Carbon Metabolic Pathways Research Articles

Oxygen sensing regulation mechanism of Thauera bacteria in simultaneous nitrogen and phosphorus removal process

Thauera is a genus of denitrifying and phosphorus-accumulating bacteria used for removing nitrogen and phosphorus from wastewater. Dissolved oxygen is one of the main factors affecting denitrification and phosphorus accumulation, and there is currently little research on the oxygen sensing regulation mechanism of Thauera bacteria. We studied denitrifying phosphorus accumulation and gene transcription expression of Thauera sp. RT1901 in anaerobic, microaerobic, and aerobic environments and analyzed the protein structure and regulation mode of two oxygen-sensing systems. The results showed that the strain could achieve the similar denitrification and phosphorus accumulation effect in microaerobic environment as in anaerobic environment. Transcriptome analysis showed that as the oxygen concentration continued to rise, the core carbon and phosphorus metabolism pathways of the strain remained unchanged, and the respiratory system shifted from nitrate respiration to aerobic respiration, thereby inhibiting the denitrification pathway. The fumarate nitrate reduction (FNR) protein and FixLJ two-component system performed oxygen sensing to jointly regulate the expression of respiratory genes. The FNR protein formed a dimer in an anaerobic environment, activating denitrification-related genes and inhibiting cytochrome oxidase-related genes. The FixLJ system conducted signal transduction through phosphorylation in a low oxygen environment and activated the transcription of the fixK gene. The FixK protein has a similar structure and function as the FNR protein but is not directly affected by oxygen. These results reveal the oxygen sensing regulation mechanism of Thauera sp. RT1901 in the denitrification and phosphorus accumulation process, providing new insights for further studying the functions of this genus of bacteria in wastewater treatment systems.

Efficient and Economic Utilization of Cellobiose for Glycosylation Modification by Regulating Carbon Source Supply and Metabolic Pathway In Vivo.

Glycosylation, one of the most common and significant modifications in nature, has prompted the development of a cellobiose phosphorolysis route for glycosylation in vivo. However, the process of glycosylation is hampered by the notably low conversion rate of cellobiose. In this work, regulation of the carbon source supply by changing the ratio of glucose to cellobiose improved the conversion rate of cellobiose, resulting in enhancing the efficiency of glycosylation and the production of vitexin. Moreover, three genes (pgm, agp, and ushA) involved in the degradation of UDP-glucose were knocked out to relieve the degradation and diversion of the cellobiose phosphorolysis route. Finally, through the optimization of conversion conditions, we observed a continuous enhancement in cellobiose conversion rate and vitexin production in BL21ΔushAΔagp-TcCGT-CepA, corresponding to an increased concentration of added glucose. The maximum production of vitexin reached 2228 mg/L with the addition of 2 g/L cellobiose and 6 g/L glucose, which was 312% of that in BL21-TcCGT-CepA with the addition of 2 g/L cellobiose. The conversion rate of cellobiose in BL21ΔushAΔagp-TcCGT-CepA reached 88%, which was the highest conversion rate of cellobiose to date. Therefore, this study presents a cost-effective and efficient method to enhance the conversion rate of cellobiose during the glycosylation process.

Multi-omics analysis reveals the mechanism underlying the dimorphic formation of Saccharomycopsis fibuligera during dough fermentation

