly negatively correlated with the changes of Massilia and Acinetobacter (|ρ| > 0.6, p < 0.05). Moreover a significant positive correlation was found between the relative abundance of Lactococcus and the contents of 3-methyl-1-butanol and ethyl acetate (|ρ| > 0.6, p < 0.05). Therefore, this study provides a valuable theoretical basis for further improving the quality and production technology of CFRW. [ABSTRACT FROM AUTHOR]

Diverse bacterial assemblages were identified in a large, open stormwater drain (vernacular: nalah) built decades ago in a densely populated suburb of Delhi, India. Illumina-based next-generation sequencing (NGS) of 16S rRNA gene amplicons was conducted with metagenomic DNAs isolated from influent sewage water and sediment samples collected from Sahibabad drain, which now carries domestic and industrial wastes to downstream sewage treatment plants. Results are discussed with respect to diversity and adaptation to unique ecological niche(s) in these drains as well as the prevalence of potentially pathogenic bacteria. Recently, it has become a common practice to cover such drains with thick cement slabs to facilitate the construction of residential/commercial complexes. However, the impact of concrete covers on microbial communities that inhabit the Sahibabad drain is unknown. Results indicated that open drains with better aeration and exposure to sunlight contained microbes that likely enhance biodegradation in sewage water. The deposition of sediments along the course of the drain was dominated by methanogenic and sulphidogenic bacteria. The covering of the drain may have contributed to an increased abundance of anaerobic pathogens which settled in sediments and/or resuspended into sewage water. Such findings are important as the microbes active in sewage can impact public health and drain infrastructure. [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]

Red sour soup is a Guizhou specialty condiment made by the natural fermentation of tomatoes and chili. In this study, three components (tomato acid, chili acid, and tomato and chili mixed acid) of split‐fermented red sour soup were explored to compare the quality characteristics and microbial communities in the middle and late fermentation stages. The titratable acidity of mixed acids was lower than that of tomato acid and chili acid in the middle stage, but it was significantly increased in the late stage. The cell viability of lactic acid bacteria was mostly higher than that of yeasts during the whole fermentation. Also significantly increased in the late stage of fermentation were sensory scores and the signal intensity of sour substances. However, the signal intensity of both bitter and salty substances decreased, and the total amount of free amino acids was reduced. In addition, the antioxidant capacity of the samples and the dominant microorganisms were different between the two fermentation stages, Lactobacillus and Kazachstania were the key common genus of the different components of split‐fermented red sour soup. It is anticipated that this study would provide us an insight into the quality characteristics and microbial communities of split‐fermented red sour soup. [ABSTRACT FROM AUTHOR]

Submerged plants and related disturbances can affect both the phosphorus (P) release and the microbial communities in sediments. In this study, a sediment resuspension system was constructed, and P variability characteristics influenced by Vallisneria natans (V. natans) and the response mechanism of the microbial community were studied. The results indicated that the total phosphorus (TP) content increased from 678.875 to 1019.133 mg/kg and from 1126.017 to 1280.679 mg/kg in sediments and suspended solids (SSs) during the sediment resuspension process, respectively. Organic P (OP) increased by 127.344 mg/kg and 302.448 mg/kg in sediments and SSs after the disturbance, respectively. The microbial communities in the sediments and the leaves of V. natans had higher Chao values after the disturbance, while Shannon values decreased after the disturbance compared to the control in SSs. Proteobacteria had the highest abundance with the value of 51.1% after the disturbance in the sediments and SSs, and the abundance values of Proteobacteria in rhizomes and leaves of V. natans could reach 73.2% on average. Chloroflexi, Acidobacteria, and Firmicutes were also the main phyla in the sediment resuspension system. Sodium hydroxide extractable P (NaOH-P) in sediments could reduce the bioavailability of this P fraction under disturbance conditions. The decrease in the abundance of Bacteroidetes and Nitrospirae indicated that they were more sensitive to the disturbance, and the rotational speed changed the survival conditions for the Bacteroidetes and Nitrospirae. The response mechanism of microbial community during the sediment resuspension process could reflect the influence of the microbial community on the changing characteristics of P and could provide a theoretical foundation for P control at the micro level. [ABSTRACT FROM AUTHOR]

