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Frontiers in microbiology 3346건

  1. [해외논문]   Cobalamin (Vitamin B12) Induced a Shift in Microbial Composition and Metabolic Activity in an in vitro Colon Simulation   SCIE

    Xu, Yuanyuan , Xiang, Shasha , Ye, Kun , Zheng, Yiqing , Feng, Xiao , Zhu, Xuan , Chen, Jie , Chen, Yuewen
    Frontiers in microbiology v.9 ,pp. 2780 , 2018 ,

    초록

    Cobalamin deficiency is believed to be related to disturbances in cell division, neuropathy, nervous system disease and pernicious anemia. Elderly people are usually advised to supplement their diets with cobalamin. As cobalamin has several forms, the effects of different forms of cobalamin on gut microbiota were investigated in this study. After 7 days of supplementation, methylcobalamin had reduced the diversity of gut microbiota compared to that in the control and cyanocobalamin groups. After supplementation with methylcobalamin, the percentage of Acinetobacter spp. had increased to 45.54%, while the percentages of Bacteroides spp., Enterobacteriaceae spp. and Ruminococcaceae spp. had declined to 11.15, 9.34, and 2.69%, respectively. However, cyanocobalamin had different influences on these bacteria. Both cobalamins increased the amount of short-chain fatty acids, particularly butyrate and propionic acid. The cyanocobalamin group showed increased activity of cellulase compared with that in the other two groups. According to CCA and PICRUSt analysis, methylcobalamin had a positive correlation with Pseudomonas bacteria, propionic acid, and butyrate. Methylcobalamin promoted lipid, terpenoid, and polyketide metabolism by gut bacteria, promoted the degradation of exogenous substances, and inhibited the synthesis of transcription factors and secondary metabolites. Our results indicate that the various forms of cobalamin in the food industry should be monitored and regulated, because the two types of cobalamin had different effects on the gut microbiome and on microbial metabolism, although they have equal bio-activity in humans. Given the effects of methylcobalamin on gut microbiota and microbial metabolism, methylcobalamin supplementation should be suggested as the first option.

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  2. [해외논문]   Development of Freeze-Thaw Tolerant Lactobacillus rhamnosus GG by Adaptive Laboratory Evolution   SCIE

    Kwon, Ye Won , Bae, Jae-Han , Kim, Seul-Ah , Han, Nam Soo
    Frontiers in microbiology v.9 ,pp. 2781 , 2018 ,

    초록

    The industrial application of microorganisms as starters or probiotics requires their preservation to assure viability and metabolic activity. Freezing is routinely used for this purpose, but the cold damage caused by ice crystal formation may result in severe decrease in microbial activity. In this study, adaptive laboratory evolution (ALE) technique was applied to a lactic acid bacterium to select tolerant strains against freezing and thawing stresses. Lactobacillus rhamnosus GG was subjected to freeze-thaw-growth (FTG) for 150 cycles with four replicates. After 150 cycles, FTG-evolved mutants showed improved fitness (survival rates), faster growth rate, and shortened lag phase than those of the ancestor. Genome sequencing analysis of two evolved mutants showed genetic variants at distant loci in six genes and one intergenic space. Loss-of-function mutations were thought to alter the structure of the microbial cell membrane (one insertion in cls ), peptidoglycan (two missense mutations in dacA and murQ ), and capsular polysaccharides (one missense mutation in wze ), resulting in an increase in cellular fluidity. Consequently, L. rhamnosus GG was successfully evolved into stress-tolerant mutants using FTG-ALE in a concerted mode at distal loci of DNA. This study reports for the first time the functioning of dacA and murQ in freeze-thaw sensitivity of cells and demonstrates that simple treatment of ALE designed appropriately can lead to an intelligent genetic changes at multiple target genes in the host microbial cell.

