Search Results (96)

Ulva prolifera (Chlorophyta), a pivotal species in green tide generation, is particularly vulnerable to abiotic stressors, including variations in temperature and light intensity, requiring specific regulatory frameworks for survival. Epigenetic modification is recognized as a molecular mechanism contributing to the flexible adaptability to environmental alterations. In this study, using DNA methylation pattern analysis, we investigated abiotic stress responsive methylation events, as well as gene and pathway expression patterns, in green macroalgae U. prolifera cultured under elevated temperature–light stress (30 °C and 300 µmol photons m⁻² s⁻¹⁾ and identified a negative correlation between CG methylation and gene expression patterns which indicated that abiotic stress caused CG demethylation and afterwards provoked the transcription response. CHG and CHH methylation exhibited an increased mutability and were preeminently found in transposable elements and intergenic regions, possibly contributing to genetic stability by restricting transposon activity. Furthermore, a rapid regeneration through spore ejection and the formation of new thalli was observed, which emphasized its tenacity capacity for stress memory. Our study also revealed an upregulation of genes associated with the glycolysis pathway and highlighted the critical roles of hexokinase, 6-phosphofructokinase-1, and fructose-6-phosphate in triggering glycolysis as a significant stress-adaptive pathway. Overall, these findings suggested that DNA methylation functions as a potential regulatory mechanism, maintaining environmental adaptability, genomic integrity, and underpinning regenerative capacity in U. prolifera. The findings elucidated the molecular resilience of U. prolifera, highlighting its feasibility for sustainable development and biotechnological applications. Full article

In line with the latest challenges, agriculture has many options to protect against stress conditions. Seed-priming treatment was applied to winter wheat genotype AG Hurrem with Dr. Green seed-priming fertilizer, which is a commonly used seed fertilizer containing macro- and microelements. Genome-wide transcriptomic analysis was performed to examine the effects of treatments. In seed-primed plants, defense response pathways such as purine and thiamine metabolism, glutathione pathway, and phenylpropanoid biosynthesis were activated. At the same time, photosynthesis and some cellular respiration processes were downregulated and suppressed. Furthermore, in samples of plants previously exposed to priming and subsequently to drought stress, biochemical pathways activated during seed priming showed positive modulation, thus confirming the long-term traces of the priming effects of previous treatments and their repeated inducibility in the genome, i.e., the presumed existence of stress memory. The in silico analyses were also supported by laboratory antioxidant enzyme activity measurements. The priming technique and the preventive approach that can be offered with it may be a promising option for developing sustainable agricultural production in the future. Full article

We conducted a comparative chromosomal analysis of 10 nominal species and 3 unidentified species in the Simulium striatum group from six countries. A total of 66 chromosomal rearrangements were found, of which 78.8% were inversions. The group is defined by 11 fixed inversions, of which 6 are unique, supporting the monophyletic status previously indicated by morphological and molecular characters. Only 1 of the 13 taxa had a unique fixed chromosomal rearrangement. Although the group demonstrates significant macrogenomic reorganization, subsequent speciation occurred largely without chromosomal rearrangement. The results conflict with the pattern seen in all other species groups of Simuliidae, in which one or more diagnostic rearrangements are typically expressed among species in the same group. The chromosomes provide limited evidence that four entities are valid species but no evidence for the nine others. The weight of evidence from combined chromosomal, molecular, and morphological data, in addition to the practical considerations made for insular species, supports the species status of seven of these nominal species; the remaining taxa require further study. The S. striatum group, accordingly, is either over-divided into nominal species or deficient in chromosomal discriminators. If most or all nominal species and unnamed species are valid, all but one are homosequential, an unprecedented condition in Simuliidae. This group illustrates the need for the integration of multiple character sets for discovering and delimiting species. Full article