To unravel the mechanism underlying the dimorphic formation of Saccharomycopsis fibuligera during dough fermentation, we assembled a high-quality chromosome-scale genome and conducted comparative genomic analysis. Furthermore, we examined the differences between the yeast-like cells and hyphae at both transcriptome and metabolome levels. The completed S. fibuligera ACX0001 genome of 19.29 Mb comprised seven chromosomes and contained 6115 predicted protein-coding genes. Comparative genomic analysis revealed that S. fibuligera possessed 51 unique gene families comprising 85 annotated genes. The advantageous genes related to carbon metabolism pathway were accumulated in S. fibuligera during evolution, including the unique genes encoding glycosyl hydrolases such as glucan endo-1,3-β glucosidase, which distinguished it from the other yeasts. Transcriptomic and metabolomic analysis identified 568 differentially expressed genes and 109 differentially abundant metabolites between the yeast-like cells and hyphae, respectively. In response to the dough environment, S. fibuligera activated the expression of the glucan endo-1,3-β glucosidase, which can soften the cell wall and promote germination of yeast-like cells. Simultaneously, the flux of acetyl-CoA was redirected towards fatty acid and steroid biosynthesis in S. fibuligera, which influenced the production of quorum-sensing molecules, thereby contributing to the dimorphic transition. Therefore, the dimorphic growth of S. fibuligera was collectively governed by the glycosyl hydrolase family genes, central carbon metabolism, and quorum-sensing molecules. This study provides a theoretical foundation for the potential application of S. fibuligera in food industry.

Biosynthesis of Ag2Se nanoparticles as a broad-spectrum antimicrobial agent with excellent biocompatibility

Silver (Ag)-containing nanomaterials have emerged as promising alternatives or adjuvants to antibiotics. Ongoing research is dedicated to enhance their antimicrobial efficacy, stability, biocompatibility, and environmental sustainability. Microorganism-synthesized Ag-containing nanomaterials offer distinct advantages, especially for various surface modification, which potentially fulfill these objectives. In this study, we present the synthesis of silver-selenium (Bio-Ag2Se) nanoparticles using a yeast strain, Rhodotorula mucilaginosa PA-1. These Bio-Ag2Se nanoparticles have small size with a narrow size distribution (12.3 ± 2.9 nm) and long-term stability. They demonstrate a broad antimicrobial spectrum and high antimicrobial efficacy at very low concentrations, effectively targeting microorganisms including Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, as well as pathogenic fungus Candida albicans. Furthermore, Bio-Ag2Se nanoparticles exhibit excellent efficacy to inhibit and eliminate biofilms formed by notorious pathogen S. aureus. In contrast, Bio-Ag2Se nanoparticles at effective antibacterial concentrations demonstrate favorable biocompatibility and do not show obvious cytotoxic effects on human and plant cells. To elucidate the antibacterial mechanisms of Bio-Ag2Se nanoparticles against S. aureus and E. coli, transcriptomic analysis and phenotypic examination were employed. The results reveal significant and broad up-regulation in carbon metabolism pathways in both S. aureus and E. coli, suggesting it as one of the major antibacterial mechanisms of Bio-Ag2Se. This study presents a green synthesis strategy for Ag-containing nanoparticles with promising applications.

Metabolomics reveals the mechanism of action of meropenem and amikacin combined in the treatment of Pseudomonas aeruginosa.

The treatment of Pseudomonas aeruginosa infection often involves the combined use of β-lactam and aminoglycoside antibiotics. In this study, we employed metabolomic analysis to investigate the mechanism responsible for the synergistic activities of meropenem/amikacin combination therapy against multidrug-resistant P. aeruginosa strains harboring OXA-50 and PAO genes. Antibiotic concentrations for meropenem (2 mg/L) monotherapy, amikacin (16 mg/L) monotherapy, and meropenem/amikacin (2/16 mg/L) combination therapy were selected based on clinical breakpoint considerations. Metabolomic analysis revealed significant alterations in relevant metabolites involved in bacterial cell membrane and cell wall synthesis within 15 min of combined drug administration. These alterations encompassed various metabolic pathways, including fatty acid metabolism, peptidoglycan synthesis, and lipopolysaccharide metabolism. Furthermore, at 1 h and 4 h, the combination therapy exhibited significant interference with amino acid metabolism, nucleotide metabolism, and central carbon metabolism pathways, including the tricarboxylic acid cycle and pentose phosphate pathway. In contrast, the substances affected by single drug administration at 1 h and 4 h demonstrated a noticeable reduction. Meropenem/amikacin combination resulted in notable perturbations of metabolic pathways essential for survival of P. aeruginosa, whereas monotherapies had comparatively diminished impacts.