Soil health is a critical factor in sustainable agriculture, particularly in fruit production, where fertilization strategies play a vital role in maintaining the soil quality and enhancing fruit production and quality. This study investigates the effects of different fertilization strategies on soil bacterial communities and honey pomelo (Citrus maxima) properties in Ji'an City, Jiangxi Province, China. Three fertilization treatments were compared: conventional fertilization (CF: botanical organic plus chemical compound fertilizers), organic material fermented fertilization (OF: organic material including duck manure fermented fertilizer plus chemical compound fertilizer), and a special honey pomelo fertilizer (SF: organic material fermented fertilizer only during the whole honey pomelo growing season). Soil samples were collected at two depths (0–20 cm and 20–40 cm) from nine plots (three treatments × three replicates) and analyzed for their soil properties, bacterial community diversity and composition, and fruit characteristics. The results indicate that the OF and SF significantly improved the soil pH, soil organic matter (SOM), and nutrient availability compared to the CF. Additionally, the OF and SF treatments led to a 13.6% and 16.6% increase in fruit weight, respectively, and higher bacterial diversity, although no significant differences were observed in fruit quality parameters such as vitamin C, soluble sugar, and titratable acid. Acidobacteriota, Proteobacteria, Actinobacteria, and Chloroflexi were the dominant bacterial phyla. The soil bacterial composition structures were significantly different among the different fertilization strategies, and were well explained by soil properties such as the pH, SOM, total phosphorus, and available nutrients. Our study suggests that applying fermented organic fertilizers which use duck manure as part of the raw materials, either alone or in combination with chemical compound fertilizers, increases honey pomelo fruit production and improves soil health, contributing to the sustainable development of orchards. [ABSTRACT FROM AUTHOR]

Soil aggregates, which are highly influenced by land conversion, play key roles in driving soil nutrient distribution and microbial colonization. However, the role of soil aggregates in shaping the responses of microbial community composition and multiple ecosystem functions, especially ecosystem multifunctionality (EMF), to land conversion remains poorly understood. In this study, we investigated the impact of the conversion of a longan orchard (LO) to a conventional tea plantation (CTP) and organic tea plantation (OTP) on soil EMF at the aggregate level and explored the underlying mechanism. Our results showed that EMF was significantly reduced in the conventional tea plantation, with 3.44, 1.79, and 1.24 times for large macro-, macro-, and micro-aggregates. In contrast, it was relatively preserved in the organic tea plantation. Notably, micro-aggregates with higher microbial biomass supported more EMF than larger aggregates under the land conversion conditions. The EMF associated with soil aggregates was found to be regulated by the differences in nutrient content and microbial community composition. Random forest analysis, redundancy analysis, and Pearson analysis indicated that both soil nutrient and microbial community composition within soil aggregates jointly determined EMF. This study highlights that soil aggregation influences the stratification of nutrients and microbial communities, which leads to the differing response of aggregate-related EMF to land conversion. [ABSTRACT FROM AUTHOR]

Microbial activity has been documented in various lacustrine environments, suggesting its fundamental role in mineral precipitation and, therefore, in the formation of organo-deposits such as microbialites. Many studies are currently focused on documenting how the association of microbes and extracellular polymeric substances (EPSs) may influence the authigenesis of Mg-rich clay minerals and the subsequent carbonate precipitation in growing microbialites in lacustrine environments. In this study, we investigate the present-day microbialites of the alkaline Bagno dell'Acqua lake (Pantelleria Island, Italy) using X-ray diffraction (XRD) scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS). Our results reveal the intimate association of Mg-smectite/carbonate minerals with the EPS and microbes, and, for the first time, we selected microbes belonging to phylum Firmicutes (Bacillus sp.), from natural microbialites, to carry out laboratory experiments that testify their direct role in the precipitation of clay and carbonate minerals. [ABSTRACT FROM AUTHOR]

Background Burkholderia: is a phosphorus solubilizing microorganism discovered in recent years, which can dissolve insoluble phosphorus compounds into soluble phosphorus. To investigate the effects of Burkholderia and calcium phosphate on the composting of Torreya grandis branches and leaves, as well as to explain the nutritional and metabolic markers related to the composting process. Methods: In this study, we employed amplicon sequencing and untargeted metabolomics analysis to examine the interplay among phosphorus (P) components, microbial communities, and metabolites during T. grandis branch and leaf waste composting that underwent treatment with calcium phosphate and phosphate-solubilizing bacteria (Burkholderia). There were four composting treatments, 10% calcium phosphate (CaP) or 5 ml/kg (1 × 108/ml Burkholderia) microbial inoculum (WJP) or both (CaP + WJP), and the control group (CK). Results: The results indicated that Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, pH, EC, and nitrogen content. Furthermore, these treatments significantly affected the diversity and structure of bacterial and fungal communities, altering microbial and metabolite interactions. The differential metabolites associated with lipids and organic acids and derivatives treated with calcium phosphate treatment are twice as high as those treated with Burkholderia in both 21d and 42d. The results suggest that calcium phosphate treatment alters the formation of some biological macromolecules. Conclusion: Both Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, nitrogen content and metabolites of T. grandis branch and leaf waste compost.These results extend our comprehension of the coupling of matter transformation and community succession in composting with the addition of calcium phosphate and phosphate-solubilizing bacteria. [ABSTRACT FROM AUTHOR]

In this experiment, alfalfa silage with different packing densities (500 kg/m3、600 kg/m3 and 700 kg/m3) was prepared under the conditions of outdoor high temperature and indoor room temperature, respectively. At the same time, the same lactobacillus additive was used for fermentation in each density treatment group. The chemical composition, fermentation quality and microbial community of alfalfa silage were analyzed. The results showed that the contents of dry matter (DM) and water-soluble carbohydrate (WSC) decreased with the increase of density during fermentation at high temperature. At the same time, when the density is 600 kg/m³, CP (crude protein) content is the highest, ADF (acid detergent fiber) content is the lowest. The contents and pH values of neutral detergent fiber (NDF), lactic acid (LA) and lactic acid bacteria (LAB) were significantly affected by temperature (p < 0.05). Density had significant effects on DM, NDF, WSC and LA contents (p < 0.05). The interaction between temperature and density had significant effects on the content of ADF and LAB (p < 0.05). At the same time, the abundance of Lactiplantibacillus plantarum in high temperature fermented silage was lower than that in normal temperature fermented feed. The number of Lactiplantibacillus plantarum in room temperature treatment group decreased with the increase of density. In summary, this study clarified the effects of different temperature and density on alfalfa fermentation quality and microbial community, and clarified that the density should be reasonably controlled within 600 kg/m³ during alfalfa silage, providing theoretical support for production practice. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Time Period Major Taxa Studied Methods Results Conclusion Ecological theory suggests that dispersal limitation and selection by climatic factors influence bacterial community assembly at a continental scale, yet the conditions governing the relative importance of each process remains unclear. The carnivorous pitcher plant Sarracenia purpurea provides a model aquatic microecosystem to assess bacterial communities across the host plant's north–south range in North America. This study determined the relative influences of dispersal limitation and environmental selection on the assembly of bacterial communities inhabiting S. purpurea pitchers at the continental scale.Eastern United States and Canada.2016.Bacteria inhabiting S. purpurea pitchers.Pitcher morphology, fluid, inquilines and prey were measured, and pitcher fluid underwent DNA sequencing for bacterial community analysis. Null modelling of β‐diversity provided estimates for the contributions of selection and dispersal limitation to community assembly, complemented by an examination of spatial clustering of individuals. Phylogenetic and ecological associations of co‐occurrence network module bacteria was determined by assessing the phylogenetic diversity and habitat preferences of member taxa.Dispersal limitation was evident from between‐site variation and spatial aggregation of individual bacterial taxa in the S. purpurea pitcher system. Selection pressure was weak across the geographic range, yet network module analysis indicated environmental selection within subgroups. A group of aquatic bacteria held traits under selection in warmer, wetter climates, and midge abundance was associated with selection for traits held by a group of saprotrophs. Processes that increased pitcher fluid volume weakened selection in one module, possibly by supporting greater bacterial dispersal.Dispersal limitation governed bacterial community assembly in S. purpurea pitchers at a continental scale (74% of between‐site comparisons) and was significantly greater than selection across the range. Network modules showed evidence for selection, demonstrating that multiple processes acted concurrently in bacterial community assembly at the continental scale. [ABSTRACT FROM AUTHOR]

Legume/cereal intercropping is an example of classic nitrogen-efficient planting that can effectively improve crop yield and nutrient-utilization efficiency. However, the interaction between rhizosphere microorganisms and rhizodeposition and the related ecological mechanisms remain unclear. We conducted a pot experiment using 13CO2 continuous labeling, DNA stable isotope probe technology, high-throughput sequencing, and the carbon-nitrogen-phosphorus functional gene chip to effectively track rhizosphere-deposited C and compare the microorganisms that utilize this C pool in the rhizosphere of a soybean/maize intercropping system at 21 days after labeling. The relative abundance of Caldalkalibacillus and Nesterenkonia that use rhizosphere-deposited C was significantly higher in the soybean/maize intercropping system than in monocropped soybean, but there were no significant differences between intercropped and monocropped maize. The soybean/maize intercropping system altered the composition of the microbial community that utilizes rhizosphere-deposited C and reduced the community richness. Moreover, intercropping improved the expression of functional genes associated with carbon fixation (acsH and exg) and nitrous oxide reduction (nosZ1). Overall, by tracking the flow of C from plant photosynthetic products to root exudates, our research provides new insights into identifying the microbial communities that assimilate and deposit carbon in soil. [ABSTRACT FROM AUTHOR]

Objective: This study investigated the impact of Aspergillus niger lysing polysaccharide monooxygenase (AnLPMO) on in vitro rumen microbial fermentation of rice straw. Methods: AnLPMO was heterologously expressed in Escherichia coli. Fourier transform infrared spectrometry and X-ray photoelectron spectroscopy analyzed the surface structure of rice straw after AnLPMO treatment. Two in vitro experiments, coupled with 16S highthroughput sequencing and quantitative real–time polymerase chain reaction techniques, assessed the influence of AnLPMO on rumen microbial fermentation of rice straw. Results: AnLPMO exhibited peak activity at 40°C and pH 6.5, with a preference for rice straw xylan hydrolysis, followed by Avicel. AnLPMO application led to the fractional removal of cellulose and hemicelluloses and a notable reduction in the levels of carbon elements and C–C groups present on the surface of rice straw. Compared to the control (no AnLPMO), supplementing AnLPMO at 1.1 to 2.0 U significantly enhanced in vitro digestibility of dry matter (IVDMD, p<0.01), total gas production (p<0.01), and concentrations of total volatile fatty acids (VFA, p<0.01), acetate (p<0.01), and ammonia-N (p<0.01). Particularly, the 1.4 U AnLPMO group showed a 14.8% increase in IVDMD. In the second experiment, compared to deactivated AnLPMO (1.4 U), supplementing bioactive AnLPMO at 1.4 U increased IVDMD (p = 0.01), total gas production (p = 0.04), and concentrations of total VFA (p<0.01), propionate (p<0.01), and ammonia-N (p<0.01), with a limited 9.6% increase in IVDMD. Supplementing AnLPMO stimulated the growth of ruminal bacterial taxa facilitating fiber degradation, including Proteobacteria, Spirochaetes, Succinivibrio, Rikenellaceae_RC9_ Gut_Group, Prevotelaceae_UCG-003, Desulfovibrio, Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Prevotella bryantii, P. ruminicola, and Treponema bryantii. Conclusion: These findings highlight AnLPMO's potential as a feed additive for improving rice straw utilization in ruminant production. [ABSTRACT FROM AUTHOR]

Background: The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem. Methods: High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure. Results: S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors. Conclusions: Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max (L.) Merr.) is an important oilseed crop, known for its rich nutritional content and high-quality protein. To address the shortage of feed protein resources and better utilize soybeans as a raw material, this study investigated the feasibility of using whole-plant soybean (WPS) as silage. As the ensiling period is a critical fermentation parameter, identifying the optimal fermentation duration was a key objective. The research involves fermenting WPS for silage production, conducted over five fermentation durations: 7, 15, 30, 60, and 90 days. The fermentation quality, microbial community, and metabolome of WPS silage were analyzed across these different time points. WPS silage fermented for 30 days exhibited optimal fermentation characteristics, with the highest lactic acid (LA) content observed at 30 days (p < 0.05), while butyric acid (BA) was detected only at 60 and 90 days. At 30 days, Enterococcus genera reached its peak relative abundance and was identified as the dominant genus. Random forest analysis highlighted Pantoea genera as the most influential biomarker. Metabolomic analysis revealed that the metabolic pathways involved in the biosynthesis of essential amino acids valine, leucine, and isoleucine were significantly enhanced during the later stages of fermentation compared to the earlier stages. Under natural fermentation conditions, the optimal fermentation period for WPS silage is approximately 30 days. These findings provide a theoretical basis for the utilization of WPS and the subsequent optimization of fermentation quality. [ABSTRACT FROM AUTHOR]