The nitrogen cycle is the key to the healthy operation of river ecosystems and plays an important role in maintaining the ecological balance, purifying water quality, and promoting the circulation of material. The Xisha River was chosen as the research object to analyze the water quality condition from 2021 to 2023, and the microbial diversity of nitrogen metabolism, functional genes, and metabolic pathways in the water body were analyzed using macro-genomics technology. The results showed that total nitrogen (TN) was the main exceedance factor in the water body, and ammonia nitrogen (NH₃-N), TN, and total phosphorus (TP) were the key factors affecting the water quality. The downstream station (W2) exhibited the most significant water quality changes, while the upstream station (W5) showed the highest biodiversity and abundance. The top five genera in abundance in the water body were unclassified__c__Actinomycetia, unclassified__p__Bacteroidota, Paenisporosarcina, Candidatus_Planktophila, and unclassified__c__Betaproteobacteria. The five most abundant nitrogen metabolism genes were K01915 (nitrate reductase), K00265 (nitrite reductase), K01673 (ammonium transporter), K00266 (nitrite reductase), and K02575 (nitrate reductase), each contributing to critical nitrogen cycling processes such as denitrification, nitrification, and nitrogen assimilation. The six major nitrogen metabolism pathways were denitrification (M00529), anisotropic nitrate reduction (M00528), anisotropic nitrate reduction (M00529). anisotropic nitrate reduction (M00530), complete nitrification (M00804), nitrate assimilation (M00615), methylaspartate cycling (M00740), and assimilatory nitrate reduction (M00531). TN was identified as the primary environmental factor influencing both microbial communities and nitrogen metabolism genes. Co-occurrence network analysis identified K01915 (nitrate reductase), K00459 (ammonium transporter), K01673 (ammonium transporter), and K00261 (nitrate reductase) as pivotal genes involved in nitrogen metabolism. This study reveals the microbial-driven nitrogen cycle and lays the foundation for mitigating nitrogen pollution in the Xisha River. Full article

The Hungarian Grey (HG) cattle breed was almost extinct after WW2; only 200 cows and six bulls survived. Despite the historical significance of the HG, no comprehensive genomic analysis has been conducted to clarify its genetic diversity and evolutionary history. Previous studies have relied on random or limited pedigree sampling, lacking a fully representative dataset determining genetic and conservation status. Here, the founder sampling of 110 individuals and the analysis of their mitochondrial DNA (mtDNA) sequence variation aim to investigate the phylogenetic placement of the breed using, for the first time, a fully representative sample. All identified haplogroups belong to the taurine T macro-haplogroup, with a predominance of T3 (89.1%), followed by T2 (4.5%), T1 (3.6%), and T1′2′3 (2.7%). The phylogenetic analysis confirms the absence of ancient haplogroups derived from European aurochs, suggesting a purely taurine origin for the HG breed. The high haplotype diversity (Hd = 0.94) and the genetic similarity to other Podolian breeds, particularly Maremmana cattle, indicate a preserved genetic background despite centuries of selective breeding. The lack of intensive crossbreeding practices has maintained the original beef production purpose of the breed, distinguishing it from the crossbred Podolian cattle used for dual-purpose or dairy production. Full article

Bacterial diseases cause high mortality and considerable losses in aquaculture. The rapid expansion of intensive aquaculture has further increased the risk of large-scale outbreaks. However, the emergence of drug-resistant bacteria, food safety concerns, and environmental regulations have severely limited the availability of antimicrobial. Compared to traditional antibiotics, antimicrobial peptides (AMPs) offer broad spectrum activity, physicochemical stability, and lower resistance development. However, their low natural yield and high extraction costs along with the time-consuming and expensive nature of traditional drug discovery, pose a challenge. In this study, we applied a machine-learning macro-model to predict AMPs from three macrogenomes in the water column of South American white shrimp aquaculture ponds. The AMP content per megabase in the traditional earthen pond (TC1) was 1.8 times higher than in the biofloc pond (ZA1) and 63% higher than in the elevated pond (ZP11). A total of 1033 potential AMPs were predicted, including 6 anionic linear peptides, 616 cationic linear peptides, and 411 cationic cysteine-containing peptides. After screening based on structural, and physio-chemical properties, we selected 10 candidate peptides. Using a rapid high-throughput cell-free protein expression system, we identified nine peptides with antimicrobial activity against aquatic pathogens. Three were further validated through chemical synthesis. The three antimicrobial peptides (K-5, K-58, K-61) showed some inhibitory effects on all four pathogenic bacteria. The MIC of K-5 against Vibrio alginolyticus was 25 μM, the cell viability of the three peptides was higher than 70% at low concentrations (≤12.5 μM), and the hemolysis rate of K-5 and K-58 was lower than 5% at 200 μM. This study highlights the benefits of machine learning in AMP discovery, demonstrates the potential of cell-free protein synthesis systems for peptide screening, and provides an efficient method for high-throughput AMP identification for aquatic applications. Full article

