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Introduction: Residue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored. Methods: In a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK). Results and discussion: Using metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both α and β) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD < SC < BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes. [ABSTRACT FROM AUTHOR]

The acquisition of microbial plant cell wall-degrading enzymes coincided with the main independent origins of specialized herbivory in beetles. Secondary loss of beetle-encoded digestive enzymes was offset by the recruitment of functionally convergent digestive symbionts. Tyrosine-supplementing symbionts were repeatedly recruited by herbivorous beetles, thereby aiding in cuticle biosynthesis. A symbiotically enforced cuticle allows herbivorous beetles to overcome biotic and abiotic challenges. Synthetic symbioses developed to tractably reconstitute natural infections in beetles. The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles. [ABSTRACT FROM AUTHOR]

The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy. Here, the authors show that different formulations of medical ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, via modifying the gut microbiome and microbial pathways associated with fiber-mediated seizure protection. [ABSTRACT FROM AUTHOR]

Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development. Here, the authors perform a global analysis of over 3000 infant gut samples revealing a universal pattern of microbial changes over the first 1.5 years, with declines in Bifidobacterium and increases in Faecalibacterium, providing a standard for early gut development. [ABSTRACT FROM AUTHOR]

Calf diarrhea is a prevalent and significant health issue in dairy farming, severely impacting feed intake, weight gain, and survival rates in young calves. This study aimed to investigate the microbial composition and antibiotic resistance profiles of diarrheic calves to provide insights into the epidemiology and management of the condition. The prevalence of diarrhea in 1685 calves was analyzed. Rectal fecal samples were collected from five healthy and five diarrheic Holstein calves on a large dairy farm in Shaanxi Province, China. High-throughput 16S-rRNA sequencing and PCR were utilized for microbial and resistance gene analysis. In 2023, the overall diarrhea rate among 1685 calves was 9.08%, with a significantly higher diarrhea rate during the suckling period (8.13%) compared to the post-weaning period (0.95%) (p < 0.001). No differences in species diversity and richness were detected among the different groups. However, LEfSe analysis identified six genera (Eubacterium, Eubacteriaceae, Prevotella, Comamonadaceae, Comamonas, and Firmicutes) significantly enriched in diarrheic calves compared to healthy ones (LDA scores > 2, p < 0.05). Additionally, antibiotic resistance genes for quinolones, β-lactams, chloramphenicol, tetracyclines, and aminoglycosides were detected, with significantly higher prevalence in diarrheic calves. These findings demonstrate distinct microbial and antibiotic resistance profiles between healthy and diarrheic calves, emphasizing the importance of microbial management in controlling calf diarrhea. [ABSTRACT FROM AUTHOR]

The anaerobic acid production experiments were conducted with the pretreated kitchen waste under pH adjustment. The results showed that pH 8 was considered to be the most suitable condition for acid production, especially for the formation of acetic acid and propionic acid. The average value of total volatile fatty acid at pH 8 was 8814 mg COD/L, 1.5 times of that under blank condition. The average yield of acetic acid and propionic acid was 3302 mg COD/L and 2891 mg COD/L, respectively. The activities of key functional enzymes such as phosphotransacetylase, acetokinase, oxaloacetate transcarboxylase and succinyl-coA transferase were all enhanced. To further explore the regulatory mechanisms within the system, the distribution of microorganisms at different levels in the fermentation system was obtained by microbial sequencing, results indicating that the relative abundances of Clostridiales, Bacteroidales, Chloroflexi, Clostridium, Bacteroidetes and Propionibacteriales , which were great contributors for the hydrolysis and acidification, increased rapidly at pH 8 compared with the blank group. Besides, the proportion of genes encoding key enzymes was generally increased, which further verified the mechanism of hydrolytic acidification and acetic acid production of organic matter under pH regulation. The anaerobic acid production of the pretreated kitchen waste was enhanced with pH regulation and pH 8 was considered to be the most suitable condition, especially for the formation of acetic acid and propionic acid. The regulatory mechanisms were adequately demonstrated by microbial sequencing and the genes encoding key enzymes. [Display omitted] [ABSTRACT FROM AUTHOR]

The interaction between host cells and commensal microbes forms a complex metaorganism that regulates mouse physiology through host and microbial genes. Experiments with a particular specific pathogen–free (SPF) inbred mouse strain performed in different laboratories often yield conflicting data due to microbiota variations that stem from housing conditions. The lower microbial richness and diversity of current SPF standards in mouse strains do not fully capture the complex interactions present in the gut microbiota of wild mice and humans. Conventional laboratory SPF murine gut microbiota can be outcompeted and replaced by natural microbiota in cohousing experiments. In the intestine, various ecological niches are occupied by specialized microbes, each adapted to their specific environments. This specialization optimizes the consumption of survival factors, limiting the integration of new species and enhancing resilience against external challenges. Global biomedical research faces two major shortcomings: the poor translation of mouse studies to clinical practice and the presence of irreproducible data across laboratories. Both issues may be attributed to the low complexity and variability of current laboratory microbiota. We recognize that stability relies on biological diversity by reconceptualizing the mammalian phenotype as a metaorganism – incorporating both the host and its coevolved microbes. We propose using naturally adapted microbiota to produce more robust, reproducible, and generalizable mouse data, reinforcing scientific rigor in global biomedical research. Laboratory mice housed under specific pathogen–free (SPF) conditions are the standard model in biomedical research. However, experiments with a particular inbred mouse strain performed in different laboratories often yield inconsistent or conflicting data due to housing-specific variations in the composition and diversity of SPF microbiota. These variations affect immune and nonimmune cell functions, leading to systemic physiological changes. Consequently, microbiota-dependent inconsistencies have raised general doubts regarding the suitability of mice as model organisms. Since stability positively correlates with biological diversity, we postulate that increasing species diversity can improve microbiota stability and mouse physiology, enhancing robustness, reproducibility, and experimental validity. Similar to the generation of inbred mouse strains in the last century, we suggest a worldwide initiative to define a transplantable 'wild' microbiota that stably colonizes mice irrespective of housing conditions. [ABSTRACT FROM AUTHOR]

Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes. [ABSTRACT FROM AUTHOR]