Background: Microplastic aging affects the dynamics of antibiotic resistance genes (ARGs) on microplastics, yet no review presents the effects of microplastic aging on the associated ARGs. Objectives: This review, therefore, aims to discuss the effects of different types of microplastic aging, as well as the other pollutants on or around microplastics and the chemicals leached from microplastics, on the associated ARGs. Results: It highlights that microplastic photoaging generally results in higher sorption of antibiotics and ARGs due to increased microplastic surface area and functional group changes. Photoaging produces reactive oxygen species, facilitating ARG transfer by increasing bacterial cell membrane permeability. Reactive oxygen species can interact with biofilms, suggesting combined effects of microplastic aging on ARGs. The effects of mechanical aging were deduced from studies showing larger microplastics anchoring more ARGs due to rough surfaces. Smaller microplastics from aging penetrate deeper and smaller places and transport ARGs to these places. High temperatures are likely to reduce biofilm mass and ARGs, but the variation of ARGs on microplastics subjected to thermal aging remains unknown due to limited studies. Biotic aging results in biofilm formation on microplastics, and biofilms, often with unique microbial structures, invariably enrich ARGs. Higher oxidative stress promotes ARG transfer in the biofilms due to higher cell membrane permeability. Other environmental pollutants, particularly heavy metals, antibacterial, chlorination by-products, and other functional genes, could increase microplastic-associated ARGs, as do microplastic additives like phthalates and bisphenols. Conclusions: This review provides insights into the environmental fate of co-existing microplastics and ARGs under the influences of aging. Further studies could examine the effects of mechanical and thermal MP aging on their interactions with ARGs. [ABSTRACT FROM AUTHOR]

Prothioconazole (PTC) is currently a popular triazole fungicide. In recent years, as the use of PTC has increased, there has been growing concern about its environmental and toxicological effects. Here, we studied the effect of PTC on the growth of soybean plants and further analyzed the enzyme activity and microbial community of rhizosphere soil after PTC treatment through 16S rRNA gene high-throughput sequencing and fungal ITS. Changes in structural diversity and species richness were measured using Simpson's diversity index, Shannon's diversity index and the Chao1 and ACE algorithms. The statistical t-test was applied to test whether the index values were significantly different between the two groups. The results showed that the contents of malondialdehyde (MDA) and H2O2 increased after the recommended dose of PTC, indicating that PTC has a strong toxic effect on plant growth, thus affecting the healthy growth of plants. In the presence of PTC, the species richness of fungi and bacteria decreased in all three soil types (black soil, yellow earth and red earth), and the community structure also changed significantly (the p-values were all less than 0.05). Proteobacteria, Actinomycetota, Bacteroidota and Acidobacteriota were the main bacteria, and the abundance of Acidobacteriota and Chloroflexi increased. The dominant fungal communities were Ascomycota and Mortierellomycota. The increased abundance of potentially beneficial microorganisms, such as Sphingomonadaceae, suggested that plants may be resistant to PTC stress by recruiting beneficial microorganisms. PICRUSt analysis showed that the metabolism-related functions and membrane transport pathway of rhizosphere bacterial community were inhibited after PTC stress. Spearman correlation analysis revealed a weak correlation between key fungal taxa and rhizosphere variables in the presence of PTC. Therefore, compared with those in the fungal community, the bacterial community was more likely to help plants resist PTC stress, indicating that these key fungal groups may indirectly help soybean growth under PTC stress by affecting the bacterial community. [ABSTRACT FROM AUTHOR]

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility. [ABSTRACT FROM AUTHOR]

Activated sludge has a high diversity of infectious agents. However, many of these microorganisms contribute greatly to the biological treatment process due to the enzyme production and capability for degrading a wide range of organic compounds in wastewater. The present review discusses the potential of aerobic granular sludge as a bio-startup (AGS-BS-up) for new wastewater treatment plants. The complex microbial community in activated sludge was investigated using 16S metagenomic analysis. The potential of aerobic granular sludge prepared from activated sludge to be used as a bio-starting medium for food wastewater treatment plants (FWWTP) was discussed. AGS-BS-up appears to have high applicability to enhance the biological treatment of food wastewater (FWW). The hypothesis behind using aerobic granular sludge as a bio-startup for FWWTP lies in the high microbial biodiversity in the aerobic granular sludge, which contributes effectively to the biological treatment of food wastewater. Based on the previous studies, the AGS-BS-up is efficient in improving the quality of FWW to meet international standards required for safe disposal into the environment. [ABSTRACT FROM AUTHOR]