The early developmental phase is a critical window for feline growth, during which immature digestive systems are susceptible to microbiome imbalances caused by environmental stressors. Our research employed macrogenomic analysis to evaluate how complex probiotic formulations influence growth metrics and gastrointestinal flora in juvenile felines. Two dozen healthy kittens were equally divided into the control group and the probiotics group following a 5-day environmental adaptation phase. Fecal scores were recorded daily for all kittens. Fresh fecal samples were collected on days 1 and 14 for macrogenomic analysis. The results showed a significantly lower rate of constipation in the probiotics group compared to the control group (p < 0.05). However, no significant differences were observed in intestinal microbial diversity or structure between the two groups. Metagenomic analysis revealed a higher relative abundance of Bifidobacterium animalis in the probiotics group compared to the control group (p < 0.05). Additionally, the probiotics group exhibited lower relative abundances of Lachnospiraceae bacterium 2 1 58FAA, Lachnospiraceae bacterium 1 1 57FAA, and Acidaminococcus intestini compared to the control group (p < 0.05). These results suggest that complex probiotics can regulate the intestinal microbiota, improve constipation, and promote intestinal health in kittens. Full article

Panax notoginseng is a prominent traditional Chinese medicinal herb, yet its yield and quality are significantly constrained by continuous cropping obstacles, primarily stemming from soil-related issues. This study analyzed soils subjected to various degrees of continuous P. notoginseng cultivation, soils without P. notoginseng planting, and natural forest floor soil without P. notoginseng planting. The objective was to investigate variations in soil microbial communities, physicochemical properties, and enzyme activities across different cropping conditions. Macro-genome sequencing was employed to reveal microbial shifts and key factors influencing rhizosphere microbial communities. Notably, the natural forest floor soil exhibited the highest levels of soil organic matter, soil organic carbon, total nitrogen, and available potassium. Furthermore, continuous cropping soils showed the highest levels of pH, available phosphorus, electrical conductivity, and total potassium. The activities of catalase, urease, acid phosphatase, sucrase, and soil FDA hydrolase decreased significantly after continuous cropping, but increased again after five years of fallowing. Microbial analysis revealed that Bacteroidetes, Firmicutes, and Chloroflexi dominated the soils without P. notoginseng planting, whereas Proteobacteria, Actinobacteria, and Acidobacteria were the predominant phyla in continuous cropping and natural forest floor soils. Continuous cropping led to an increase in Acidobacteria, Gemmatimonadetes, and Chloroflexi, while fallowing reduced Actinobacteria. Gemmatimonades was almost exclusively present in the continuous cropping soils. Overall, continuous P. notoginseng planting altered the soil nutrients and microbial composition. Key factors influencing microbial communities included pH, nitrate nitrogen, available phosphorus, available potassium, and electrical conductivity. The study suggests that attention should be paid to scientific and rational fertilization practices to mitigate the effects of continuous cropping. Additionally, a fallow period of more than five years is recommended. The proper application of probiotic fertilizers is also advised. Finally, cultivating P. notoginseng under forest conditions is recommended as a viable method. Full article

Inflammatory bowel disease remains a significant challenge in clinical settings. This study investigated the therapeutic potential of sea cucumber ovum hydrolysates (SCH) in a dextran sulfate sodium (DSS)-induced colitis mouse model. SCH, defined by its elevated stability and solubility, with a molecular weight below 1000 Da, significantly alleviated DSS-induced colitis, as evidenced by enhanced splenic index, reduced colonic damage, and diminished serum pro-inflammatory cytokines. