Changes In Functional Genes Research Articles

Eutrophication driven macrophyte-derived organic matter decomposition to methane emission relates to co-metabolism effect in freshwater sediments

Lakes and wetlands play pivotal roles in global organic matter storage, receiving significant inputs of organic material. However, the co-metabolic processes governing the decomposition of these organic materials and their impact on greenhouse gas emissions remain inadequately understood. This study aims to assess the effects of mixed decomposition involving macrophytes and cyanobacteria on carbon emissions. A series of microcosms was established to investigate the decomposition of macrophyte residues and algae over a period of 216 days. A two-component kinetic model was utilized to estimate methane (CH4) production rates. Gas isotope technology was employed to discern the contributions of CH4 produced by macrophyte residues or algae. Quantitative PCR and analysis of 16S rRNA gene amplicons were employed to assess changes in functional genes and microbial communities. There were significant differences in the cumulative carbon release from the decomposition of different plant types due to the addition of carbon sources. After adding algae, the cumulative emission of CH4 increased significantly. The δ13C–CH4 partitioning indicated that CH4 originated exclusively from the fresh organic carbon of macrophyte residues, while it shifted to algae source after adding algae. The synergistic effect of the mixed decomposition on the CH4 emissions was greater than the sum of the individual decompositions. The microbial community richness was higher in the single plant residue treatment compared to the mixed treatment with algae addition, while microbial evenness in the sediment increased steadily in each treatment. Our findings emphasize the pronounced co-metabolic effect observed during the mixed decomposition of macrophytes and cyanobacteria.

Responses of Soil Phosphorus Cycling-Related Microbial Genes to Thinning Intensity in Cunninghamia lanceolata Plantations

Background: Microorganisms are important regulators of soil phosphorus cycling and phosphorus availability in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) plantations. However, the effects of thinning on soil phosphorus cycling by microbes in C. lanceolata plantations remain unclear. Methods: We performed a metagenomic sequencing analysis to investigate how thinning intensities (weak, moderate, and heavy) alter phosphorus cycling related microbial genes and their regulatory effects on soil phosphorus availability in C. lanceolata plantations. Results: Following heavy thinning, the contents of available and labile phosphorus increased by 13.8% and 36.9%, respectively, compared to moderate and weak thinning. Moreover, the relative abundance of genes associated with inorganic phosphorus solubilization increased significantly with the increase in thinning intensity, whereas genes associated with phosphorus uptake and transport significantly decreased. The metagenomic analysis results indicate that Acidobacteria (47.6%–53.5%), Proteobacteria (17.9%–19.1%), and Actinobacteria (11.7%–12.8%) are the major contributors to the functional phosphorus cycling genes in the soil. The random forest analysis results suggested that gcd, plc, phoN, ugpA, and phoR were the critical genes involved in the transformation and use of phosphorus, which in turn increased soil phosphorus availability. Structural equation modeling revealed that soil pH was the primary factor influencing changes in functional genes associated with phosphorus cycling in C. lanceolata plantations. Specifically, soil pH (ranging from 4.3 to 4.9) were positively correlated with genes involved in inorganic phosphate solubilization and organic phosphate mineralization, while negatively correlated with genes related to phosphorus uptake and transport. Conclusions: Taken together, our results demonstrate that the enhanced microbe-mediated mineralization of organic phosphorus and solubilization of inorganic phosphorus are suppressed when uptake and transportation are the mechanisms responsible for the increased soil phosphorus availability under appropriate thinning intensities. Changes in the soil microbial community and phosphorus cycling genes in response to different thinning intensities may maintain soil functionality and nutrient balance in C. lanceolata plantations. These findings contribute to a better understanding of the mechanisms underlying the microbial mediation of phosphorus cycling in the soil of C. lanceolata plantations.

Integrated metagenomic and metaproteomic analyses reveal bacterial micro-ecological mechanisms in coral bleaching.