Esters are vital flavor compounds in Chinese Nongxiangxing baijiu and greatly affect the quality of baijiu. Microbial communities inhabiting fermented grains (FGs) have a marked impact on esters. However, the specific microorganisms and their assembly patterns remain unclear. This study utilized high-throughput sequencing and a culture-based method to reveal ester-producing microorganisms. A total of 33 esters were detected, including 19 ethyl esters, 9 linear chain esters, and 2 branched chain esters. A correlation analysis indicated that the bacterial genus Lactobacillus (relative abundance in average: 69.05%) and fungal genera Pichia (2.40%), Aspergillus (11.84%), Wickerhamomyces (0.60%), Thermomyces (3.57%), Saccharomycopsis (7.87%), Issatchenkia (0.96%), and Thermoascus (10.83%) were dominant and associated with esters production and their precursors. The numbers of esters positively correlated with them were 1, 17, 3, 2, 1, 1, 1, and 1, respectively. The modified stochasticity ratio (MST) index and Sloan neutral model revealed that bacteria were predominantly governed by deterministic processes while fungal assemblies were more stochastic. Saturnispora silvae and Zygosaccharomyces bailii were isolated and identified with ester synthesis potential. PICRUSt2 analysis showed that fungi in FG had a high potential for synthesizing ethanol, while 14 enzymes related to esters synthesis were all produced by bacteria, especially enzymes catalyzing the synthesis of acyl-CoA. In addition, ester synthesis was mainly catalyzed by carboxylesterase, acylglycerol lipase and triacylglycerol lipase. These findings may provide insights into ester production mechanism and potential strategies to improve the quality of Nongxiangxing baijiu. [ABSTRACT FROM AUTHOR]

In this study, the differences in physicochemical properties, microbial community structure, and metabolic characteristics between various fortified Muqu and their corresponding high-temperature Daqu (HTD) were investigated using multiphase detection methods. The results demonstrated that the physicochemical properties, community structure, dominant bacterial composition, and metabolic components varied significantly among the different types of fortified HTD. The differences between HTDs became more pronounced when fortified HTD was used as Muqu. Compared to HTD, Muqu exhibited a more complex volatile profile, while HTD contained higher levels of characteristic non-volatile components. The cultivable bacteria count in Muqu was significantly higher than that in HTD, while the cultivable fungi count was slightly lower than that in HTD. The fungal profiles in HTD were primarily associated with starch hydrolysis and ethanol synthesis, while bacterial activity was more prominent in Muqu. Additionally, pyrazine synthesis was mainly attributed to fungi in Muqu and bacteria in HTD. Source Tracker analysis indicated that 8.11% of the bacteria and 26.76% of the fungi originated from Muqu. This study provides a theoretical foundation for the controlled production of HTD, contributing to improvements in its quality and consistency. [ABSTRACT FROM AUTHOR]

Composite produce leaf samples from commercial production rarely test positive for pathogens, potentially due to low pathogen prevalence or the relatively small number of plants sampled. Aggregative sampling may offer a more representative alternative. This pilot study investigated whether aggregative swab samples performed similarly to produce leaf samples in their ability to recover quality indicators (APCs and coliforms), detect Escherichia coli, and recover representative microbial profiles. Aggregative swabs of the outer leaves of romaine plants (n = 12) and composite samples consisting of various grabs of produce leaves (n = 14) were collected from 60 by 28 ft sections of a one-acre commercial romaine lettuce field. Aerobic plate counts were 9.17 ± 0.43 and 9.21 ± 0.42 log(CFU/g) for produce leaf samples and swabs, respectively. Means and variance were not significantly different (p = 0.38 and p = 0.92, respectively). Coliform recoveries were 3.80 ± 0.76 and 4.19 ± 1.15 log(CFU/g) for produce leaf and swabs, respectively. Means and variances were not significantly different (p = 0.30 and p = 0.16, respectively). Swabs detected generic E. coli in 8 of 12 samples, more often than produce leaf samples (3 of 14 positive, Fisher's p = 0.045). Full-length 16S rRNA microbial profiling revealed that swab and produce leaf samples did not show significantly different alpha diversities (p = 0.75) and had many of the most prevalent bacterial taxa in common and in similar abundances. These data suggest that aggregative swabs perform similarly to, if not better than, produce leaf samples in recovering indicators of quality (aerobic and coliform bacteria) and food safety (E. coli), justifying further method development and validation. [ABSTRACT FROM AUTHOR]