An examination of the carbon metabolic pathways in Acinetobacter sp. TAC-1 in the context of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) utilization

The present study aimed to unravel the carbon metabolism pathway of Acinetobacter sp. TAC-1, a heterotrophic nitrification-aerobic denitrification (HN-AD) strain that utilizes poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as a carbon source. Sodium acetate was employed as a control to assess the gene expression of carbon metabolic pathways in the TAC-1 strain. The results of genome sequencing demonstrated that the TAC-1 strain possessed various genes encoding carbon metabolic enzymes, such as gltA, icd, sucAB, acs, and pckA. KEGG pathway database analysis further verified the presence of carbon metabolism pathways, including the glycolytic pathway (EMP), pentose phosphate pathway (PPP), glyoxylate cycle (GAC), and tricarboxylic acid (TCA) cycle in the TAC-1 strain. The differential expression of metabolites derived from distinct carbon sources provided further evidence that the carbon metabolism pathway of TAC-1 utilizing PHBV follows the sequential process of PHBV (via the PPP pathway)→gluconate (via the EMP pathway)→acetyl-CoA (entering the TCA cycle)→CO2+H2O (generating electron donors and releasing energy). This study is expected to furnish a theoretical foundation for the advancement and implementation of novel denitrification processes based on HN-AD and solid carbon sources.

Adsorption of PCBs on microplastics mitigated greenhouse gas emission by changing C/N metabolism in freshwater sediment

Microplastics (MPs) and polychlorinated biphenyls (PCBs) might coexist in freshwater sediments. However, the effect of the adsorption of PCBs on MPs on greenhouse gas emissions and microbial communities is still not clear. In this paper, incubation experiment was conducted by pre-treating different particle sizes of MPs with and without adsorption of PCBs into the sediments for 30 days. The results showed that the coexistence of MPs and PCBs suppressed carbon dioxide (CO2) emissions. The treatment group without adsorption promoted methane (CH4) emissions by increasing the functional gene of mcrA, mcrB, mcrG, mtbC, and mtmC, while the adsorption attenuates this effect. At the same time, the coexistence of the two pollutants reduced alpha diversity in the sediment, especially when the MPs were small in size and in that with adsorbed PCBs. The principal component analysis showed that the pre-adsorption of PCBs on MPs reduced the differences among microbial communities as compared to that without pre-adsorption. It was also found that the coexistence of MPs and PCBs affected carbon (C) and nitrogen (N) metabolic pathways in the sediment, especially, CH4 metabolism, and increased norC content with the potential to increase nitrous oxide (N2O) emissions. The results suggest that sediment pollution with MPs and PCBs should be paid attention, which is important in affecting greenhouse gas emission and achieving sustainability.

Improving the production of recombinant L-Asparaginase-II in Escherichia coli by co-expressing catabolite repressor activator (cra) gene

Identification of a single genetic target for microbial strain improvement is difficult due to the complexity of the genetic regulatory network. Hence, a more practical approach is to identify bottlenecks in the regulatory networks that control critical metabolic pathways. The present work focuses on enhancing cellular physiology by increasing the metabolic flux through the central carbon metabolic pathway. Global regulator cra (catabolite repressor activator), a DNA-binding transcriptional dual regulator was selected for the study as it controls the expression of a large number of operons that modulate central carbon metabolism. To upregulate the activity of central carbon metabolism, the cra gene was co-expressed using a plasmid-based system. Co-expression of cra led to a 17% increase in the production of model recombinant protein L-Asparaginase-II. A pulse addition of 0.36% of glycerol every two hours post-induction, further increased the production of L-Asparaginase-II by 35% as compared to the control strain expressing only recombinant protein. This work exemplifies that upregulating the activity of central carbon metabolism by tuning the expression of regulatory genes like cra can relieve the host from cellular stress and thereby promote the growth as well as expression of recombinant hosts.

Analysis of immune infiltration and cuproptosis-related genes in acute myocardial infarction

Abstract Background Acute myocardial infarction (AMI) is a major global health concern. The identification of key genes associated with AMI and cuproptosis is crucial for developing effective diagnostic and prognostic tools. Purpose To identify differentially expressed genes (DEGs) associated with AMI, and investigate their correlation with cuproptosis and immune infiltration to improve diagnosis and prognosis. Methods Six datasets (GSE48060, GSE83500, GSE97320, GSE974, GSE19339, and GSE66360) containing normal control and AMI samples were integrated from the Gene Expression Omnibus (GEO) database. DEGs between AMI and control samples were identified and cross-referenced with ferroptosis-associated genes. GO and KEGG analyses were performed to explore the functions and pathways associated with the identified genes. Immune infiltration analysis was also conducted to investigate the correlation between the genes and immune infiltration. An AMI prediction model was constructed using statistical analysis. Results Fifteen DEGs were identified, including nine upregulated and six downregulated genes. Among these genes, 11 were found to be associated with cuproptosis, including SLC31A1, PDHB, PDHA1, LIPT1, LIAS, FDX1, DLS1, DLD, DLAT, DBT, and ATP7B. These genes were mainly enriched in the TCA cycle, pyruvate metabolism, glycolysis/gluconeogenesis, and carbon metabolism pathways. Immune infiltration analysis revealed significant differences in macrophages, Th1 cells, Th2 cells, tumor-infiltrating lymphocytes, cytolytic activity, and MHC class 1 between normal and AMI samples. A correlation between these genes and immune infiltration was also observed. The AMI prognostic model constructed had an AUC of 0.61047. Conclusion Cuproptosis-related genes (SLC31A1, PDHB, PDHA1, LIPT1, LIAS, FDX1, DLS1, DLD, DLAT, DBT, and ATP7B) may play significant roles in AMI and its immune infiltration. The identified genes and pathways could potentially serve as biomarkers for improving the diagnosis and prognosis of AMI.Flow chart of research designCuproptosis-related AMI genes

203 The Effects of Daily Supplementation of Selected Probiotic and Postbiotic on the Microbiome of Adult Cats

Abstract Probiotics, defined as “live microorganisms, which when administered in adequate amounts confer a health benefit on the host” have been shown to beneficially affect health aspects, including body mass index, immune system modulation, and oxidative stress. There are still limited data on the microbiome and the probiotic effects in cats compared with humans. Looking into the feline microbiome could help us understand more about the gut health of these animals. This study was a complete randomized design with 36 cats [mean age = 4.98 1.97 yr; mean body condition score (BCS) = 6.33 1.08] divided into 3 treatments (n = 12/trt). Animals were fed a standard extruded commercial diet. The treatments used were control diet + placebo (maltodextrin carrier; CON), control diet + Probiotic (Bifidobacterium animalis subsp. Lactis CECT8145; daily dosage: CFU/cat; PRO), and control diet + postbiotic (Heat-killed B. animalis subsp. lactis CECT8145; daily dosage: CFU/cat; POST). The objective of this study was to identify and analyze the effects of a selected probiotic and its heat-killed form on the feline microbiome. Fresh fecal samples were collected on days 0 and 90, DNA was extracted and sequenced using the method of ‘Whole Shotgun Sequencing’, abundance comparisons were carried out with the R limma voom package (3.48.3v) to find taxonomic groups and for pathway analysis, it was performed a differential abundance analysis at L3 between day 0 and 90 in each group and abundance comparisons between groups depending on time. Relative abundance of B. animalis increased (P < 0.05) over time in cats in the PRO group, which suggests potential colonization of the B. animalis fed in the live form in the feline gut. Cats in the CON group had an increment abundance of metabolites involved in carbon metabolism pathways and amino acid biosynthesis when compared with PRO and POST, whilst there was a decrease in the abundance of membrane transport, biofilm formation, and bacterial motility pathways in the CON group. In conclusion, the use of the probiotic and postbiotic had a similar effect on the overall feline metabolism, although more studies are needed to determine if B. animalis subsp. Lactis CECT 8145 can induce beneficial outcomes to the feline microbiome.

