Search Results (10)

This study explores the effects of afforestation in infertile mountainous areas on soil microbial communities and functional nutrient cycling genes in young Cyclobalanopsis gilva forests, aiming to provide a scientific basis for promoting C. gilva growth. Employing metagenomic sequencing coupled with integrative analyses of microbial community structure and functional genes, this study took 7-year-old C. gilva forest stands in infertile mountainous areas of Shouchang Forest Farm, Zhejiang Province as the research object, using adjacent 7-year-old C. gilva forest in woodland areas as a control, to analyze the differences in soil microbial community structure and nutrient cycling functional genes in the rhizosphere (SCG) and non-rhizosphere (SNR) of infertile mountainous areas, as well as from the rhizosphere (FCG) and non-rhizosphere (FNR) of control woodland areas, and further explore their relationships with the growth of C. gilva. The results indicated that the contents of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and microbial biomass nitrogen (MBN) in SNR were significantly lower than those in FNR by 59.50%, 39.57%, 29.32%, and 53.13%, respectively. Bradyrhizobium and Trebonia were the dominant genera in both site conditions; however, the relative abundance of these genera was lower in infertile mountainous areas compared to the control. Notably, the Shannon and Simpson indices of SCG were significantly lower by 0.49 and 0.01 than those of SNR (p < 0.05), respectively. Additionally, the relative abundances of carbon fixation and nitrogen fixation of SCG were significantly higher than those of SNR. And the relative abundances of functional genes involved in carbon cycling (glyA, fdhA), nitrogen cycling (nasA, narfC, narC, and nirB), and phosphorus cycling (phoB) in infertile mountainous areas were significantly higher than those in the control. The nutrient cycling processes and the expression of functional genes in SCG are coordinately regulated by soil nutrients (SOC and TN) and microbial biomass [MBC (microbial biomass carbon) and MBN]. This work provides a mechanistic foundation for optimizing afforestation strategies and ecological restoration in nutrient-limited mountainous ecosystems, highlighting the critical role of microbial functional plasticity in overcoming edaphic constraints. Full article

Phaeodactylum tricornutum is rich in bioactive substances, rendering it valuable in nutrition and medicine. Epigenetic editing mediated by human RNA demethylase FTO can significantly increase the yields of rice and potato and offers significant potential for the genetic breeding of microalgae. This study aimed to enhance the production of certain metabolites in P. tricornutum via FTO-mediated epigenetic editing. Phenotypic analysis revealed that transgenic P. tricornutum exhibits significantly reduced RNA m⁶A modification levels and faster growth, producing markedly higher levels of lipids, proteins, and carotenoids than the wild type. Transcriptome analysis revealed 1009 upregulated genes and 378 downregulated genes. KEGG analysis demonstrated the upregulated expression of multiple key enzymes involved in long-chain fatty acid synthesis (e.g., ACSL, fabF, and fabG), carotenoid synthesis (e.g., crtQ, PDS, and PSY1), and amino acid synthesis (e.g., dapF, glyA, and aroK) in transgenic P. tricornutum, consistent with our phenotypic results. These results indicate that FTO can promote growth and increase the bioactive compound content in P. tricornutum by regulating the m⁶A modification of RNA, and further suggest that FTO has the potential to serve as a new tool for the epigenetic editing of microalgae. Full article

Bacterial and eukaryotic dihydrofolate reductase (DHFR) enzymes are essential for DNA synthesis and are differentially sensitive to the competitive inhibitors trimethoprim and methotrexate. Unexpectedly, trimethoprim did not reduce Wolbachia abundance, and the wStri DHFR homolog contained amino acid substitutions associated with trimethoprim resistance in E. coli. A phylogenetic tree showed good association of DHFR protein sequences with supergroup A and B assignments. In contrast, DHFR is not encoded by wFol (supergroup E) and wBm (supergroup D) or by genomes of the closely related genera Anaplasma, Ehrlichia, Neorickettsia, and possibly Orientia. In E. coli and humans, DHFR participates in a coupled reactions with the conventional thymidylate synthase (TS) encoded by thyA to produce the dTMP required for DNA synthesis. In contrast, Wolbachia and other Rickettsiales express the unconventional FAD-TS enzyme encoded by thyX, even when folA is present. The exclusive use of FAD-TS suggests that Wolbachia DHFR provides a supplementary rather than an essential function for de novo synthesis of dTMP, possibly reflecting the relative availability of, and competing demands for, FAD and NAD coenzymes in the diverse intracellular environments of its hosts. Whether encoded by thyA or thyX, TS produces dTMP by transferring a methyl group from methylene tetrahydrofolate to dUMP. In the Rickettsiales, serine hydroxymethyltransferase (SMHT), encoded by a conserved glyA gene, regenerates methylene tetrahydrofolate. Unlike thyA, thyX lacks a human counterpart and thus provides a potential target for the treatment of infections caused by pathogenic members of the Rickettsiales. Full article

Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (Lactuca sativa L.) plants were grown under low, medium, and high light intensities. High light intensity remarkably induced the leaf contents of soluble proteins and chlorophylls, whereas it reduced the contents of leaf nitrate. In comparison, medium light intensity exhibited the highest contents of soluble sugar, cellulose, and free amino acids. Meanwhile, light intensity resulted in significant changes in the composition of functional genes but not in the taxonomic compositions of the prokaryotic community (bacteria and archaea) in the phyllosphere. Notably, garden lettuce plants under high light intensity treatment harbored more sulfur-cycling mdh and carbon-cycling glyA genes than under low light intensity, both of which were among the 20 most abundant prokaryotic genes in the leaf phyllosphere. Furthermore, the correlations between prokaryotic functional genes and lettuce leaf metabolite groups were examined to disclose their interactions under varying light intensities. The relative abundance of the mdh gene was positively correlated with leaf total chlorophyll content but negatively correlated with leaf nitrate content. In comparison, the relative abundance of the glyA gene was positively correlated with leaf total chlorophyll and carotenoids. Overall, this study revealed that the functional composition of the phyllosphere prokaryotic community and leaf metabolite groups were tightly linked in response to changing light intensities. These findings provided novel insights into the interactions between plants and prokaryotic microbes in indoor farming systems, which will help optimize environmental management in indoor farms and harness beneficial plant–microbe relationships for crop production. Full article

The application of fermented soybean meal (FSBM) is an effective strategy to alleviate the shortage of fish meal (FM) in aquaculture. However, an excessive substitution ratio often reduces fish growth and induces liver oxidative stress, while the mechanism remains poorly understood. Here, an 8-week feeding trial was conducted in largemouth bass (initial weight: 6.82 ± 0.09 g) to establish an oxidative stress model by replacing 50% of FM with FSBM (fermented by Bacillus subtilis). The results showed that FSBM substitution significantly reduced the growth performance of largemouth bass, including the weight gain rate and specific growth rate. Moreover, FSBM significantly reduced the contents of essential amino acids and total free amino acids in muscle, along with the mRNA expression of amino acids and small peptide transporters. Enzyme activity detection and liver sections showed that FSBM substitution caused liver oxidative stress, indicating the successful construction of an oxidative stress model. An integrated analysis of transcriptomic and metabolomic data revealed that FSBM substitution impaired glycine, serine and threonine metabolism, as well as glutathione metabolism. In addition, the ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG) was decreased in the FSBM group, which may explain the mechanism of oxidative stress caused by FSBM substitution. Considering that glycine is an important component of glutathione synthesis, key genes involved in glycine metabolism (glya, gnmt and agxt) and dietary glycine supplementation should be valued to improve the availability of FSBM. This study reveals for the first time the importance of non-essential amino acids in improving the utilization of plant-based protein sources and provides original insight for the optimization of aquatic feeds. Full article

L-serine is widely used in the food, cosmetic, and pharmaceutical industries. However, the complicated metabolic network and regulatory mechanism of L-serine production lead to the suboptimal productivity of the direct fermentation of L-serine and limits its large-scale industrial production. In this study, a high-yield L-serine production Escherichia coli strain was constructed by a series of defined genetic modification methodologies. First, L-serine-mediated feedback inhibition was removed and L-serine biosynthetic pathway genes (serA^fr, serC, and serB) associated with phosphoglycerate kinase (pgk) were overexpressed. Second, the L-serine conversion pathway was further examined by introducing a glyA mutation (K229G) and deleting other degrading enzymes based on the deletion of initial sdaA. Finally, the L-serine transport system was rationally engineered to reduce uptake and accelerate L-serine export. The optimally engineered strain produced 35 g/L L-serine with a productivity of 0.98 g/L/h and a yield of 0.42 g/g glucose in a 5-L fermenter, the highest productivity and yield of L-serine from glucose reported to date. Furthermore, transcriptome and intermediate metabolite of the high-yield L-serine production Escherichia coli strain were analyzed. The results demonstrated the regulatory mechanism of L-serine production is delicate, and that combined metabolic and bioprocess engineering strategies for L-serine producing strains can improve the productivity and yield. Full article