Biogeochemical redox cycling of iron (Fe) essentially governs various geochemical processes in nature. However, the mechanistic underpinnings of Fe-redox cycling in deep-sea sediments remain poorly understood, due to the limited access to the deep-sea environment. Here, abyssal sediment collected from a depth of 5800 m in the Pacific Ocean was characterized for its elemental, mineralogical, and biological properties. The sedimentary environment was determined to be oligotrophic with limited nutrition, yet contained a considerable amount of trace elements. Fe-redox reactions in sediment progressed through an initial lag phase, followed by a fast Fe(II) reduction and an extended period of Fe(III) oxidation before achieving equilibrium after 58 days. The presence of an external H2 electron donor significantly increased the extent of Fe(III) bio-reduction by 7.73% relative to an amendment-free control under high pressure of 58 MPa. A similar enhancement of 11.20% was observed following lactate amendment under atmospheric pressure. Fe(II) bio-oxidation occurred after 16 days' anaerobic culturing, coupled with nitrate reduction. During Fe bio-redox reactions, microbial community composition was significantly shaped by the presence/absence of an electron donor, while the hydrostatic pressure levels were the controlling factor. Shewanella spp. emerged as the primary Fe(III)-reducing microorganisms, and were stimulated by supplemented lactate. Marinobacter hydrocarbonoclasticus was the predominant Fe(II)-oxidizing microorganism across all conditions. Our findings illustrate continuous Fe-redox reactions occurring in the deep-sea environment, with coexisting Fe-redox microorganisms determining the oscillation of Fe valence states within the abyssal sediment. [ABSTRACT FROM AUTHOR]

Magnetic fields, as a form of physical energy, exert an influence on biological activities. However, our current understanding of the impact of magnetic fields on wheat yield remains limited. In this study, our objective was to investigate the effects of magnetic field treatment of wheat plants on their yield, root growth, absorption of nitrogen and phosphorus and soil bacterial diversity. The experiments were conducted at two agricultural research stations in China, Zhengzhou and Xuchang. Plants were treated with magnetic fields of 20, 40, 60, and 80 mT induced by permanent magnets for chronic exposure. Untreated plants were considered as controls. Our result showed that soil nutrients were found to have a substantial impact on wheat nitrogen and phosphorus absorption, and wheat nitrogen and phosphorus absorption significantly affected wheat yield. The change in soil nutrient content was caused by the change in soil bacterial community diversity and abundance, and increased soil nutrients increased wheat yield. The results suggest that magnetic field treatment stimulated wheat plant growth and yield, and changed soil nutrient content through improved soil bacterial community diversity and increased soil nitrogen and phosphorous absorption. [ABSTRACT FROM AUTHOR]

Introduction: Carotenoids are important precursors of various aroma components in tobacco and play an important role in the sensory quality of tobacco. Phaffia rhodozyma is a species of Xanthophyllomyces capable of synthesizing a highly valuable carotenoid-astaxanthin, but has not yet been used in improving tobacco quality. Methods: The dynamic changes of microbial community and metabolites during tobacco fermentation were analyzed in combination with microbiome and metabolome, and the quality of tobacco after fermentation was evaluated by sensory scores. Results: P. rhodozyma could grow and produce carotenoids in tobacco extract, with a maximum biomass of 6.50 g/L and a maximum carotenoid production of 36.13 mg/L at 100 g/L tobacco extract. Meanwhile, the correlation analysis combined with microbiome and metabolomics showed that P. rhodozyma was significantly positively correlated with 11 metabolites such as 6-hydroxyluteolin and quercetin. Furthermore, the contents of alcohols, ketones and esters, which were important aromatic components in fermented tobacco, reached 77.57 μg/g, 58.28 μg/g and 73.51 μg/g, increasing 37.39%, 265.39% and 266.27% compared to the control group, respectively. Therefore, the aroma and flavor, and taste scores of fermented tobacco increased by 0.5 and 1.0 points respectively. Discussion: This study confirmed that P. rhodozyma fermentation could effectively improve the sensory evaluation of tobacco, and provided a novel microbial fermentation method to improve tobacco quality. [ABSTRACT FROM AUTHOR]

Corn (C), wheat (W), and paddy rice (PR) are important energy sources and are commonly used in feed production for swine. This study mainly focuses on the variation and regularities of microbiota and metabolites in the gastrointestinal tract (GIT) of pigs in response to C, W, and PR. A total of 18 pigs were allotted into three dietary groups with six replicated pigs and received diets containing C, W, or PR as the sole energy source, respectively. The results showed that digestive parts significantly affected the diversity of microbial communities. Cereal grain sources significantly influenced the β-diversity of microbial communities in the colon and rectum. Campylobacterota and Proteobacteria are mainly distributed in the duodenum, Lactobacillus in the jejunum, and Bacteroidota in the colon and rectum. The W diet increased the Bacteroidota, Spirochaetota, and Prevotellaceae_NK3B31_group abundances and showed the highest concentrations of all short-chain fatty acids (SCFAs) in the hindgut. Fibrobacterota, Bacteroidota, Spirochaetota, Prevotellaceae_NK3B31_group, Prevotella, and Treponema in the colon or rectum were positively correlated with acetate, propionate, butyrate, and total SCFAs. These findings suggested that aerobic bacteria and facultative anaerobes in the foregut will gradually be replaced by anaerobes in the hindgut. The W diet had the best fermentability and was beneficial to the colonization of microbial communities that mainly used carbohydrates. The hindgut flora of the PR diet group may be more balanced with fewer potential pathogenic bacteria. Many microbial communities have been identified to contribute positively to the SCFA production of the hindgut. Collectively, our study revealed the spatial variation regularities of GIT microbial communities in an adult pig model and provided new insights into GIT microbiota and responses of metabolites to cereal grain diets. [ABSTRACT FROM AUTHOR]

Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray–Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats. [ABSTRACT FROM AUTHOR]

Background: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. Results: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. Conclusion: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands. [ABSTRACT FROM AUTHOR]

Background: Paddy soil is a typical soil type affected by anthropogenic management and factors related to natural soil formation. The evolution from mudflats to typical paddy soils can significantly affect the soil microecology. Previous studies have reported the evolution of soil physicochemical properties, microbes, and related soil environmental factors in a millennium paddy soil chronosequence. However, the potential biological mechanisms of changes in metabolites and microbes–metabolites interaction are poorly understood. Therefore, a combination of high-throughput sequencing and environmental pseudotargeted metabolomics techniques was adopted to explore the effects of the millennium paddy soil chronosequence on microbial communities, metabolites, and their functions and interactions. Results: The soil ecology changed greatly in the first 60 years of the transition from mudflat to paddy planting. Among the microbial communities, the response of the bacteria to the chronosequence was more sensitive than that of fungi. Among them, the bacterial communities of Proteobacteria, Bacteroidetes, Acidobacteria, and Nitrospirae exhibited regular succession over the chronosequence, but the fungal communities did not show regular changes. Bacterial function prediction revealed that the beginning of the critical stage of the evolution from mudflat to paddy soil involved the organic matter cycle and energy flow. In contrast, fungi were characterized mainly by pathogenic and saprophytic functions. The results of the principal component analysis of the metabolites revealed a similar pattern of change as that of the microbes. Seventy-five characteristic metabolites exhibited three trends of change during the development of the paddy soil chronosequence. Twenty-five differentially active metabolic pathways, including glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and galactose metabolism, were enriched. In addition, correlation analysis revealed that long-chain fatty acids, short-chain fatty acids, phenolic acids, carbohydrates, and polyalcohols significantly regulate the microbial communities in paddy soil. Conclusions: Combining metabolome and microbiome has expanded the overall understanding of the development of paddy soil under anthropogenic management. During the development of a paddy soil chronosequence, the synergistic regulation of soil physicochemical properties and metabolites in the microbial community results in increased productivity. This study provides a new perspective on microbes and metabolites interaction. [ABSTRACT FROM AUTHOR]