Effect of HRT on nitrogen removal from low carbon source wastewater enhanced by slurry and its mechanism

Insufficient carbon sources in low-carbon wastewater have consistently hindered nitrogen removal performance. This work utilized slurry after anaerobic digestion as an additional carbon source, and the optimal hydraulic retention time (HRT) parameters were obtained through adjustment. The findings revealed that, under HRT conditions of 24–12 h, the discharge standards of wastewater treatment plants (WWTPs) could be met. It had been proven that HRT 12 h was the more cost-effective parameter for application in WWTPs, and the removal efficiencies for COD, NH4+-N, NO3–-N, and TN reached impressive levels of 82.43%, 95.24%, 77.49%, and 86.70%, respectively. However, the HRT 6 h struggled to achieve efficient wastewater treatment. Mechanistic analysis demonstrated that shortening the HRT resulted in considerably higher microbial richness, diversity, and evenness, causing notable shifts in microbial community structure. Additionally, a shortened HRT reduced the enrichment abundance of key bacterial phyla (Proteobacteria, Bacteroidetes) and genera (Hydrogenophaga, Filimonas, Meganema) that played an important role in nitrogen and organic matter removal. Furthermore, a shortened HRT increased hydraulic shear forces, impeding the enrichment of carbon and nitrogen metabolism pathways, and reducing the abundance of essential genes associated with glycolysis (HK, pfkA, FBA, GAPDH) and nitrogen metabolism processes (narG, narH, narI, norB, nirS, nosZ). It was noteworthy that the microbial community under the HRT 6 h condition carried the highest risk of microbial pathogenicity. This work revealed the optimal parameters, and carbon and nitrogen metabolism mechanism of wastewater treatment systems with slurry as a carbon source for the first time, and provided novel ideas and insights for low-carbon wastewater treatment.

Mycoplasma synoviae lipid-associated membrane proteins identification and expression changes when exposed to chicken cells.

Mycoplasma synoviae is a significant cause of respiratory disease and synovitis among chickens, and has an adverse economic impact on broiler breeding efforts. The present study was designed to develop a systematic understanding of the role that M. synoviae lipid-associated membrane proteins (LAMPs) may play in the virulence of this pathogen. Bioinformatics tools were used to identify 146 predicted membrane proteins and lipoproteins in the M. synoviae proteome. Then, Triton X-114 was used to extract LAMPs that were subsequently identified via LC-MS/MS. This approach enabled the detection of potential LAMPs, and the top 200 most abundant proteins detected using this strategy were subject to further analysis. M. synoviae cells (100 MOI) were exposed to chicken fibroblasts (DF-1) and macrophages (HD-11) in a 1:1 mixed culture. Analysis of LAMP transcripts identified 72 up-regulated LAMP genes which were analyzed in depth by bioinformatics. GO analysis revealed these genes to be enriched in the nucleotide binding, sulfur amino acid transmembrane transporter activity, tRNA binding, rRNA modification, and transition metal ion transport pathways. Moreover, KEGG enrichment analysis suggested that these genes were enriched in the biosynthesis of secondary metabolites, carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism pathways.

High synthetic mechanisms and concentration improvement of menaquinone-7 from Bacillus subtilis subsp.natto

A strain MMH-56 of Bacillus subtilis subsp. natto with a high productivity of menaquinone-7 (MK-7) was obtained by physico-chemical mutagenesis. Transcriptomic analysis demonstrated that the efficient synthesis of MK-7 in strain MMH-56 was correlated to the enhanced central carbon metabolic and shikimate pathways, along with the activated fatty acid metabolic pathway in the MK-7 synthesis process. Especially, the expressions of menA, menB, menD, and menE in the shikimate pathway were upregulated; while, AroA, AroC, AroH, AroK, and TyrA were down-regulated, compared to the wild-type. Such ingenious regulations released the feedback-inhibition of MK-7 synthesis from aromatic amino acids, and promoted the biosynthesis of MK-7. Additionally, fermentation medium for MK-7 production were further optimized by response surface methodology. A final concentration of 161.74 mg/L MK-7 was acquired, which was 62.93-fold higher than the wild-type. Such productivity was sufficient for the industrial production of MK-7.