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  3. [해외논문]   Investigation of the Role That NADH Peroxidase Plays in Oxidative Stress Survival in Group B Streptococcus   SCIE

    Korir, Michelle L. (Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, MI , United States ) , Flaherty, Rebecca A. (Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, MI , United States ) , Rogers, Lisa M. (Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center , Nashville, TN , United States ) , Gaddy, Jennifer A. (Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center , Nashville, TN , United States ) , Aronoff, David M. (Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center , Nashville, TN , United States ) , Manning, Shannon D. (Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, MI , United States )
    Frontiers in microbiology v.9 ,pp. 2786 , 2018 ,

    초록

    Macrophages play an important role in defending the host against infections by engulfing pathogens and containing them inside the phagosome, which consists of a harsh microbicidal environment. However, many pathogens have developed mechanisms to survive inside macrophages despite this challenge. Group B Streptococcus (GBS), a leading cause of sepsis and meningitis in neonates, is one such pathogen that survives inside macrophages by withstanding phagosomal stress. Although a few key intracellular survival factors have been identified, the mechanisms by which GBS detoxifies the phagosome are poorly defined. Transcriptional analysis during survival inside macrophages revealed strong upregulation of a putative NADH peroxidase ( npx ) at 1 and 24 h post-infection. A deletion mutant of npx (Δ npx ) was more susceptible to killing by a complex in vitro model of multiple phagosomal biochemical/oxidant stressors or by hydrogen peroxide alone. Moreover, compared to an isogenic wild type GBS strain, the Δ npx strain demonstrated impaired survival inside human macrophages and a reduced capacity to blunt macrophage reactive oxygen species (ROS) production. It is therefore likely that Npx plays a role in survival against ROS production in the macrophage. A more thorough understanding of how GBS evades the immune system through survival inside macrophages will aid in development of new therapeutic measures.

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  4. [해외논문]   The XRE-DUF397 Protein Pair, Scr1 and Scr2, Acts as a Strong Positive Regulator of Antibiotic Production in Streptomyces   SCIE

    Santamarí (Instituto de Biología Funcional y Genómica, Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca , Salamanca , Spain ) , a, Ramó (Instituto de Biología Funcional y Genómica, Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca , Salamanca , Spain ) , n I. (Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Granada , Spain ) , Sevillano, Laura (Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Granada , Spain ) , Martí (Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Granada , Spain ) , n, Jesú (Instituto de Biolog&ia) , s , Genilloud, Olga , Gonzá , lez, Ignacio , Dí , az, Margarita
    Frontiers in microbiology v.9 ,pp. 2791 , 2018 ,

    초록

    The xenobiotic response element (XRE) transcription factors belong to a regulator family frequently found in Streptomyces that are often followed by small proteins with a DUF397 domain. In fact, the pair XRE-DUF397 has been proposed to comprise toxin–antitoxin (TA) type II systems. In this work, we demonstrate that one of these putative TA-systems, encoded by the genes SCO4441 and SCO4442 of Streptomyces coelicolor , and denominated Scr1/Scr2 (which stands for S . c oelicolor r egulator ), does not behave as a toxin–antitoxin system under the conditions used as was originally expected. Instead the pair Scr1/Scr2 acts as a strong positive regulator of endogenous antibiotic production in S. coelicolor . The analysis of the 19 Streptomyces strains tested determined that overexpression of the pair Scr1/Scr2 drastically induces the production of antibiotics not only in S. coelicolor , but also in Streptomyces lividans , Streptomyces peucetius, Streptomyces steffisburgensis and Streptomyces sp. CA-240608. Our work also shows that Scr1 needs Scr2 to exert positive regulation on antibiotic production.

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  5. [해외논문]   Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H 2 S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model   SCIE

    Burrichter, Anna (Department of Biology, University of Konstanz , Konstanz , Germany ) , Denger, Karin (Department of Biology, University of Konstanz , Konstanz , Germany ) , Franchini, Paolo (Department of Biology, University of Konstanz , Konstanz , Germany ) , Huhn, Thomas (The Konstanz Research School Chemical Biology, University of Konstanz , Konstanz , Germany ) , Mü (Department of Biology, University of Konstanz , Konstanz , Germany ) , ller, Nicolai (Department of Biology, University of Konstanz , Konstanz , Germany ) , Spiteller, Dieter (Department of Biology, University of Konstanz , Konstanz , Germany ) , Schleheck, David
    Frontiers in microbiology v.9 ,pp. 2792 , 2018 ,