Alpine wet meadows are known as N2O sinks due to nitrogen (N) limitation. However, phosphate addition and N deposition can modulate this limitation, and little is known about their combinative effects on N2O emission from the Qinghai-Tibet Plateau in wet meadows. This study used natural wet meadow as the control treatment (CK) and conducted experiments with N (CON2H4 addition, N15), P (NaH2PO4 addition, P15), and their combinations (CON2H4 and NaH2PO4 addition, N15P15) to investigate how N and P supplementation affected soil N2O emissions in wet meadow of QTP. Contrary to previous studies on grasslands, the effect of phosphate addition treatment on soil N2O flux was not detectable during the growing seasons of 2019 and 2020. Over a span of two years, the N addition treatment significantly increased the N2O flux by 3.45 μg⋅m–2⋅h–1 due to increased soil N availability. Noticeably, phosphate addition intensified the effect of N deposition treatment on soil N2O flux with high significance in the early growth season of 2020. This augmentation can be attributed to the alleviation of limiting factors imposed by plants and microorganisms on soil N and P, fostering the mineralization and decomposition of litter and soil nutrients by microorganisms. Consequently, the results showed that total nitrogen and nitrate nitrogen were the main controls on soil N2O emission under N and P addition. In addition, redundancy analysis showed that the relative abundance of NirK genes in soil microorganisms (Bradyrhizobium , Devosia , Ochrobactrum , Alcaligenes , Rhizobium) is the main factor affecting N2O flux and available nitrogen. We project that if nutrient input continues to increase, the main limiting factor of soil will change from N restriction to P restriction due to the unique microbial nitrogen conversion process in the alpine meadow, significantly increasing N2O emissions. Consequently, the heightened contribution of alpine wet meadows to global warming and ozone depletion hinges on the dynamics of nutrient input regimes, spotlighting the urgent need for informed environmental management strategies. [ABSTRACT FROM AUTHOR]

This study evaluated the relationships and sensitivity of denitrifying microbial gene abundance, as well as the activities of soil enzymes β-glucosidase (GLU) and arylsulfatase (ARYL), to assess the quality of sugarcane soils managed with vinasse (V), filter cake (FC), and mineral fertilizer (MF). Composite soil samples were collected using a systematic sampling approach that included two soil classes (Ferralsol and Acrisol), two textures (clayey and sandy), three management systems (V, V+FC, and MF), two sampling seasons (rainy and dry), and three replicates, totaling 72 samples. Analysis of soil organic carbon (SOC), and macro- and micronutrients differentiated the Ferralsol and Acrisol samples into distinct groups based on agricultural management (Global R = 0.554) and showed some overlap based on soil texture (Global R = 0.369). The number of nir K, nir S, and nos Z I gene copies per gram of soil, determined by Real-Time Quantitative PCR (qPCR) based on genomic DNA isolated from the 72 soil samples, was higher in the rainy season compared to the dry season (P <0.05). None of the genes evaluated revealed a consistent response to different sugarcane soil managements, showing specific response patterns for each soil class and texture. In the Ferralsol, the activities of GLU and ARYL increased in the following order: V < MF < V+FC, regardless of soil texture (sandy or clayey) and sampling season. The average activity of the two enzymes in both V+FC and MF treatments was 1.8 times higher in sandy soil and 3.9 times higher in clayey soil compared to soil managed with vinasse. In the Acrisol, no significant differences among the treatments were observed. Statistical analyses revealed negative correlations (P <0.05) between the number of copies of the nir K and nos Z I genes and GLU and ARYL activities in the soil during both seasonal periods analyzed. The number of copies of these two microbial genes was also negatively correlated with the soil organic matter in the rainy season. Thus, the indications of sugarcane soil quality based on enzymatic analyses were corroborated by the lower abundance of genes associated with denitrification process. The findings of this study open the possibilities to infer about the potential for N2O emission from these sugarcane soils based on GLU and ARYL activities. [ABSTRACT FROM AUTHOR]

Peatlands are invaluable but threatened ecosystems that store huge amounts of organic carbon globally and emit the greenhouse gasses carbon dioxide (CO2) and methane (CH4). Trophic interactions of microbial groups essential for methanogenesis are poorly understood in such systems, despite their importance. Thus, the present study aimed at unraveling trophic interactions between fermenters and methanogens in a nitrogen-limited, subarctic, pH-neutral fen. In situ CH4 emission measurements indicated that the fen is a source of CH4, and that CH4 emissions were higher in plots supplemented with ammonium compared to unsupplemented plots. The amino sugar N-acetylglucosamine was chosen as model substrate for peat fermenters since it can serve as organic carbon and nitrogen source and is a monomer of chitin and peptidoglycan, two abundant biopolymers in the fen. Supplemental N-acetylglucosamine was fermented to acetate, ethanol, formate, and CO2 during the initial incubation of anoxic peat soil microcosms without preincubation. Subsequently, ethanol and formate were converted to acetate and CH4. When methanogenesis was inhibited by bromoethanesulfonate, acetate and propionate accumulated. Long-term preincubation considerably increased CH4 production in unsupplemented microcosms and microcosms supplemented with methanogenic substrates. Supplemental H2-CO2 and formate stimulated methanogenesis the most, whereas acetate had an intermediary and methanol a minor stimulatory effect on methane production in preincubated microcosms. Activity of acetogens was suggested by net acetate production in microcosms supplemented with H2-CO2, formate, and methanol. Microbial community analysis of field fresh soil indicated the presence of many physiologically unresolved bacterial taxa, but also known primary and secondary fermenters, acetogens, iron reducers, sulfate reducers, and hydrogenotrophic methanogens (predominately Methanocellaceae and Methanoregulaceae). Aceticlastic methanogens were either not abundant (Methanosarcinaceae) or could not be detected due to limited coverage of the used primers (Methanotrichaceae). The collective results indicate a complex interplay of synergy and competition between fermenters, methanogens, acetogens, and potentially iron as well as sulfate reducers. While acetate derived from fermentation or acetogenesis in this pH-neutral fen likely plays a crucial role as carbon source for the predominant hydrogenotrophic methanogens, it remains to be resolved whether acetate is also converted to CH4 via aceticlastic methanogenesis and/or syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. [ABSTRACT FROM AUTHOR]