l-Cysteine is an important sulfur-containing amino acid with numerous applications in the pharmaceutical and cosmetic industries. The microbial production of l-cysteine has received substantial attention, and the supply of the precursor l-serine is important in l-cysteine biosynthesis. In this study, to achieve l-cysteine overproduction, we first increased l-serine production by deleting genes involved in the pathway of l-serine degradation to glycine (serine hydroxymethyl transferase, SHMT, encoded by glyA genes) in strain 4W (with l-serine titer of 1.1 g/L), thus resulting in strain 4WG with l-serine titer of 2.01 g/L. Second, the serine-biosensor based on the transcriptional regulator NCgl0581 of C. glutamicum was constructed in E. coli, and the validity and sensitivity of the biosensor were demonstrated in E. coli. Then 4WG was further evolved through adaptive laboratory evolution (ALE) combined with serine-biosensor, thus yielding the strain 4WGX with 4.13 g/L l-serine production. Moreover, the whole genome of the evolved strain 4WGX was sequenced, and ten non-synonymous mutations were found in the genome of strain 4WGX compared with strain 4W. Finally, 4WGX was used as the starting strain, and deletion of the l-cysteine desulfhydrases (encoded by tnaA), overexpression of serine acetyltransferase (encoded by cysE) and the key enzyme of transport pathway (encoded by ydeD) were performed in strain 4WGX. The recombinant strain 4WGX-∆tnaA-cysE-ydeD can produce 313.4 mg/L of l-cysteine using glycerol as the carbon source. This work provides an efficient method for the biosynthesis of value-added commodity products associated with glycerol conversion. Full article

Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30–40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant. Full article

Gaining an insight into the mechanism underlying antimicrobial-resistance development in Staphylococcus aureus is crucial for identifying effective antimicrobials. We isolated S. aureus sequence type 72 from a patient in whom the S. aureus infection was highly resistant to various antibiotics and lysostaphin, but no known resistance mechanisms could explain the mechanism of lysostaphin resistance. Genome-sequencing followed by subtractive and functional genomics revealed that serine hydroxymethyltransferase (glyA or shmT gene) plays a key role in lysostaphin resistance. Serine hydroxymethyltransferase (SHMT) is indispensable for the one-carbon metabolism of serine/glycine interconversion and is linked to folate metabolism. Functional studies revealed the involvement of SHMT in lysostaphin resistance, as ΔshmT was susceptible to the lysostaphin, while complementation of the knockout expressing shmT restored resistance against lysostaphin. In addition, the ΔshmT showed reduced virulence under in vitro (mammalian cell lines infection) and in vivo (wax-worm infection) models. The SHMT inhibitor, serine hydroxymethyltransferase inhibitor 1 (SHIN1), protected the 50% of the wax-worm infected with wild type S. aureus. These results suggest SHMT is relevant to the extreme susceptibility to lysostaphin and the host immune system. Thus, the current study established that SHMT plays a key role in lysostaphin resistance development and in determining the virulence potential of multiple drug-resistant S. aureus. Full article

Sogunjung-tang (SGJT) is a traditional herbal prescription that has been used in Korea for the treatment of abdominal pain since ancient times. In this study, an analytical method for the simultaneous quantification of 12 marker analytes (gallic acid (GA), albiflorin (ALB), paeoniflorin (PAE), liquiritin apioside (LIAP), liquiritin (PIQ), benzoic acid (BA), coumarin (COU), liquiritigenin (LIQG), cinnamic acid (CINA), benzoylpaeoniflorin (BPAE), cinnamaldehyde (CINAD), and glycyrrhizinic acid (GLYA)) for quality evaluation of SGJT was developed based on high-performance liquid chromatography (HPLC) combined with a photodiode array detector. A Waters SunFire reverse-phased C₁₈ column was used for the chromatographic separation of the 12 marker analytes in SGJT using a two-mobile phases system consisting of 0.1% (v/v) aqueous formic acid and 0.1% (v/v) formic acid in acetonitrile. The developed analytical method was validated by assessment of linearity, limit of detection, limit of quantification, recovery, and precision. Using the developed and validated HPLC method, the 12 marker analytes were determined to be present in 0.10–32.83 mg/g in SGJT. Full article