[Response Characteristics of Soil Fungal Community Structure to Long-term Continuous Cropping of Pepper]

This study aimed to clarify the effect of long-term continuous cropping of pepper on soil fungal community structure, reveal the mechanism of continuous cropping obstacles, and provide a theoretical basis for the ecological safety and sustainable development of pepper industry. We took the pepper continuous cropping soil in the vegetable greenhouse planting base of Tongren City as the research object. The diversity and community structure of fungi in farmland soil were analyzed using Illumina MiSeq high-throughput sequencing, the responses of soil physio-chemical properties and fungal community characteristics to long-term continuous pepper cropping were discussed, and the relationships between the characteristics of fungal community structure and environmental factors were determined using CCA and correlation network analysis. The results showed that with the extension of pepper continuous cropping years, the soil pH value and organic matter (OM) content decreased, total phosphorus (TP) and available phosphorus (AP) contents increased, hydrolyzed nitrogen (AN) and available potassium (AK) contents decreased first and then increased, and total nitrogen (TN) and total potassium (TK) contents did not change significantly. Long-term continuous cropping decreased the Chao1 index and observed species index and decreased the Shannon index and Simpson index. The change in continuous cropping years had a significant effect on the relative abundance of soil fungal dominant flora. At the phylum level, the relative abundance of Mortierellomycota decreased with the extension of pepper continuous cropping years, the relative abundance of Ascomycota increased first and then decreased, and the relative abundance of Basidiomycota decreased first and then increased. At the genus level, with the increasing of pepper continuous cropping years, the relative abundance of Fusarium increased, and the relative abundance of Mortierella and Penicillium decreased. In addition, long-term continuous cropping simplified the soil fungal symbiosis network. CCA analysis indicated that pH, OM, TN, AN, AP, and AK were the driving factors of soil fungal community structure, and correlation network analysis showed that pH, OM, TN, TP, TK, AN, AP, and AK were the driving factors of soil fungal community structure, including Fusarium, Lophotrichus, Penicillium, Mortierella, Botryotrichum, Staphylotrichum, Plectosphaerella, and Acremonium. In conclusion, continuous cropping changed the soil physical and chemical properties, affected the diversity and community structure of the soil fungal community, changed the interaction between microorganisms, and destroyed the microecological balance of the soil, which might explain obstacles associated with continuous cropped pepper.

Metabolic Profiling Early Post-Allogeneic Haematopoietic Cell Transplantation in the Context of CMV Infection

Immune dysfunction resulting from allogeneic haematopoietic stem cell transplantation (aHSCT) predisposes one to an elevated risk of cytomegalovirus (CMV) infection. Changes in metabolism have been associated with adverse outcomes, and in this study, we explored the associations between metabolic profiles and post-transplantation CMV infection using plasma samples collected 7-33 days after aHSCT. We included 68 aHSCT recipients from Rigshospitalet, Denmark, 50% of whom experienced CMV infection between days 34-100 post-transplantation. First, we investigated whether 12 metabolites selected based on the literature were associated with an increased risk of post-transplantation CMV infection. Second, we conducted an exploratory network-based analysis of the complete metabolic and lipidomic profiles in relation to clinical phenotypes and biological pathways. Lower levels of trimethylamine N-oxide were associated with subsequent CMV infection (multivariable logistic regression: OR = 0.63; 95% CI = [0.41; 0.87]; p = 0.01). Explorative analysis revealed 12 clusters of metabolites or lipids, among which one was predictive of CMV infection, and the others were associated with conditioning regimens, age upon aHSCT, CMV serostatus, and/or sex. Our results provide evidence for an association between the metabolome and CMV infection post-aHSCT that is independent of known risk factors.

Deciphering the microbial community structures and functions of wastewater treatment at high-altitude area

Introduction: The proper operation of wastewater treatment plants is a key factor in maintaining a stable river and lake environment. Low purification efficiency in winter is a common problem in high-altitude wastewater treatment plants (WWTPs), and analysis of the microbial community involved in the sewage treatment process at high-altitude can provide valuable references for improving this problem. Methods: In this study, the bacterial communities of high- and low-altitude WWTPs were investigated using Illumina high-throughput sequencing (HTS). The interaction between microbial community and environmental variables were explored by co-occurrence correlation network. Results: At genus level, Thauera (5.2%), unclassified_Rhodocyclaceae (3.0%), Dokdonella (2.5%), and Ferribacterium (2.5%) were the dominant genera in high-altitude group. The abundance of nitrogen and phosphorus removal bacteria were higher in high-altitude group (10.2% and 1.3%, respectively) than in low-altitude group (5.4% and 0.6%, respectively). Redundancy analysis (RDA) and co-occurrence network analysis showed that altitude, ultraviolet index (UVI), pH, dissolved oxygen (DO) and total nitrogen (TN) were the dominated environmental factors (p < 0.05) affecting microbial community assembly, and these five variables explained 21.4%, 20.3%, 16.9%, 11.5%, and 8.2% of the bacterial assembly of AS communities. Discussion: The community diversity of high-altitude group was lower than that of low-altitude group, and WWTPs of high-altitude aeras had a unique microbial community structure. Low temperature and strong UVI are pivotal factors contributing to the reduced diversity of activated sludge microbial communities at high-altitudes.

The TaGSK1, TaSRG, TaPTF1, and TaP5CS Gene Transcripts Confirm Salinity Tolerance by Increasing Proline Production in Wheat (Triticum aestivum L.)

Salinity is an abiotic stress factor that reduces yield and threatens food security in the world's arid and semi-arid regions. The development of salt-tolerant genotypes is critical for mitigating yield losses, and this journey begins with the identification of sensitive and tolerant plants. Numerous physiologic and molecular markers for detecting salt-tolerant wheat genotypes have been developed. One of them is proline, which has been used for a long time but has received little information about proline-related genes in wheat genotypes. In this study, proline content and the expression levels of proline-related genes (TaPTF1, TaDHN, TaSRG, TaSC, TaPIMP1, TaMIP, TaHKT1;4, TaGSK, TaP5CS, and TaMYB) were examined in sensitive, moderate, and tolerant genotypes under salt stress (0, 50, 150, and 250 mM NaCl) for 0, 12, and 24 h. Our results show that salt stress increased the proline content in all genotypes, but it was found higher in salt-tolerant genotypes than in moderate and sensitive genotypes. The salinity stress increased gene expression levels in salt-tolerant and moderate genotypes. While salt-stress exposure for 12 and 24 h had a substantial effect on gene expression in wheat, TaPTF1, TaPIMP1, TaMIP, TaHKT1;4, and TaMYB genes were considerably upregulated in 24 h. The salt-tolerant genotypes showed a higher positive interaction than a negative interaction. The TaPTF1, TaP5CS, TaGSK1, and TaSRG genes were found to be more selective than the other analyzed genes under salt-stress conditions. Despite each gene's specific function, increasing proline biosynthesis functioned as a common mechanism for separating salt tolerance from sensitivity.

[Characteristics of Microbial Community Structure in the Surrounding Farmlands of a Mercury Mining Area and Its Environmental Driving Factors]

In order to investigate the characteristics of soil microbial community structure and their relationships with environmental factors in the surrounding farmlands of a mercury mining region, we analyzed soil physical and chemical properties, Hg pollution, enzyme activity, and microbial community structure characteristics in the surrounding farmlands of a mercury mining region in Tong Ren (Bahuang Town, Bijiang District; Huaqiao Town, Shiqian County; Kaide Town, Jiangkou County; and Chuantong town, Bijiang District; referred to as BJ, SQ, JK, and TR, respectively). The relationships between the characteristics of soil microbial community structure and environmental factors were determined using redundancy analysis (RDA) and correlation network analysis. The results showed that the degree of soil Hg contamination varied depending on the sampling locations in the study region. The soils in JK and TR were categorized as having light-level Hg contamination, whereas those in SQ and BJ were at moderate-level Hg contamination. The potential ecological risk indicated that the soil suffered different degrees of Hg contamination (TR was at a medium level, BJ and JK were at a serious level, and SQ was at a high severe level of pollution). The dominant bacteria flora were Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi, whereas the dominant flora of fungi included Ascomycota, Basidiomycota, and Mortierellomycota. RDA analysis showed that pH, sucrase (SC), and catalase (CAT) activities were the key environmental factors of soil bacterial community structure. Soil pH, available nitrogen (AN), available potassium (AK), HCl-Hg, acid phosphatase (ACP), and urease (URE) activities were the key environmental factors that affected soil fungal community structure. Correlation network analysis indicated that pH, available phosphorus (AP), HCl-Hg, SC, ACP, and CAT were the key environmental factors affecting soil bacterial community structure, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Rokubacteria, and Planctomycetes. AK, pH, total nitrogen (TN), AP, AN, ACP, URE, and SC activities were the key environmental factors affecting soil fungal community structure, such as Ascomycota, Basidiomycota, Mortierellomycota, Glomeromycota, Chytridiomycota, Rozellomycota, Kickxellomycota, and Mucoromycota.

Metabolic Profiling and Metabolite Correlation Network Analysis Reveal That Fusarium solani Induces Differential Metabolic Responses in Lotus japonicus and Lotus tenuis against Severe Phosphate Starvation

Root fungal endophytes are essential mediators of plant nutrition under mild stress conditions. However, variations in the rhizosphere environment, such as nutrient depletion, could result in a stressful situation for both partners, shifting mutualistic to nonconvenient interactions. Mycorrhizal fungi and dark septate endophytes (DSEs) have demonstrated their ability to facilitate phosphate (Pi) acquisition. However, few studies have investigated other plant-fungal interactions that take place in the root environment with regard to phosphate nutrition. In the present research work, we aimed to analyze the effect of extreme Pi starvation and the fungal endophyte Fusarium solani on the model Lotus japonicus and the crop L. tenuis. We conducted metabolomics analysis based on gas chromatography-mass spectrometry (GC-MS) on plant tissues under optimal conditions, severe Pi starvation and F.solani presence. By combining statistical and correlation network analysis strategies, we demonstrated the differential outcomes of the two plant species against the combination of treatments. The combination of nutritional stress and Fusarium presence activated significant modifications in the metabolism of L. japonicus affecting the levels of sugars, polyols and some amino acids. Our results display potential markers for further inspection of the factors related to plant nutrition and plant-fungal interactions.

Signal Deconvolution and Noise Factor Analysis Based on a Combination of Time-Frequency Analysis and Probabilistic Sparse Matrix Factorization

Nuclear magnetic resonance (NMR) spectroscopy is commonly used to characterize molecular complexity because it produces informative atomic-resolution data on the chemical structure and molecular mobility of samples non-invasively by means of various acquisition parameters and pulse programs. However, analyzing the accumulated NMR data of mixtures is challenging due to noise and signal overlap. Therefore, data-cleansing steps, such as quality checking, noise reduction, and signal deconvolution, are important processes before spectrum analysis. Here, we have developed an NMR measurement informatics tool for data cleansing that combines short-time Fourier transform (STFT; a time-frequency analytical method) and probabilistic sparse matrix factorization (PSMF) for signal deconvolution and noise factor analysis. Our tool can be applied to the original free induction decay (FID) signals of a one-dimensional NMR spectrum. We show that the signal deconvolution method reduces the noise of FID signals, increasing the signal-to-noise ratio (SNR) about tenfold, and its application to diffusion-edited spectra allows signals of macromolecules and unsuppressed small molecules to be separated by the length of the T₂* relaxation time. Noise factor analysis of NMR datasets identified correlations between SNR and acquisition parameters, identifying major experimental factors that can lower SNR.

Dietary Bioactive Lipid Compounds Rich in Menthol Alter Interactions Among Members of Ruminal Microbiota in Sheep