Simple Summary: Numerous microorganisms found in the gastrointestinal tracts of donkeys are challenging to cultivate due to their unique and often unknown growth requirements. This study provides a comprehensive catalog of donkey gut microbial genes and expands our understanding of the donkey gut microbiome. For the first time, metagenome-assembled genomes from the donkey hindgut have been characterized. Our dataset serves as a valuable resource for the discovery of novel carbohydrate-degrading enzymes and for further research on the donkey gut microbiome. The gut microbiota plays an important role in the digestion, absorption, and metabolism of nutrients, as well as in the immunity, health, and behavior of donkeys. While reference genomes and gut microbial gene catalogs have been helpful in understanding the composition of the donkey, there is still a significant gap in sequencing and understanding the functional aspects of donkey gut microbial genomes. In this study, we analyzed metagenomic sequencing data from 26 donkeys' gut samples and successfully assembled 844 microbial metagenome-assembled genomes (MAGs). Surprisingly, 678 (80.33%) of these MAGs appear to belong to previously unidentified species. Our analysis further revealed a total of 292,980 predicted carbohydrate-active enzymes (CAZymes) and 257,893 polysaccharide utilization loci (PULs). Interestingly, these enzymes and loci displayed relatively low similarity matches in public databases. We found that the higher abundances of 36 MAGs in the cecum (such as Prevotella, Desulfovibrio, Alistipes, and Treponema_D) and 9 MAGs in the dorsal colon (such as Limimorpha, Saccharofermentans, and Lactobacillus) were associated with a diverse array of carbohydrate-degrading pathways. Network analysis identified Prevotella and Dysosmobacter as connectors, while Saccharofermentans and Akkermansia were shown as provincial hubs. This suggests their crucial roles in complex carbohydrate degradation and hindgut metabolism in donkeys. These findings underscore the complexity of hindgut metabolism in donkeys and expand our understanding of their gut microbiome. Overall, this study provides a comprehensive catalog of donkey gut microbial genes, revealing novel carbohydrate-degrading enzymes and offering new insights for future research on the donkey gut microbiome. [ABSTRACT FROM AUTHOR]

Arsenic contamination in sludge and sediment has emerged as a pressing environmental issue with far-reaching implications. This review delves into the multifaceted problem of arsenic contamination, focusing on its complex interactions with microbial resistance genes (MRGs). It explores the key role of microorganisms in the biogeochemical cycling of arsenic, including processes such as reduction, oxidation, methylation, and volatilization. It describes how microorganisms resist arsenic through resistance genes that encode proteins such as efflux pumps, enzymatic detoxification, and intracellular sequestration. Arsenic, a naturally occurring element, can enter sludge and sediment through various natural and anthropogenic pathways, leading to detrimental effects on environmental quality. Understanding the role of microorganisms in arsenic mobilization, transformation, and their ability to resist arsenic toxicity through MRGs is essential for effective mitigation and remediation strategies. This review discusses the sources and distribution of arsenic in sludge and sediment, the intricate mechanisms of microbial arsenic resistance, and the potential implications for environmental management and human health. It also examines current research trends and identifies areas requiring further investigation. By unraveling the interplay between arsenic contamination, microorganisms, and MRGs, this review aims to contribute to a deeper understanding of the issue and guide future research and environmental protection efforts. [ABSTRACT FROM AUTHOR]

Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates. [ABSTRACT FROM AUTHOR]

For the first time, a comprehensive assessment of the biological activity of the supraglacial systems of the IGAN Glacier—the largest glacier of the Polar Urals—was carried out. The stocks and structure of microbial biomass were estimated using luminescent microscopy and substrate-induced respiration methods; basal respiration, the intensity of methanogenesis and nitrogen fixation, the number of copies of ribosomal genes of microorganisms (bacteria, archaea, and fungi), and the numbers (CFU/g soil) of cultivated micromycetes, saprotrophic bacteria, and actinomycetes were also studied. The highest biological activity was found in the supraglacial zone, and the lowest—along its periphery and in the near periglacial zone. In all zones of the glacier, Geomyces pannorum, G. vinaceus, and Teberdinia hygrophila dominated among micromycetes, and representatives of the Arthrobacter and Bacillus genera dominated among bacteria. The microbiome structure of supraglacial bodies depended on their location on the glacier and differed significantly at the periphery and in the center of the supraglacial zone, as well as in comparison with soils and sediments in the adjacent periglacial landscape. The material released from the glacier body with a high content of organic matter affects the biological activity of supraglacial microbial communities. [ABSTRACT FROM AUTHOR]

Beneficial plant–microbe interactions are critical to plant productivity in both natural and agricultural ecosystems due to benefits such as improved plant nutrition and abiotic stress tolerance. The legume–rhizobia symbiosis and plant–arbuscular mycorrhizal fungi symbiosis both involve continuous signaling and coordination between two organisms. Within symbioses, the development of novel microbial and plant structures is driven by symbiosis-specific gene expression in a few specific cell populations. Genetic engineering to take better advantage of these interactions relies on the identification of symbiosis-responsive plant and microbial genes that can serve as targets for modification. Applying single-cell and spatial RNA-seq to study plant–microbe endosymbiosis can facilitate the identification of such genes and improve our general understanding of the complex biology of symbiotic interactions. Plant–microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant–microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells. [ABSTRACT FROM AUTHOR]

Autotrophic microorganisms play a significant role in atmospheric CO2 fixation and soil organic carbon (SOC) sequestration in diverse ecosystems, but little is known about their role in karst forests. To investigate the composition and changes of autotrophic microbial communities during degraded karst forest restoration, the related functional genes and microorganisms from three restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) were examined through metagenomic sequencing. Their underlying drivers and contributions to SOC were investigated using structural equation modeling (SEM) and regression analysis. Karst forest restoration resulted in the synchronous recovery of above-ground plants and soil conditions. When TG was restored to OG, soil autotrophic CO2 fixation microbes changed significantly, indicated by an increase in microbial functional strength and diversity. Among the six examined functional pathways, the rTCA cycle contributed the most (0.074–0.082%), while the WL pathway contributed the least (0.008–0.010%) to CO2 fixation functions. Except the Calvin cycle, genes involved in the other five pathways showed an increase with karst forest restoration. SEMs further revealed that soil pH and available nitrogen directly drive the increase in microbial autotrophic CO2 fixation functions. In karst forests, autotrophic CO2-fixing microorganisms play a crucial role in enhancing SOC, particularly through the DC/4-HB cycle, 3-HP/4-HB cycle, and WL pathway. Soil microbial communities involved in autotrophic CO2 fixation were predominantly attributed to Proteobacteria (43.02–32.42%) and Actinobacteria (18.83–30.89%), although their contributions varied across different stages. These results highlight the significant contribution of autotrophic microorganisms to the SOC of karst forests and enhance our understanding of the microbial mechanisms behind soil C sequestration. [ABSTRACT FROM AUTHOR]

The fixation and transfer of biological nitrogen from peanuts to maize in maize–peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective. Summary Statement: The metagenomic analyses and structural equation modelling indicated that Bradyrhizobium significantly affected the nitrogen fixation, whereas the nrfC and nirA influenced the nitrogen transfer. Overall, our study identified key bacterial genus and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective. [ABSTRACT FROM AUTHOR]

Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high‐depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well‐phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome‐assembled genomes (MAGs) which were further clustered into 256 species‐level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that Mesomycoplasma hyopneumoniae (M. hyopneumoniae) MAG_47 and its adhesion‐related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion‐ and immunomodulation‐related VFs likely determined the heterogenicity of adhesion and pathogenicity among M. hyopneumoniae strains. M. hyopneumoniae adhesion activated several pathways, including nuclear factor kappa‐light‐chain‐enhancer of activated B, mitogen‐activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin‐6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with Mycoplasma pneumoniae and pigs infected with M. hyopneumoniae. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health. Highlights: We constructed a comprehensive microbial gene catalog of lower respiratory tract microbiome, containing 10,031,593 nonredundant genes and obtained 356 nonredundant metagenome‐assembled genomes using five representative pig populations.Significant associations of Mesomycoplasma hyopneumoniae (M. hyopneumoniae) strains and their adhesion‐related virulence factors with lung lesions were observed and confirmed in two different pig populations, as well as through in vitro infection of porcine bronchial epithelial cells.M. hyopneumoniae adhesion activated several pathways, such as nuclear factor kappa‐light‐chain‐enhancer of activated B, mitogen‐activated protein kinase, cell apoptosis and response to reactive oxygen species, which resulted in cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is the third most prevalent cancer. Ongoing research aims to uncover the causes of CRC, with a growing focus on the role of gut microbiota (GM) in carcinogenesis. The GM influences CRC development, progression, treatment efficacy, and therapeutic toxicities. For example, Fusobacterium nucleatum and Escherichia coli can regulate microbial gene expression through the incorporation of human small noncode RNA and potentially contribute to cancer progression. Metallic nanoparticles (MNPs) have both negative and positive impacts on GM, depending on their type. Several studies state that titanium dioxide may increase the diversity, richness, and abundance of probiotics bacteria, whereas other studies demonstrate dose‐dependent GM dysbiosis. The MNPs offer cytotoxicity through the modulation of MAPK signaling pathways, NF‐kB signaling pathways, PI3K/Akt signaling pathways, extrinsic signaling pathways, intrinsic apoptosis, and cell cycle arrest at G1, G2, or M phase. MNPs enhance drug delivery, enable targeted therapy, and may restore GM. However, there is a need to conduct well‐designed clinical trials to assess the toxicity, safety, and effectiveness of MNPs‐based CRC therapies. [ABSTRACT FROM AUTHOR]

This study investigated the purification of pollutants in runoff rainwater by constructing a micro-ecosystem using waste-activated sludge (WAS) and riverbed sludge (RBS) as inoculums in combination with pervious concrete. The research results showed that the best hydraulic retention time (HRT) was 9 h. The COD and ammonia nitrogen (NH4+-N) removal of the waste-activated sludge ecosystem (WASE) was 62.67% and 71.21%, respectively, while the riverbed sludge ecosystem (RBSE) showed COD and NH4+-N removal percentages of 46.05% and 66.55%, respectively. The analysis of the genetic metabolism of microbial genes showed that the system was microbially enhanced with extensive and diverse populations. At the phylum level, the microorganisms responsible for degrading organic matter were mainly Firmicutes and Actinobacteriota. At the genus level, the Trichococcus genus was dominant in the WASE, while the Dietzia, norank_f__Sporomusaceae and norank_f__norank_o__norank_c__BRH-c20a genera were the central bacterial populations in the RBSE. The proliferation of phylum-level bacteria in the WASE was relatively large, and the genus-level bacteria demonstrated a better removal efficiency for pollutants. The overall removal effect of the WASE was better than that of the RBSE. The application analyses showed that a WASE is capable of effectively accepting and treating all rainfall below rainstorm levels and at near-full rainstorm levels under optimal removal efficiency conditions. This study innovatively used wastewater plant waste-activated sludge combined with pervious concrete to construct a micro-ecosystem to remove runoff rainwater pollutants. The system achieved pollutant removal comparable to that of pervious concrete modified with adsorbent materials. An effective method for the collection and pollutant treatment of urban runoff rainwater is provided. [ABSTRACT FROM AUTHOR]

Nitrogen cycling in freshwater ecosystems is critical for maintaining water quality, and understanding the processes of nitrification and denitrification is essential for effective nitrogen management, particularly in areas with diverse pollution sources. This study investigated the nitrification and denitrification processes in three tributaries of the Jinjing River—Tuojia (agricultural), Jinjing (residential), and Guanjia (woodland)—during both the wet and dry seasons. The potential nitrification rates (PNRs) and potential denitrification rates (PDNRs) were measured across these sites. The highest rates were observed in Tuojia during the wet season, with the PNR reaching 39.7 μg·kg−1 h−1 and the PDNR reaching 3.25 mg·kg−1·h−1, while the rates were considerably lower in Jinjing and Guanjia. The ammonia-oxidizing archaea (AOA) abundance was higher than the ammonia-oxidizing bacteria (AOB) abundance at all sites, with Tuojia exhibiting the highest AOA abundance (5.9 × 10⁷ copies·g−1) during the wet season. The nitrate-nitrogen (NO₃−-N) content was a key factor influencing denitrification, and the AOA abundance was significantly correlated with nitrification rates (r = 0.69; p < 0.05). These findings highlight the spatial and seasonal variability in nitrogen cycling and emphasize the importance of developing targeted nitrogen management strategies in regions with mixed land uses and pollution sources. [ABSTRACT FROM AUTHOR]

Background: Wound infections are a common complication of injuries negatively impacting the patient's recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden. Methods: This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR). Results: Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity. Conclusions: This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications. [ABSTRACT FROM AUTHOR]

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L , ASS1 , and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2 , EGR3 , GSTM3 , and GPR61 genes and the abundance of microorganisms, such as Trueperella , Victivallis , and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005 , Prevotellaceae_UCG-003 , Prevotellaceae_NK3B31_group , Prevotella_1 , Prevotella_9 , and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding. [ABSTRACT FROM AUTHOR]