270 Cellular Response to Heat Exposure: Influences on the Growth Potential of Bovine Skeletal Muscle and Adipose Tissue

Abstract Our lack of understanding regarding how heat exposure affects major tissue growth and meat attributes impedes our ability to counteract more frequent climate extremes and promote profitability in the beef cattle industry. The objective of the study was to determine pathways that heat shock proteins (HSPs) regulate in beef cattle’s skeletal muscle and adipose tissue growth and metabolism. Bovine satellite cells (BSCs) were isolated from the longissimus muscle of 3-month-old Holstein bulls (n = 5). Preadipose cells were isolated from the subcutaneous fat of 18-month-old Angus steers (n = 5) and induced adipogenic differentiation. Satellite, myofibers, and adipose cells were incubated at 38°C (control; CON), 39.5°C (moderate heat stress; MHS), and 41°C (extreme heat stress; EHS) and harvested for mRNA gene expressions, protein level, proteomics, immunostaining. Heat exposure cued bovine satellite cell proliferation and may increase the self-renewing satellite cell population. After 3 h of heat exposure, the mRNA gene expression and protein levels of Pax3 and Myf5 were downregulated, while HSPs 20, 27, 70, and 90 were upregulated. Small heat shock proteins, especially HSP27, appear to be essential in regulating satellite cell activity under heat stress. When HSP27 knock-down BSCs were exposed to EHS for 3 h, Myf5 gene expressions and protein levels returned to normal. This may indicate that HSP27 directly regulates Myf5 under heat stress and temporarily activates the self-renewal mechanism instead of committing myogenic differentiation. Results from proteomics showed that pathways related to oxidative phosphorylation, NADH dehydrogenase activity, and transmembrane transport were upregulated by EHS while MHS upregulated biosynthesis of amino acids, PI3K-Akt signaling pathway. Heat exposure during myogenic differentiation of satellite cells seemingly stimulates the commitment of myogenesis. Heat treatments increased mRNA gene expressions of IGF I, MHC I, MyoD, and myogenin and protein levels. Heat exposure also improved the muscle protein synthesis pathway by regulating the phosphorylation of mTOR, Akt, and P70S6. Heat stress triggered adipogenic differentiation and lipid storage, followed by increased expression of HSP. Extreme heat stress increased adipose cell growth by upregulating C/EBPα and PPARγ, key regulators of adipogenesis. Lipogenic genes FAS and SCD were also increased, accompanied by HSPs. Adipocytes exposed to EHS also increased intracellular lipid accumulation. Proteomic analysis revealed that carbon and pyruvate metabolism pathways were upregulated by MHS, whereas glycolysis/ gluconeogenesis, protein processing in the endoplasmic reticulum, RNA transport, and biosynthesis of amino acids were upregulated by EHS. Cellular mechanisms related to skeletal muscle hypertrophy and adipose tissue growth are responsive in in-vitro settings; however, the results are controversial depending on cell type and animal species. Various factors such as metabolic, hormonal, and immunologic regulation need to be considered to accurately assess the effect of HS on the postnatal growth of major tissues at the animal level.

Transcriptomic and metabolomic analyses to study the key role by which Ralstonia insidiosa induces Listeria monocytogenes to form suspended aggregates.