This study aimed to investigate the effects of two practically relevant doses of menthol-rich plant bioactive lipid compounds (PBLC) on fermentation, microbial community composition, and their interactions in sheep rumen. Twenty-four growing Suffolk sheep were divided into three treatments and were fed hay ad libitum plus 600 g/d of concentrate containing no PBLC (Control) or PBLC at low dose (80 mg/d; PBLC-L) or high dose (160 mg/d; PBLC-H). After 4 weeks on the diets, samples of ruminal digesta were collected and analyzed for short-chain fatty acid (SCFA), ammonia, and microbiota; microbiota being analyzed in the solid and the liquid digesta fractions separately. Ruminal SCFA and ammonia concentrations were not affected by the PBLC treatments. The microbiota in the solid fraction was more diverse than that in the liquid fraction, and the relative abundance of most taxa differed between these two fractions. In the solid fraction, phylogenetic diversity increased linearly with increased PBLC doses, whereas evenness (lowest in PBLC-L) and Simpson diversity index (greatest in PBLC-H) changed quadratically. In the liquid fraction, however, the PBLC supplementation did not affect any of the microbial diversity measurements. Among phyla, Chloroflexi (highest in PBLC-L) and unclassified_bacteria (lowest in PBLC-L) were altered quadratically by PBLC. Lachnospiraceae, Bacteroidaceae (increased linearly), BS11 (increased in PBLC-L), Christensenellaceae (decreased in PBLC treatments), and Porphyromonadaceae (increased in PBLC treatments) were affected at the family level. Among genera, Butyrivibrio increased linearly in the solid fraction, YRC22 increased linearly in the liquid fraction, whereas Paludibacter increased and BF311 increased linearly with increasing doses of PBLC in both fractions. The PBLC treatments also lowered methanogens within the classes Thermoplasmata and Euryarchaeota. Correlation network analysis revealed positive and negative correlations among many microbial taxa. Differential network analysis showed that PBLC supplementation changed the correlation between some microbial taxa and SCFA. The majority of the predicted functional features were different between the solid and the liquid digesta fractions, whereas the PBLC treatments altered few of the predicted functional gene categories. Overall, dietary PBLC treatments had little influence on the ruminal fermentation and microbiota but affected the associations among some microbial taxa and SCFA.

A correlation network analysis of dissociative experiences

The interrelationships between the symptom domains of dissociation, such as the loss of continuity in subjective experience, the inability to access personal information, and the distortions about the perception of self and the environment, need to be better understood. In the current study, 2274 adults from Italy completed the Dissociative Experiences Scale-II (DES-II), and their responses were examined within a correlation network analysis framework. Fifteen dissociative experiences showed the strongest associations with the other dissociative experiences included in the measure, and they were selected for further analysis. A partial correlation network was calculated to reveal the associations between such experiences, and a community detection analysis was used to explore whether they formed distinct clusters in the network. Subsequently, a Bayesian network was estimated to examine the direction of the associations among the dissociative experiences, and a directed acyclic graph (DAG) was generated to estimate a potentially causal model of their relationships. The community detection analysis revealed three clusters of experiences that were conceptualized in terms of trance, experiential disconnectedness, and segregated behaviors. Dissociative amnesia was a common denominator of all the three clusters. The analysis of the DAG further suggested that dissociation can be conceptualized as a network in which dissociative experiences are layered into groups of symptoms that interact among them. Cognizance of the configuration and interactions among the dissociative domains and their related symptoms may be critical for better understanding the internal logic behind the dissociative processes and for addressing them effectively in clinical practice.

Covariation and phenotypic integration in chemical communication displays: biosynthetic constraints and eco-evolutionary implications

Chemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking. We assessed the phenotypic integration of CCDs in a meta-analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules. Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated than those of plants (i.e. stronger covariation), suggesting that animals communicate via fixed proportions among compounds. Both plant and animal CCDs were composed of modules, which are groups of strongly covarying compounds. Biosynthetic similarity of compounds revealed biosynthetic constraints in the covariation patterns of plant CCDs. We provide a novel perspective on chemical communication and a basis for future investigations on structural properties of CCDs. This will facilitate identifying modules and biosynthetic constraints that may affect the outcome of selection and thus provide a predictive framework for evolutionary trajectories of CCDs in plants and animals.

Nuclear magnetic resonance-based metabolomics approach to evaluate preventive and therapeutic effects of Gastrodia elata Blume on chronic atrophic gastritis

Chronic atrophic gastritis (CAG) is one of the most common digestive system diseases worldwide which defined by WHO as initial step of cancer. Gastrodia elata Blume (GEB) is a traditional herbal with multiple pharmacological activities which was widely used in Asian countries. This study aims to explore the preventive and therapeutical effects of Gastrodia elata Blume on auto-immune induced CAG in rats. Tissues of stomachs were collected and submitted to ¹H NMR-based metabolomics analysis and histopathological inspection. The biochemical indexes of MDA, SOD, GSH, NO and XOD were measured. Gastrodia elata Blume could apparently ameliorate the damaged gastric glands and the biochemical parameters, enhance gastric acid secretion, and significantly relieve the inflammation of the stomach. Orthogonal signal correction-partial least squares-discriminant analysis (OSC-PLS-DA) of NMR profiles and correlation network analysis revealed that Gastrodia elata Blume could effectively treat CAG via regulating energy and purine metabolisms, and by anti-oxidation and anti-inflammation effects.

Nuclear Magnetic Resonance-Based Metabolomics Approach to Evaluate the Prevention Effect of Camellia nitidissima Chi on Colitis-Associated Carcinogenesis

Colorectal cancer (CRC) is one of the most common malignant tumors worldwide, occurring in the colon or rectum portion of large intestine. With marked antioxidant, anti-inflammation and anti-tumor activities, Camellia nitidissima Chi has been used as an effective treatment of cancer. The azoxymethane/dextran sodium sulfate (AOM/DSS) induced CRC mice model was established and the prevention effect of C. nitidissima Chi extracts on the evolving of CRC was evaluated by examination of neoplastic lesions, histopathological inspection, serum biochemistry analysis, combined with nuclear magnetic resonance (NMR)-based metabolomics and correlation network analysis. C. nitidissima Chi extracts could significantly inhibit AOM/DSS induced CRC, relieve the colonic pathology of inflammation and ameliorate the serum biochemistry, and could significantly reverse the disturbed metabolic profiling toward the normal state. Moreover, the butanol fraction showed a better efficacy than the water-soluble fraction of C. nitidissima Chi. Further development of C. nitidissima Chi extracts as a potent CRC inhibitor was warranted.

Tumor-infiltrating T lymphocytes improve clinical outcome of therapy-resistant neuroblastoma

Neuroblastoma grows within an intricate network of different cell types including epithelial, stromal and immune cells. The presence of tumor-infiltrating T cells is considered an important prognostic indicator in many cancers, but the role of these cells in neuroblastoma remains to be elucidated. Herein, we examined the relationship between the type, density and organization of infiltrating T cells and clinical outcome within a large collection of neuroblastoma samples by quantitative analysis of immunohistochemical staining. We found that infiltrating T cells have a prognostic value greater than, and independent of, the criteria currently used to stage neuroblastoma. A variable in situ structural organization and different concurrent infiltration of T-cell subsets were detected in tumors with various outcomes. Low-risk neuroblastomas were characterized by a higher number of proliferating T cells and a more structured T-cell organization, which was gradually lost in tumors with poor prognosis. We defined an immunoscore based on the presence of CD3⁺, CD4⁺ and CD8⁺ infiltrating T cells that associates with favorable clinical outcome in MYCN-amplified tumors, improving patient survival when combined with the v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN) status. These findings support the hypothesis that infiltrating T cells influence the behavior of neuroblastoma and might be of clinical importance for the treatment of patients.

Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation

Although hepatic encephalopathy (HE) is linked to the gut microbiota, stool microbiome analysis has not found differences between HE and no-HE patients. This study aimed to compare sigmoid mucosal microbiome of cirrhotic patients to controls, between HE vs. no-HE patients, and to study their linkage with cognition and inflammation. Sixty cirrhotic patients (36 HE and 24 no-HE) underwent cognitive testing, stool collection, cytokine (Th1, Th2, Th17, and innate immunity), and endotoxin analysis. Thirty-six patients (19 HE and 17 no-HE) and 17 age-matched controls underwent sigmoid biopsies. Multitag pyrosequencing (including autochthonous genera, i.e., Blautia, Roseburia, Fecalibacterium, Dorea) was performed on stool and mucosa. Stool and mucosal microbiome differences within/between groups and correlation network analyses were performed. Controls had significantly higher autochthonous and lower pathogenic genera compared with cirrhotic patients, especially HE patients. HE patients had worse MELD (model for end-stage liver disease) score and cognition and higher IL-6 and endotoxin than no-HE. Mucosal microbiota was different from stool within both HE/no-HE groups. Between HE/no-HE patients, there was no difference in stool microbiota but mucosal microbiome was different with lower Roseburia and higher Enterococcus, Veillonella, Megasphaera, and Burkholderia abundance in HE. On network analysis, autochthonous genera (Blautia, Fecalibacterium, Roseburia, and Dorea) were associated with good cognition and decreased inflammation in both HE/no-HE, whereas genera overrepresented in HE (Enterococcus, Megasphaera, and Burkholderia) were linked to poor cognition and inflammation. Sigmoid mucosal microbiome differs significantly from stool microbiome in cirrhosis. Cirrhotic, especially HE, patients' mucosal microbiota is significantly different from controls with a lack of potentially beneficial autochthonous and overgrowth of potentially pathogenic genera, which are associated with poor cognition and inflammation.