    초록

    Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is produced by plants and other phototrophs and its biodegradation is a relevant component of the biogeochemical carbon and sulfur cycles. SQ is known to be degraded by aerobic bacterial consortia in two tiers via C 3 -organosulfonates as transient intermediates to CO 2 , water and sulfate. In this study, we present a first laboratory model for anaerobic degradation of SQ by bacterial consortia in two tiers to acetate and hydrogen sulfide (H 2 S). For the first tier, SQ-degrading Escherichia coli K-12 was used. It catalyzes the fermentation of SQ to 2,3-dihydroxypropane-1-sulfonate (DHPS), succinate, acetate and formate, thus, a novel type of mixed-acid fermentation. It employs the characterized SQ Embden-Meyerhof-Parnas pathway, as confirmed by mutational and proteomic analyses. For the second tier, a DHPS-degrading Desulfovibrio sp. isolate from anaerobic sewage sludge was used, strain DF1. It catalyzes another novel fermentation, of the DHPS to acetate and H 2 S. Its DHPS desulfonation pathway was identified by differential proteomics and demonstrated by heterologously produced enzymes: DHPS is oxidized via 3-sulfolactaldehyde to 3-sulfolactate (SL) by two NAD + -dependent dehydrogenases (DhpA, SlaB); the SL is cleaved by an SL sulfite-lyase known from aerobic bacteria (SuyAB) to pyruvate and sulfite. The pyruvate is oxidized to acetate, while the sulfite is used as electron acceptor in respiration and reduced to H 2 S. In conclusion, anaerobic sulfidogenic SQ degradation was demonstrated as a novel link in the biogeochemical sulfur cycle. SQ is also a constituent of the green-vegetable diet of herbivores and omnivores and H 2 S production in the intestinal microbiome has many recognized and potential contributions to human health and disease. Hence, it is important to examine bacterial SQ degradation also in the human intestinal microbiome, in relation to H 2 S production, dietary conditions and human health.

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  6. [해외논문]   The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy   SCIE

    Ma, Jing-E , Jiang, Hai-Ying , Li, Lin-Miao , Zhang, Xiu-Juan , Li, Guan-Yu , Li, Hui-Ming , Jin, Xue-Jun , Chen, Jin-Ping
    Frontiers in microbiology v.9 ,pp. 2793 , 2018 ,

    초록

    The characteristics of flora in the intestine of an animal, including the number and abundance of different microbial species and their functions, are closely related to the diets of the animal and affect the physical condition of the host. The Malayan pangolin ( Manis javanica ) is an endangered species that specializes in myrmecophagy. Analyzing the microbiome in the intestine of the pangolin is imperative to protect this species. By sequencing the metagenomes of the feces of four pangolins, we constructed a non-redundant catalog of 211,868 genes representing 1,811 metagenomic species. Taxonomic annotation revealed that Bacteroidetes (49.9%), Proteobacteria (32.2%), and Firmicutes (12.6%) are the three main phyla. The annotation of gene functions identified 5,044 genes from 88 different glycoside hydrolase (GH) families in the Carbohydrate-Active enZYmes database and 114 gene modules related to chitin-degrading enzymes, corresponding to the catalytic domains of GH18 family enzymes, containing chitinase genes of classes III and V in the dataset. Fourteen gene modules corresponded to the catalytic domains of GH19 family enzymes, containing chitinase genes of classes I, II, and IV. These genes were found in 37 species belonging to four phyla: Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Moreover, when the metabolic pathways of these genes were summarized, 41,711 genes were associated with 147 unique KEGG metabolic pathways, and these genes were assigned to two Gene Ontology terms: metabolic process and catalytic activity. We also found several species that likely play roles in the digestion of cellulose and may be able to degrade chitin, including Enterobacter cloacae, Lactococcus lactis, Chitinimonas koreensis , and Chitinophaga pinensis . In addition, we identified some intestinal microflora and genes related to diseases in pangolins. Twenty-seven species were identified by STAMP analysis as differentially abundant in healthy and diseased animals: 20 species, including Cellulosilyticum lentocellum and Lactobacillus reuteri , were more abundant in healthy pangolins, while seven species, including Odoribacter splanchnicus, Marinilabilia salmonicolor, Xanthomonas citri, Xanthomonas vasicola, Oxalobacter formigenes, Prolixibacter bellariivorans , and Clostridium bolteae , were more abundant in diseased pangolins. These results will support the efforts to conserve pangolins.

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  7. [해외논문]   Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments   SCIE

    Arce, Maria Isabel (Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin , Germany ) , von Schiller, Daniel (Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU) , Bilbao , Spain ) , Bengtsson, Mia M. (Institute of Microbiology, University of Greifswald , Greifswald , Germany ) , Hinze, Christian (Institute of Microbiology, University of Greifswald , Greifswald , Germany ) , Jung, Hoseung (Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys), Humboldt University of Berlin , Berlin , Germany ) , Alves, Ricardo J. Eloy (Department of Ecogenomics and Systems Biology, University of Vienna , Vienna , Austria ) , Urich, Tim (Institute of Microbiology, University of Greifswald , Greifswald , Germany ) , Singer, Gabriel (Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin , Germany )
    Frontiers in microbiology v.9 ,pp. 2794 , 2018 ,

    초록

    Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N 2 O) to the atmosphere. While ammonium (NH 4 + ) pool size decreased, nitrate (NO 3 − ) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N 2 O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH 4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N 2 O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases – a hydrological scenario expected to become more important in the future.

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  8. [해외논문]   Sucrose-Induced Proteomic Response and Carbohydrate Utilization of Lactobacillus sakei TMW 1.411 During Dextran Formation   SCIE

    Prechtl, Roman M. (Lehrstuhl für Technische Mikrobiologie, Technische Universität München ) , Janßen, Dorothee (Lehrstuhl für Technische Mikrobiologie, Technische Universität München ) , Behr, Jü (Bavarian Center for Biomolecular Mass Spectrometry ) , rgen (Bavarian Center for Biomolecular Mass Spectrometry ) , Ludwig, Christina (Bavarian Center for Biomolecular Mass Spectrometry ) , Kü (Lehrstuhl für Technische Mikrobiologie, Technische Universität München ) , ster, Bernhard (Lehrstuhl für Technische Mikrobiologie, Technische Universität München ) , Vogel, Rudi F. , Jakob, Frank
    Frontiers in microbiology v.9 ,pp. 2796 , 2018 ,

    초록

    Lactobacillus (L.) sakei belongs to the dominating lactic acid bacteria in indigenous meat fermentations, while diverse strains of this species have also been isolated from plant fermentations. We could recently show, that L. sakei TMW 1.411 produces a high molecular weight dextran from sucrose, indicating its potential use as a dextran forming starter culture. However, the general physiological response of L. sakei to sucrose as carbohydrate source has not been investigated yet, especially upon simultaneous dextran formation. To address this lack of knowledge, we sequenced the genome of L. sakei TMW 1.411 and performed a label-free, quantitative proteomics approach to investigate the sucrose-induced changes in the proteomic profile of this strain in comparison to its proteomic response to glucose. In total, 21 proteins were found to be differentially expressed at the applied significance criteria (FDR ≤ 0.01). Among these, 14 were associated with the carbohydrate metabolism including several enzymes, which enable sucrose and fructose uptake, as well as, their subsequent intracellular metabolization, respectively. The plasmid-encoded, extracellular dextransucrase of L. sakei TMW 1.411 was expressed at high levels irrespective of the present carbohydrate and was predominantly responsible for sucrose consumption in growth experiments using sucrose as sole carbohydrate source, while the released fructose from the dextransucrase reaction was more preferably taken up and intracellularly metabolized than sucrose. Genomic comparisons revealed, that operons coding for uptake and intracellular metabolism of sucrose and fructose are chromosomally conserved among L. sakei , while plasmid-located dextransucrase genes are present only in few strains. In accordance with these findings, all 59 different L. sakei strains of our strain collection were able to grow on sucrose as sole carbohydrate source, while eight of them exhibited a mucous phenotype on agar plates indicating dextran formation from sucrose. Our study therefore highlights the intrinsic adaption of L. sakei to plant environments, where sucrose is abundant, and provides fundamental knowledge regarding the use of L. sakei as starter culture for sucrose-based food fermentation processes with in-situ dextran formation.

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  9. [해외논문]   A Rhodococcal Transcriptional Regulatory Mechanism Detects the Common Lactone Ring of AHL Quorum-Sensing Signals and Triggers the Quorum-Quenching Response   SCIE

    Barbey, Corinne (Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) –) , Chane, Andrea (Normandie Université) , Burini, Jean-Franç (–) , ois (LMSM , Évreux , France ) , Maillot, Olivier (Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) –) , Merieau, Annabelle (Normandie Université) , Gallique, Mathias (–) , Beury-Cirou, Amé (LMSM , Évreux , France ) , lie (Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) –) , Konto-Ghiorghi, Yoan (Normandie Université) , Feuilloley, Marc (–) , Gobert, Virginie (LMSM , Évreux , France ) , Latour, Xavier (Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) –)
    Frontiers in microbiology v.9 ,pp. 2800 , 2018 ,

    초록

    The biocontrol agent Rhodococcus erythropolis disrupts virulence of plant and human Gram-negative pathogens by catabolizing their N -acyl-homoserine lactones. This quorum-quenching activity requires the expression of the qsd ( q uorum-sensing s ignal d egradation) operon, which encodes the lactonase QsdA and the fatty acyl-CoA ligase QsdC, involved in the catabolism of lactone ring and acyl chain moieties of signaling molecules, respectively. Here, we demonstrate the regulation of qsd operon expression by a TetR-like family repressor, QsdR. This repression was lifted by adding the pathogen quorum signal or by deleting the qsdR gene, resulting in enhanced lactone degrading activity. Using interactomic approaches and transcriptional fusion strategy, the qsd operon derepression was elucidated: it is operated by the binding of the common part of signaling molecules, the homoserine lactone ring, to the effector-receiving domain of QsdR, preventing a physical binding of QsdR to the qsd promoter region. To our knowledge, this is the first evidence revealing quorum signals as inducers of the suitable quorum-quenching pathway, confirming this TetR-like protein as a lactone sensor. This regulatory mechanism designates the qsd operon as encoding a global disrupting pathway for degrading a wide range of signal substrates, allowing a broad spectrum anti-virulence activity mediated by the rhodococcal biocontrol agent. Understanding the regulation mechanisms of qsd operon expression led also to the development of biosensors useful to monitor in situ the presence of exogenous signals and quorum-quenching activity.

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  10. [해외논문]   Nematodes and Microorganisms Interactively Stimulate Soil Organic Carbon Turnover in the Macroaggregates   SCIE

    Jiang, Yuji (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Zhou, Hu (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Chen, Lijun (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Yuan, Ye (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Fang, Huan (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Luan, Lu (State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China ) , Chen, Yan (State Key Laboratory of Soil and Sustainable A) , Wang, Xiaoyue , Liu, Manqiang , Li, Huixin , Peng, Xinhua , Sun, Bo
    Frontiers in microbiology v.9 ,pp. 2803 , 2018 ,

    초록

    The intra-aggregate architecture of soil macroaggregates provides suitable microhabitats for nematodes to graze on microorganisms. However, it is not fully clear how nematodes and microbial communities interactively mediate soil organic carbon (SOC) turnover. Here, we aimed to illustrate the relationships between nematodes, microbial community, and SOC turnover in the macroaggregates of a red soil receiving long-term manure application. Soil macroaggregates (>2 mm) were sampled from an 11-year field experiment including four manure treatments: no manure (M0), low manure rate (M1), high manure rate (M2), and high manure rate with lime (M3). The abundances of nematodes and microbial communities were substantially increased under manure treatments. Bacterivores dominated under the M2 and M3 treatments, while plant parasites were enriched under the M1 treatment. Phospholipid fatty acid analysis indicated that the ratio of bacteria to fungi significantly increased, but the ratio of Gram-positive bacteria to Gram-negative bacteria declined with the increasing manure addition. Random forest modeling showed that soil porosity had a primary effect on nematode assemblages, while pH and SOC contributed profoundly to the structure of the microbial community and carbon metabolic capacity. Structural equation modeling suggested that nematode grazing promoted carbon metabolic activities predominantly due to increased microbial biomass. Taken together, the mechanistic understanding of nematode-microorganism interactions may have important implications for improving soil fertility by nematode-mediated microbial processes.

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