Ralstonia insidiosa can survive in a wide range of aqueous environments, including food processing areas, and is harmful to humans. It can induce Listeria monocytogenes to form suspended aggregates, resulting from the co-aggregation of two bacteria, which allows for more persistent survival and increases the risk of L. monocytogenes contamination. In our study, different groups of aggregates were analyzed and compared using Illumina RNA sequencing technology. These included R. insidiosa under normal and barren nutrient conditions and in the presence or absence of L. monocytogenes as a way to screen for differentially expressed genes (DEGs) in the process of aggregate formation. In addition, sterile supernatants of R. insidiosa were analyzed under different nutrient conditions using metabolomics to investigate the effect of nutrient-poor conditions on metabolite production by R. insidiosa. We also undertook a combined analysis of transcriptome and metabolome data to further investigate the induction effect of R. insidiosa on L. monocytogenes in a barren environment. The results of the functional annotation analysis on the surface of DEGs and qPCR showed that under nutrient-poor conditions, the acdx, puuE, and acs genes of R. insidiosa were significantly upregulated in biosynthetic processes such as carbon metabolism, metabolic pathways, and biosynthesis of secondary metabolites, with Log2FC reaching 4.39, 3.96, and 3.95 respectively. In contrast, the Log2FC of cydA, cyoB, and rpsJ in oxidative phosphorylation and ribosomal pathways reached 3.74, 3.87, and 4.25, respectively. Thirty-one key components were identified while screening for differential metabolites, which mainly included amino acids and their metabolites, enriched to the pathways of biosynthesis of amino acids, phenylalanine metabolism, and methionine metabolism. Of these, aminomalonic acid and Proximicin B were the special components of R. insidiosa that were metabolized under nutrient-poor conditions.

Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities

Soil ecosystems are being more contaminated with polyhalogenated carbazoles (PHCZs), which raising much attention about their impact on soil microorganisms. 3-Bromocarbazole (3-BCZ) and 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) are two typical PHCZs with high detection rates in the soil environment. However, ecological risk research on these two PHCZs in soil is still lacking. In the present study, after 80 days of exposure, the ecological influence of 3-BCZ and 1,3,6,8-TBCZ was investigated based on 16S rDNA sequencing, ITS sequencing, gene (16S rDNA, ITS, amoA, nifH, narG and cbbL) abundance and soil enzyme activity. The results showed that the bacterial 16S rDNA gene abundance significantly decreased under 3-BCZ and 1,3,6,8-TBCZ exposure after 80 days of incubation. The fungal ITS gene abundance significantly decreased under 1,3,6,8-TBCZ (10 mg/kg) exposure. PHCZs contributed to the alteration of bacteria and fungi community abundance. Bacteria Sphingomonas, RB41 and fungus Mortierella, Cercophora were identified as the most dominant genera. The two PHCZs consistently decreased the relative abundance of Sphingomonas, Lysobacter, Dokdonella, Mortierella and Cercophora etc at 80th day. These keystone taxa are related to the degradation of organic compounds, carbon metabolism, and nitrogen metabolism and may thus have influence on soil ecological functions. Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. The nitrogen and carbon metabolism pathway were affected by 3-BCZ and 1,3,6,8-TBCZ. The soil nitrogen-related functions of aerobic ammonia oxidation were decreased but the soil carbon-related functions of methanol oxidation, fermentation, and hydrocarbon degradation were increased at 80th day. The effects of 3-BCZ and 1,3,6,8-TBCZ on the abundances of the amoA, nifH, narG, and cbbL genes showed a negative trend. These results elucidate the ecological effects of PHCZs and extend our knowledge on the structure and function of soil microorganisms in PHCZ-contaminated ecosystems.

Anaerobic production and biosynthesis mechanism of exopolysaccharides in Schizophyllum commune 20R-7-F01

Exopolysaccharides (EPS) produced by microorganisms play a vital role in physiological and ecological processes. However, the mechanisms of EPS synthesis and release in anaerobic environments remain poorly understood. Here, we provide the first evidence of anaerobic EPS synthesis by the fungus Schizophyllum commune 20R-7-F01, isolated from coal-bearing sediments ~2.0 km below the seafloor. Under anaerobic conditions, the fungus exhibited significantly higher specific EPS production (1.57 times) than under aerobic conditions. Transcriptomic analysis revealed 2057 differentially expressed genes (DEGs) in the strain cultured anaerobically for 7 days compared to aerobically. Among these genes, 642 were significantly upregulated, while 1415 were significantly downregulated, mainly associated with carbon metabolism pathways. Genes involved in glycolysis and EPS synthesis, including hexokinase (HK), phosphoglucomutase (PGM), and (1 → 3)-β-glucan synthase (GLS), were significantly upregulated, while those related to the TCA cycle, respiratory chain, and pentose phosphate pathway were downregulated under anaerobic conditions. These findings highlight the oxygen-dependent regulation of EPS synthesis and suggest that EPS may serve as a key mechanism for fungal adaptation to anaerobic environments.

Candida auris-macrophage cellular interactions and transcriptional response.

The pathogenic yeast Candida auris represents a global threat of the utmost clinical relevance. This emerging fungal species is remarkable in its resistance to commonly used antifungal agents and its persistence in the nosocomial settings. The innate immune system is one the first lines of defense preventing the dissemination of pathogens in the host. C. auris is susceptible to circulating phagocytes, and understanding the molecular details of these interactions may suggest routes to improved therapies. In this work, we examined the interactions of this yeast with macrophages. We found that macrophages avidly phagocytose C. auris; however, intracellular replication is not inhibited, indicating that C. auris resists the killing mechanisms imposed by the phagocyte. Unlike Candida albicans, phagocytosis of C. auris does not induce macrophage lysis. The transcriptional response of C. auris to macrophage phagocytosis is very similar to other members of the CUG clade (C. albicans, C. tropicalis, C. parapsilosis, C. lusitaniae), i.e., downregulation of transcription/translation and upregulation of alternative carbon metabolism pathways, transporters, and induction of oxidative stress response and proteolysis. Gene family expansions are common in this yeast, and we found that many of these genes are induced in response to macrophage co-incubation. Among these, amino acid and oligopeptide transporters, as well as lipases and proteases, are upregulated. Thus, C. auris shares key transcriptional signatures shared with other fungal pathogens and capitalizes on the expansion of gene families coding for potential virulence attributes that allow its survival, persistence, and evasion of the innate immune system.

Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways.

One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S rRNA sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment using reference genomes of PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization by different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.

Labile Metabolite Profiling in Human Blood Using Phosphorus NMR Spectroscopy.

Phosphorus metabolites occupy a unique place in cellular function as critical intermediates and products of cellular metabolism. Human blood is the most widely used biospecimen in the clinic and in the metabolomics field, and hence an ability to profile phosphorus metabolites in blood, quantitatively, would benefit a wide variety of investigations of cellular functions in health and diseases. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the two premier analytical platforms used in the metabolomics field. However, detection and quantitation of phosphorus metabolites by MS can be challenging due to their lability, high polarity, structural isomerism, and interaction with chromatographic columns. The conventionally used 1H NMR, on the other hand, suffers from poor resolution of these compounds. As a remedy, 31P NMR promises an important alternative to both MS and 1H NMR. However, numerous challenges including the instability of phosphorus metabolites, their chemical shift sensitivity to solvent composition, pH, salt, and temperature, and the lack of identified metabolites have so far restricted the scope of 31P NMR. In the current study, we describe a method to analyze nearly 25 phosphorus metabolites in blood using a simple one-dimensional (1D) NMR spectrum. Establishment of the identity of unknown metabolites involved a combination of (a) comprehensively analyzing an array of 1D and two-dimensional (2D) 1H/31P homonuclear and heteronuclear NMR spectra of blood; (b) mapping the central carbon metabolic pathway; (c) developing and using 1H and 31P spectral and chemical shift databases; and finally (d) confirming the putative metabolite peaks with spiking using authentic compounds. The resulting simple 1D 31P NMR-based method offers an ability to visualize and quantify the levels of intermediates and products of multiple metabolic pathways, including central carbon metabolism, in one step. Overall, the findings represent a new dimension for blood metabolite analysis and are anticipated to greatly impact the blood metabolomics field.