The rhizosphere microbial community helps govern biogeochemical cycling and facilitates complex plant-soil feedback. Understanding the evolutionary dynamics of microbial community structure and functional genes during vegetation succession is crucial for quantifying and understanding ecosystem processes and functions in restored sandy deserts. In this study, the rhizosphere microbial community structure of 11–66-year-old dominant shrubs in a desert revegetation area was examined using shotgun metagenomic sequencing. The interactions between the microbial community structure, functional gene abundances, soil properties, and plant characteristics of different stand ages were comprehensively investigated. The abundance of unique species first increased before subsequently decreasing with stand age, with shared species accounting for only 47.33%–59.42% of the total operational taxonomic units (OTUs). Copiotrophs such as Actinobacteria and Proteobacteria were found to dominate the rhizosphere soil microbial community, with their relative abundance accounting for 75.28%–81.41% of the total OTUs. There was a gradual shift in dominant microbial functional genes being involved in cellular processes towards those involved in environmental information processing and metabolism as stand age increased. Additionally, temporal partitioning was observed in both the microbial co-occurrence network complexity and topological parameters within the rhizosphere soil. Redundancy analysis revealed that dissolved organic carbon was the primary determinant influencing shifts in microbial community structure. Understanding the evolution of microbial community structure and function contributes to identifying potential mechanisms associating the soil microbiome with dominant sand-fixing shrubs as well as understanding the rhizosphere microbiome assembly process. These results shed light on the role of the rhizosphere microbiome in biogeochemical cycling and other ecosystem functions following revegetation of temperate sandy deserts. [ABSTRACT FROM AUTHOR]

While metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process. [ABSTRACT FROM AUTHOR]

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Small peptides produced by plants (SPPs) and microbes (SPMs) function as crucial mediators in plant–rhizosphere microbe interactions, with SPPs facilitating long-distance signaling through extracellular vesicles and SPMs modulating plant immunity and hormone signaling to enhance communication. SPPs may directly alter the rhizosphere microbiomes by modifying microbial gene expression or indirectly by influencing root morphology, exudate release, and immune responses, thus affecting microbial community structure and composition. Leveraging the bidirectional signaling facilitated by SPPs and SPMs between plants and their rhizosphere microbes offers a novel strategy in holobiont engineering, and the potential of exploring transgenic microbes to synthesize small peptides on a large scale merits further investigations. The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant–rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering. [ABSTRACT FROM AUTHOR]

Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. [ABSTRACT FROM AUTHOR]

Ecological restoration technologies have become effective measures for improving urban water systems. In this study, water quality monitoring, acute biological toxicity tests, and microorganism and antibioticresistance gene analyses were conducted to comprehensively understand the contribution of ecological restoration projects to improving the water quality of reclaimed water-replenishing urban rivers. The results showed that the concentrations of chemical oxygen demand (COD), total nitrogen, total phosphorus, and ammonia nitrogen (NH4 +-N) exhibited a downward trend along the flow direction throughout the ecological restoration engineering area. The amounts of NH4 +-N and COD were further reduced through ecological restoration engineering to approximately 75% and 35%, respectively. It demonstrates a notable mitigating effect on the acute biological toxicity of organisms, leading to a substantial rise in the half-inhibitory concentration for Luminous bacteria, Chlorella, and Daphnia magnas. The increases are observed within the ranges of 4.94 to 6.91 N, 10.85 to 46.04 N, and 2.98 to 5.80 N, respectively. In addition, it has a better control effect on pathogenic bacteria, drug-resistant bacteria, and antibiotic-resistance genes. Therefore, ecological restoration projects are more promising measures to further improve reclaimed water before the replenishment of urban rivers. This is an effective and feasible method to ensure the safety and quality of reclaimed water. [ABSTRACT FROM AUTHOR]

Milk is rich in a variety of essential nutrients, including fats, proteins, and trace elements that are important for human health. In particular, milk fat has an alleviating effect on diseases such as heart disease and diabetes. Fatty acids, the basic units of milk fat, play an important role in many biological reactions in the body, including the involvement of glycerophospholipids and sphingolipids in the formation of cell membranes. However, milk fat synthesis is a complex biological process involving multiple organs and tissues, and how to improve milk fat of dairy cows has been a hot research issue in the industry. There exists a close relationship between milk fat synthesis, genes, and microbial functions, as a result of the organic integration between the different tissues of the cow's organism and the external environment. This review paper aims (1) to highlight the synthesis and regulation of milk fat by the first and second genomes (gastrointestinal microbial genome) and (2) to discuss the effects of ruminal microorganisms and host metabolites on milk fat synthesis. Through exploring the interactions between the first and second genomes, and discovering the relationship between microbial and host metabolite in the milk fat synthesis pathway, it may become a new direction for future research on the mechanism of milk fat synthesis in dairy cows. [ABSTRACT FROM AUTHOR]

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites. [ABSTRACT FROM AUTHOR]

Permafrost peatlands are sensitive to changes in nitrogen levels because they are largely nitrogen-limited ecosystems. However, the microbial mechanisms by which the addition of nitrogen increases the emission of greenhouse gasses from permafrost peatlands remain unclear. This study was conducted to decipher the relationship between greenhouse gas emissions and soil microorganisms under nitrogen addition. Here, we performed a 154-day experimental investigation in order to assess the release of greenhouse gasses such as CO2, CH4, and N2O from the soils. Additionally, we examined the correlation between the rates of these gas emissions and the presence of crucial microbial functional genes in the soil. The results showed that the addition of low (0.01 g kg−1), medium (0.02 g kg−1), and high (0.04 g kg−1) levels of nitrogen increased the cumulative CO2 emissions by 2.35%–90.42%, respectively. The cumulative emissions of CH4 increased by 17.29%, 25.55% and 21.77%, respectively. The cumulative emissions of N2O increased 2.97, 7.49 and 7.72-fold. The addition of nitrogen increased the abundance of functional genes in the bacteria, fungi, methanogens, denitrifying bacteria, and nitrogen-fixing bacteria in soil by modifying abiotic soil variables and providing sufficient substrates for microorganisms. The results indicated that the addition of nitrogen can significantly promote the emission of greenhouse gasses by increasing the abundance of functional microbial genes in the soil of permafrost peatlands. These findings highlight the importance of considering nitrogen deposition and the nitrogen released from thawing permafrost when predicting the future greenhouse gasses emitted from permafrost peatlands. [ABSTRACT FROM AUTHOR]

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi‐omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi‐omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process. [ABSTRACT FROM AUTHOR]

The construction period of pumped storage power stations (PSPS) generates amounts of production wastewater, which may contain pathogenic bacteria and antibiotic resistance genes (ARGs) in these bacteria, potentially posing environmental and health risks. This study used the metagenome approach to analyze the distribution of microorganisms, ARGs and their correlation with water quality indicators in wastewater collected from two typical PSPSs. Coagulation system wastewater exhibits strong alkalinity (11.88), and aggregate system wastewater has high suspended solids (SS, 8 × 104 mg/L), resulting in lower richness and diversity of bacterial communities. Serpentinimonas, a kind of alkaliphilic bacteria, had the highest relative abundance (48.58–99.7%). The ARG subtypes obtained conferred wastewater resistance to tetracycline, macrolide, fluoroquinolone and so on, but wastewater treatment has limited removal effect on ARGs. The results indicate that resistant bacteria and resistance genes can still be present and distributed under highly alkaline conditions, and the removal efficiency of ARGs by wastewater treatment in PSPS is limited. Attention should be given to the environmental and health risks posed by production wastewater, thereby providing a theoretical basis for the sustainable development of the PSPS industry. [ABSTRACT FROM AUTHOR]

Denitrification, anaerobic ammonium oxidation (Anammox), and ferric iron reduction coupled with anaerobic ammonium oxidation (Feammox) are the nitrogen removal pathways in natural ecosystems. In this study, the differences between these three nitrogen removal pathways in a Phragmites australis covered site (LW), artificial grassland covered site (CD), poplar covered site (YD), and topsoil tillage after harvesting reed site (GD) in the Yinchuan Yellow River wetland were investigated using isotope tracing, metagenome, and quantitative polymerase chain reaction (Q-PCR) techniques. No 30N2 accumulation was detected in 15NH4 + addition incubations, indicating that Feammox was weak in all sites, which is consistent with a low abundance of the Feammox functional bacteria Acidimiprobiaceae sp. A6. The denitrification rates were 0.36 (LW), 0.5 (CD), 0.76 (YD) and 0.12 (GD) mg N/kg/day. The Anammox rates were 0.18 (LW) and 0.26 (GD) mg N/kg/day; other sites did not detect Anammox rate. Denitrification was the dominant pathway except for the CD site. The YD site had the highest abundance of denitrification genes, which was consistent with the denitrification rate. [ABSTRACT FROM AUTHOR]

Background: L-Tyrosine (L-Tyr) is a significant aromatic amino acid that is experiencing an increasing demand in the market due to its distinctive characteristics. Traditional production methods exhibit various limitations, prompting researchers to place greater emphasis on microbial synthesis as an alternative approach. Results: Here, we developed a metabolic engineering-based method for efficient production of L-Tyr from Corynebacterium crenatum, including the elimination of competing pathways, the overexpression of aroB, aroD, and aroE, and the introduction of the mutated E. coli tyrAfbr gene for elevating L-Tyr generation. Moreover, the mtlR gene was knocked out, and the mtlD and pfkB genes were overexpressed, allowing C. crenatum to produce L-Tyr from mannitol. The L-Tyr production achieved 6.42 g/L at a glucose-to-mannitol ratio of 3:1 in a shake flask, which was 16.9% higher than that of glucose alone. Notably, the L-Tyr production of the fed-batch fermentation was elevated to 34.6 g/L, exhibiting the highest titers among those of C. glutamicum previously reported. Conclusion: The importance of this research is underscored by its pioneering application of mannitol as a carbon source for the biosynthesis of L-Tyr, as well as its examination of the influence of mannitol-associated genes in microbial metabolism. A promising platform is provided for the production of target compounds that does not compete with human food source. [ABSTRACT FROM AUTHOR]

Background: The rapid advancements in deep neural network models have significantly enhanced the ability to extract features from microbial sequence data, which is critical for addressing biological challenges. However, the scarcity and complexity of labeled microbial data pose substantial difficulties for supervised learning approaches. To address these issues, we propose DNASimCLR, an unsupervised framework designed for efficient gene sequence data feature extraction. Results: DNASimCLR leverages convolutional neural networks and the SimCLR framework, based on contrastive learning, to extract intricate features from diverse microbial gene sequences. Pre-training was conducted on two classic large scale unlabelled datasets encompassing metagenomes and viral gene sequences. Subsequent classification tasks were performed by fine-tuning the pretrained model using the previously acquired model. Our experiments demonstrate that DNASimCLR is at least comparable to state-of-the-art techniques for gene sequence classification. For convolutional neural network-based approaches, DNASimCLR surpasses the latest existing methods, clearly establishing its superiority over the state-of-the-art CNN-based feature extraction techniques. Furthermore, the model exhibits superior performance across diverse tasks in analyzing biological sequence data, showcasing its robust adaptability. Conclusions: DNASimCLR represents a robust and database-agnostic solution for gene sequence classification. Its versatility allows it to perform well in scenarios involving novel or previously unseen gene sequences, making it a valuable tool for diverse applications in genomics. [ABSTRACT FROM AUTHOR]

Eriocheir sinensis is the main aquaculture species in China. With the continuous expansion of the aquaculture scale, the demand for E. sinensis seedlings was also increased. The water used in breeding has well-nourished and its discharge into the sea posed significant risks. This study sampled the wastewater discharge points of the E. sinensis seedlings in Sheyang County, Jiangsu Province, and the areas far from the discharge points that were not affected in March and May 2023, respectively. A large number of antibiotic resistance genes (ARGs) were found in the sediment of the wastewater discharge area, and the highest ARG was sulfonamide ARG-sul1 using qPCR analysis, while ARGs were almost undetectable in the areas not affected by wastewater discharge. The 16S rRNA sequence analysis results showed that the main bacterial phyla at the wastewater discharge point were Bacteroidetes, Proteobacteria, and Thermodesulfobacteria. In the control point, the main bacterial phyla were Proteobacteria, Chlorobacterium, and Thermodesulfobacteria. There were significant differences in the composition of microbial communities between the two points, and the samples at the wastewater discharge point were more clustered and had higher similarity. The correlation network and redundancy analysis indicated that the phyla Bacteroidetes, Firmicutes, and Proteobacteria at the wastewater discharge points were positively correlated with most ARGs. The wastewater discharge had no effect on heavy metals from the two points. This study sets a foundation for future research by identifying key microbial taxa as potential ARG carriers and examining the interactions between microbial communities, ARGs, and heavy metals. [ABSTRACT FROM AUTHOR]

• Novel carbon source and corncob had better denitrification efficiency than polycaprolactone and polyvinyl alcohol-sodium alginate. • The taxonomical composition of bacterial, fungal and archaeal communities can be altered by types of solid carbon source. • Some fungi and archaea species were conducive to solid-phase denitrification (SPD) systems. • Co-occurring network showed some potential collaboration between bacterial fungal and archaeal communities in SPD systems. • Amplicon sequence variant (ASV) can identify more taxonomies that operational taxonomic unit (OTU) cannot in this study. There is a lack of understanding about the bacterial, fungal and archaeal communities' composition of solid-phase denitrification (SPD) systems. We investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit (OTU) and amplicon sequence variant (ASV). The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone (CPSP, 0.86±0.04 mg NO 3 −-N/(g·day)) and corncob (0.85±0.06 mg NO 3 −-N/(g·day)) had better denitrification efficiency than polycaprolactone (PCL, 0.29±0.11 mg NO 3 −-N/(g·day)) and polyvinyl alcohol-sodium alginate (PVA-SA, 0.24±0.07 mg NO 3 −-N/(g·day)). The bacterial, fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL (OTU: 83.72%, ASV: 82.49%) and Rozellomycota in PVA-SA (OTU: 71.99%, ASV: 81.30%). ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum, unclassified_ f_ Xanthobacteraceae genus, etc., indicating ASV may be more conducive to understand SPD microbial communities. The co-occurring network showed some correlation between the bacteria fungi and archaea species, indicating different species may collaborate in SPD systems. Similar KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD systems. These results may be beneficial for understanding microbial communities in SPD systems. [Display omitted] [ABSTRACT FROM AUTHOR]

Cow dung liquid mulch (CDLM), which uses cow dung as a raw material, has a good degradability and is a potential alternative to traditional plastic agricultural mulch, but there is a lack of research on the effects of CDLM on rhizosphere soil physicochemical properties, rhizosphere soil microbial functions, and crop yields. In this study, the link between maize yield, environmental factors, and functional genes as well as the responses of microbial community functions to CDLM and polyethylene mulch (PE) were studied using metagenomic sequencing. Functional annotation was also performed on clusters of orthologous groups of proteins, the Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme sequencing data. The results showed that CDLM significantly increased maize yield by 30.9% compared to CK while maintaining lower soil microplastic levels. CDLM promotes the enrichment of beneficial microorganisms such as Mycolicibacterium and Pseudomonas. The relative abundance of functional genes related to microbial metabolism, soil element cycling pathways, and organic matter degradation was significantly higher in CDLM than in CK. Microbial functional genes were positively correlated with maize yield and environmental factors such as soil nutrients. These results suggested that CDLM can improve maize yield by enriching beneficial microorganisms, reducing rhizosphere soil environmental risks, and enhancing rhizosphere soil microbial function. Rhizosphere soil nutrients and microbial functional genes together mediated the positive response of maize yield to CDLM. This study can provide a scientific basis and data support for the safe use of mulch in the future. [ABSTRACT FROM AUTHOR]

Straw returning enhances soil fertility and increases corn yield, but the impact on soil fertility varies with different incorporation methods. To explore the optimal straw-returning method, this study, based on a long-term field experiment, investigated the following different corn-straw-returning methods: deep plowing and straw returning (B), rotary tillage and straw returning (RT), crushing and mixing straw returning (TM), pulverized cover straw returning (C), high-stubble-retention straw returning (LHS), strip cover (S), and flat no-tillage without straw returning (CK). High-throughput sequencing technology was employed to analyze the soil bacterial community composition and structural changes under different straw-returning methods. The study further explored the relationships between the soil bacterial community and nutrient content. The results indicated that different straw-returning methods altered the composition and structure of the soil bacterial community. The TM treatment significantly increased the richness and diversity of the soil bacterial communities. Shredding and covering (C and TM) effectively improved the soil nutrient content and bacterial community structure. In the C treatment, the abundance of Blastococcus, Nocardioides, and Microvirga increased the most, by 241.02%, 77.79%, and 355.08%, respectively, compared with CK. In the TM treatment, Pseudarthrobacter showed the highest abundance, increasing by 343.30%. The genes involved in soil carbon hydrolysis (pulA), nitrification (hao), organic nitrogen degradation and synthesis (gudB), and the nitrogen limitation response (glnR) significantly decreased by 56.21%, 78.75%, 66.46%, and 67.40%, respectively, in the C treatment. The genes involved in soil carbon hydrolysis (IMA), carbon fixation (pccB-A), methane metabolism (moxF), nitrate reduction in soil (nirD), organic nitrogen degradation and synthesis (gdh, ureAB, ureE), and phosphate absorption (glpT) significantly increased by 93.37%, 92.68%, 95.00%, 23.42%, 35.40%, 114.21%, 59.14%, and 75.86%, respectively, in the C treatment. The nitrate reduction gene (nrfA) significantly increased by 80.27% in the TM treatment. Therefore, we concluded that straw primarily stimulates the activity of bacterial communities and regulates the bacterial community by changing the relative abundance of the soil microorganisms and functional genes, thereby improving the soil nutrient content. This study considered pulverized cover straw returning and crushing and mixing straw returning to be the most reasonable methods. [ABSTRACT FROM AUTHOR]

Background and aims: Soil microbiome is the key driver mediating soil P transformation in agroecosystems. However, the underlying genomic information related to soil P cycling in response to organic C inputs is largely unknown. Methods: By using metagenomic sequencing, we investigated the effect of P fertilization and C input (i.e., glucose and lignin) on functional profiles of microbial genes related to P cycling in bulk and rhizosphere soils. Maize plants were grown for 47 days in Ultisols with or without P-fertilizer history. Results: Glucose decreased rhizosphere H2O-Pi concentrations in soil with P history, increased that in soil without P history; while lignin increased that in both soils. Ogranic C inputs increased the relative abundances of phnGHIJLMNP and pit genes by 17–138% and 2.3–31%, decreased those of phoB, phoR and pstABCS genes by 3.6–18%, 12–31% and 11–26%, respectively, in rhizosphere soils irrespective of P history. In the rhizosphere rather than bulk soil, the proportion of P starvation regulation-related genes was higher in lignin treated-soils without than with P history. Proteobacteria (10–89%) and Acidobacteria (0.41–57%) were the dominant phyla and main contributors to soil P transformation-related genes (e.g., appA, phoAD, gcd). Elevated soil pH induced by organic C inputs also diversified the composition of genes involved in P transformation. Conclusions: Organic C altered P cycling-related gene composition irrespective of soil P status, which facilitated P transformation. Proteobacteria and Acidobacteria were vital in mediating C and P metabolisms. [ABSTRACT FROM AUTHOR]

Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library being reported. Here, we describe the construction and characterization of DNA libraries from a single cultured phage (FT4), five cultured Escherichia coli phages, and three metagenomic viral sets built from freshwater, seawater, and wastewater samples. Through next-generation sequencing of five independent samplings of the libraries, we found a consistent number of recovered genes per replicate for each library, with many genes classifiable via the KEGG and Pharokka databases. By characterizing the size of the genes and inserts, we found that our libraries contain a median of one to two genes per contig with a median gene length of 303-381 bp for all libraries, reflective of the small genomes of viruses. The environmental libraries were genetically diverse compared to the single phage and multi-phage libraries. Additionally, we found reduced coverage of individual genomes when five phages were used as opposed to one. Taken together, this work provides a comprehensive analysis of the DNA libraries from phage genomes that can be used for metagenomic exploration and functional screens to infer and identify new biology. IMPORTANCE Functional metagenomics is an approach that aims to characterize the putative biological function of genes in the microbial world. This includes an examination of the sequencing data collected from a pooled source of diverse microbes and inference of gene function by comparison to annotated and studied genes from public databases. At times, DNA libraries are made from these genes, and the library is screened for a specific function. Hits are validated using a combination of biological, computational, and structural analysis. Left unresolved is a detailed characterization of the library, both its diversity and content, for the purposes of imputing function entirely by computational means, a process that may yield findings that aid in designing useful screens to identify novel gene functions. In this study, we constructed libraries from cultured phages and uncultured viromes from the environment and characterized some important parameters, such as gene number, genes per contig, ratio of hypothetical to known proteins, total genomic coverage and recovery, and the effect of pooling genetic information from multiple sources, to provide a better understanding of the nature of these libraries. This work will aid the design and implementation of future screens of pooled DNA libraries to discover and isolate viral genes with novel biology across various biomes. [ABSTRACT FROM AUTHOR]

Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers. [ABSTRACT FROM AUTHOR]

While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai–Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows' digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds. [ABSTRACT FROM AUTHOR]

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The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies. In this large-scale metagenomics study encompassing 3,483 human host-derived samples from seven body sites, researchers identify 583 unreported single-genome bins and report 314 metagenome-disease as well as 814 biosynthetic gene-disease associations. [ABSTRACT FROM AUTHOR]

The gastrointestinal (GI) microbiome of chelonians (testudines) plays an important role in their metabolism, nutrition, and overall health but the GI microbiome of three-toed box turtles (Terrapene carolina triunguis) has yet to be characterized. How the GI microbiome responds to rapidly rising environmental temperatures has also not been studied extensively in ectotherms, specifically chelonians. In this study, twenty (20) T.c.triunguis were split into control and experimental groups. The experimental group experienced 4.5°C increases every two weeks while the control group stayed at a constant ambient temperature (24°C) through the entirety of the experiment. Before each temperature increase, all turtles had cloacal swab samples taken. These samples underwent DNA extraction followed by 16S rRNA gene sequencing and microbial community analyses. Differences in diversity at the community level in the controls compared to the experimental groups were not statistically significant, indicating microbiome resilience to rapid temperature changes in T.c.triunguis, although some differentially abundant lineages were identified. Interestingly, an amplicon sequence variant belonging to the Erysipelothrix spp. was exclusively enriched in the highest temperature group relative to controls. Overall, our work suggests that there may be an innate robustness to rapid temperature swings in the microbiome of T.c.triunguis which are native to temperate North America. Despite this resilience, Erysipelothrix spp. was enriched at the highest temperature. Phylogenetic analysis of this amplicon variant showed that it is a close relative of Erysipelothrix rhusiopathiae, a pathogen of zoonotic importance associated with both wildlife and livestock. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this systematic bioinformatics analysis was to describe the compositions and differences in submucosal microbial profiles of peri-implants’ diseases and healthy implant. Material and methods: PubMed, Embase, ETH Z, Scopus, CNKI, and Wanfang databases were searched to screen relevant literature on the analysis of peri-implant microflora based on the sequencing analysis technique of 16S ribosomal RNA (16S rRNA) gene. High-throughput sequencing of the 16S rRNA gene of microorganisms from healthy implants, peri-implant mucositis, and periimplantitis was downloaded from the screened articles. EasyAmplicon and Usearch global algorithm were used to match the reads from each dataset to a full length of 16S rRNA or ITS gene sequence. The microorganisms based on the Human Oral Microbiome Database (HOMD) were re-classified, and the microbial diversity, flora composition, and differential species of the samples were reanalyzed, including taxonomic classification and alpha and beta diversity calculations. The co-occurrence network was also re-analyzed. Results: A total of seven articles with 240 implants were included. Among them, 51 were healthy implants (HI), 43 were in the peri-implant mucositis (PM) group, and 146 were in the peri-implantitis (PI) group. A total of 26,483 OTUs were obtained, and 877 microorganisms were annotated. The alpha diversity including Chao1 (healthy implants, 121.04 ± 92.76; peri-implant mucositis, 128.21 ± 66.77; peri-implantitis, 131.15 ± 84.69) and Shannon (healthy implants, 3.25 ± 0.65; peri-implant mucositis, 3.73 ± 0.61; peri-implantitis, 3.53 ± 0.67) of the samples from the three groups showed a significant difference. The beta diversity of the three samples was statistically different among groups. The genera of Treponema and Fretibacterium were significantly more abundant in the PI group than in the other two groups, and the genus of Streptococcus was more abundant in the HI group. The relative abundance of Porphyromonas in the peri-implantitis group was 6.1%. The results of the co-occurrence network showed differences in the network topology among the three groups of samples. The most connected three genera in the healthy implants were Halomonas, Fusobacterium, and Fretibacterium. The most connected three genera in peri-implant mucositis were Alistipes, Clostridia UCG-014, and Candidatus Saccharimonas. The most connected three genera in the peri-implantitis group were Lachnoanaerobaculum, Fusobacterium, and Atopobium. The betweenness of Porphvromonas gingivalis (red complex) in the PI group (7,900) was higher than in the HI group (23). Conclusions: The community compositions of peri-implant submucosal microorganisms were significantly different in healthy implants, peri-implant mucositis, and peri-implantitis. The submucosal microbial communities in peri-implantitis were characterized by high species richness and diversity compared with the healthy implants; the relative abundance of red complex, some members of the yellow complex, and some novel periodontal pathogens was higher in the peri-implantitis and peri-implant mucositis groups than in the healthy implant group. The core flora of the co-occurrence network of healthy implants, peri-implant mucositis, and peri-implantitis varied considerably. The peri-implantitis site presented a relative disequilibrium microbial community, and Porphyromonas may play an important role in the co-occurrence network. [ABSTRACT FROM AUTHOR]