Coral reefs worldwide are facing rapid decline due to coral bleaching. However, knowledge of the physiological characteristics and molecular mechanisms of coral symbionts respond to stress is scarce. Here, metagenomic and metaproteomic approaches were utilized to shed light on the changes in the composition and functions of coral symbiotic bacteria during coral bleaching. The results demonstrated that coral bleaching significantly affected the composition of symbionts, with bacterial communities dominating in bleached corals. Through differential analyses of gene and protein expression, it becomes evident that symbionts experience functional disturbances in response to heat stress. These disturbances result in abnormal energy metabolism, which could potentially compromise the health and resilience of the symbionts. Furthermore, our findings highlighted the highly diverse microbial communities of coral symbionts, with beneficial bacteria providing critical services to corals in stress responses and pathogenic bacteria driving coral bleaching. This study provides comprehensive insights into the complex response mechanisms of coral symbionts under heat stress from the micro-ecological perspective and offers fundamental data for future monitoring of coral health.

Advances in DNA methylation and demethylation in medicinal plants: a review.

DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the DNA sequence. They can thus affect phenotype formation in medicinal plants. However, a comprehensive review of the literature summarizing current research trends in this field is lacking. Thus, this review aims to provide an up-to-date summary of current methods for the detection of 5-mC DNA methylation, identification and analysis of DNA methyltransferases and demethyltransferases, and regulation of DNA methylation in medicinal plants. The data showed that polyploidy and environmental changes can affect DNA methylation levels in medicinal plants. Changes in DNA methylation can thus regulate plant morphogenesis, growth and development, and formation of secondary metabolites. Future research is required to explore the mechanisms by which DNA methylation regulates the accumulation of secondary metabolites in medicinal plants.

Characterization of Hsp17, a Novel Small Heat Shock Protein, in Sphingomonas melonis TY under Heat Stress.

Bacteria are constantly exposed to a variety of environmental stresses. Temperature is considered one of the most important environmental factors affecting microbial growth and survival. As ubiquitous environmental microorganisms, Sphingomonas species play essential roles in the biodegradation of organic contaminants, plant protection, and environmental remediation. Understanding the mechanism by which they respond to heat shock will help further improve cell resistance by applying synthetic biological strategies. Here, we assessed the transcriptomic and proteomic responses of Sphingomonas melonis TY to heat shock and found that stressful conditions caused significant changes in functional genes related to protein synthesis at the transcriptional level. The most notable changes observed were increases in the transcription (1,857-fold) and protein expression (11-fold) of Hsp17, which belongs to the small heat shock protein family, and the function of Hsp17 in heat stress was further investigated in this study. We found that the deletion of hsp17 reduced the capacity of the cells to tolerate high temperatures, whereas the overexpression of hsp17 significantly enhanced the ability of the cells to withstand high temperatures. Moreover, the heterologous expression of hsp17 in Escherichia coli DH5α conferred to the bacterium the ability to resist heat stress. Interestingly, its cells were elongated and formed connected cells following the increase in temperature, while hsp17 overexpression restored their normal morphology under high temperature. In general, these results indicate that the novel small heat shock protein Hsp17 greatly contributes to maintaining cell viability and morphology under stress conditions. IMPORTANCE Temperature is generally considered the most important factor affecting metabolic functions and the survival of microbes. As molecular chaperones, small heat shock proteins can prevent damaged protein aggregation during abiotic stress, especially heat stress. Sphingomonas species are widely distributed in nature, and they can frequently be found in various extreme environments. However, the role of small heat shock proteins in Sphingomonas under high-temperature stress has not been elucidated. This study greatly enhances our understanding of a novel identified protein, Hsp17, in S. melonis TY in terms of its ability to resist heat stress and maintain cell morphology under high temperature, leading to a broader understanding of how microbes adapt to environmental extremes. Furthermore, our study will provide potential heat resistance elements for further enhancing cellular resistance as well as the synthetic biological applications of Sphingomonas.

Long-term nitrogen and phosphorus fertilization reveals that phosphorus limitation shapes the microbial community composition and functions in tropical montane forest soil

Microorganisms govern soil nutrient cycling. It is therefore critical to understand their responses to human-induced increases in N and P inputs. We investigated microbial community composition, biomass, functional gene abundance, and enzyme activities in response to 10-year N and P addition in a primary tropical montane forest, and we explored the drivers behind these effects. Fungi were more sensitive to nutrient addition than bacteria, and the fungal community shift was mainly driven by P availability. N addition aggravated P limitation, to which microbes responded by increasing the abundance of P cycling functional genes and phosphatase activity. In contrast, P addition alleviated P deficiency, and thus P cycling functional gene abundance and phosphatase activity decreased. The shift of microbial community composition, changes in functional genes involved in P cycling, and phosphatase activity were mainly driven by P addition, which also induced the alteration of soil stoichiometry (C/P and N/P). Eliminating P deficiency through fertilization accelerated C cycling by increasing the activity of C degradation enzymes. The abundances of C and P functional genes were positively correlated, indicating the intensive coupling of C and P cycling in P-limited forest soil. In summary, a long-term fertilization experiment demonstrated that soil microorganisms could adapt to induced environmental changes in soil nutrient stoichiometry, not only through shifts of microbial community composition and functional gene abundances, but also through the regulation of enzyme production. The response of the microbial community to N and P imbalance and effects of the microbial community on soil nutrient cycling should be incorporated into the ecosystem biogeochemical model.

Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis.

Heterografting induced intraclonal epigenetic variations were detected among rubber plants. Interaction between genetically divergent root stock and scion tissues might have triggered these epigenetic changes which may eventually lead to intraclonal variability in rubber. DNA methylation in response to stress may be associated with the alteration in gene transcription leading to morphological changes in plants. Rubber tree is commercially propagated by bud grafting where the scion of a high yielding variety is grafted on to a genetically divergent root stock. Still, significant levels of intraclonal variations exist among them. Epigenetic changes associated with heterografting may be partly responsible for this conundrum. In the present study, an attempt was made to identify the impact of divergent root stock on the epigenome of scion in grafted rubber plants. Heterografts were developed by grafting eye buds from a single polyembryony derived seedling on to genetically divergent root stocks of unknown parentage. The plants were uniformly maintained and their DNA was subjected to MSAP analysis. Polymorphic DNA methylation bands corresponding to CG as well as the plant-specific CHG types of methylation were observed. Cloning of selected polymorphic regionsand bisulfite sequencing confirmed the presence of methylation in the promoter and coding region of important genes including an LRR receptor kinase gene. Since divergent root stock is the major factor differentiating the grafted plants, the changes in DNA methylation patterns might have been triggered by the interaction between the two genetically different tissues of stock and scion. The study assumes importance in Hevea, because accumulation and maintenance of epigenetic changes in functional genes and promoters during subsequent cycles of vegetative propagation may contribute towards intraclonal variability eventually leading to altered phenotypes.

Benzyldimethyldodecyl ammonium chloride shifts the proliferation of functional genes and microbial community in natural water from eutrophic lake.

Benzylalkyldimethylethyl ammonium compounds are pervasive in natural environments and toxic at high concentrations. The changes in functional genes and microbial diversity in eutrophic lake samples exposed to benzyldimethyldodecyl ammonium chloride (BAC) were assessed. BAC exerted negative effects on bacteria abundance, particularly at concentrations of 100 μg L-1 and higher. A significant increase in the number of the quaternary ammonium compound-resistant gene qacA/B was recorded within the 10 μg L-1 treatment after the first day of exposure. Not all antibiotic resistance genes increased in abundance as the concentrations of BAC increased; rather, gene abundances were dependent on the gene type, concentrations of BAC, and contact time. The nitrogen fixation-related gene nifH and ammonia monooxygenase gene amoA were inhibited by high concentrations of BAC after the first day, whereas an increase of the nitrite reductase gene nirK was stimulated by exposure. Microbial communities within higher treatment levels (1000 and 10 000 μg L-1) exhibited significantly different community composition compared to other treatment levels and the control. Selective enrichment of Rheinheimera, Pseudomonas, and Vogesella were found in the higher treatment levels, suggesting that these bacteria have some resistance or degradation capacity to BAC. Genes related with RNA processing and modification, transcription, lipid transport and metabolism, amino acid transport and metabolism, and cell motility of microbial community function were involved in the process exposed to the BAC stress.

Combination of metagenomics and culture-based methods to study the interaction between ochratoxin a and gut microbiota.

Gut microbiota represent an important bridge between environmental substances and host metabolism. Here we reported a comprehensive study of gut microbiota interaction with ochratoxin A (OTA), a major food-contaminating mycotoxin, using the combination of metagenomics and culture-based methods. Rats were given OTA (0, 70, or 210 μg/kg body weight) by gavage and fecal samples were collected at day 0 and day 28. Bacterial genomic DNA was extracted from the fecal samples and both 16S rRNA and shotgun sequencing (two main methods of metagenomics) were performed. The results indicated OTA treatment decreased the within-subject diversity of the gut microbiota, and the relative abundance of Lactobacillus increased considerably. Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system, and mismatch repair were observed. To further understand the biological sense of increased Lactobacillus, Lactobacillus selective medium was used to isolate Lactobacillus species from fecal samples, and a strain with 99.8% 16S rRNA similarity with Lactobacillus plantarum strain PFK2 was obtained. Thin-layer chromatography showed that this strain could absorb but not degrade OTA, which was in agreement with the result in metagenomics that no genes related to OTA degradation increased. In conclusion, combination of metagenomics and culture-based methods can be a new strategy to study intestinal toxicity of toxins and find applicable bacterial strains for detoxification. When it comes to OTA, this kind of mycotoxin can cause compositional and functional changes of gut microbiota, and Lactobacillus are key genus to detoxify OTA in vivo.

Viral RNA Trans-Splicing: Chance Event or Product of Evolution?

One year after the discovery of exons and introns in the adenoviral hexon gene by the teams of Roberts and Sharp [1,2], Walther Gilbert suggested that the employment of different exons of a single gene could lead to the generation of various mRNA isoforms [3], a process that is today known as alternative splicing. Alternative splicing implies a number of distinct mechanisms including exon skipping, intron retention, mutually exclusive exons, alternative splice site selection as well as alternative promoter usage and alternative polyadenylation. Constitutive and alternative splicing isn’t mutually exclusive which solves the former problem that for a steady evolutionary process, essential genes don’t need to duplicate before one version can mutate to a new gene function. Alternative splicing generates new functions by creating new exons within existing genes and can relax the negative selection pressure against evolutionary changes in functional genes. Thus, alternative splicing might open nearly neutral paths for evolutionary changes.

NMR-based metabonomic and quantitative real-time PCR in the profiling of metabolic changes in carbon tetrachloride-induced rat liver injury

Carbon tetrachloride (CCl4) is commonly used as a model toxicant to induce chronic and acute liver injuries. In this study, metabolite profiling and gene expression analysis of liver tissues were performed by nuclear magnetic resonance and quantitative real-time polymerase chain reaction to understand the responses of acute liver injury system in rats to CCl4. Acute liver injury was successfully induced by CCl4 as revealed by histopathological results and significant increase in alanine aminotransferase and serum aspartate aminotransferase. We found that CCl4 caused a significant increase in lactate, succinate, citrate, dimethylgycine, choline and taurine. CCl4 also caused a decrease in some of the amino acids such as leucine/isoleucine, glutamine/glutathione and betaine. Gene function analysis revealed that 10 relevant enzyme genes exhibited changes in expressions in the acute liver injury model. In conclusion, the metabolic pathways, including tricarboxylic acid cycle, antioxidant defense systems, fatty acid β-oxidation, glycolysis and choline and mevalonate metabolisms were impaired in CCl4-treated rat livers. These findings provided an overview of the biochemical consequences of CCl4 exposure and comprehensive insights into the metabolic aspects of CCl4-induced hepatotoxicity in rats. These findings may also provide reference of the mechanisms of acute liver injury that could be used to study the changes in functional genes and metabolites.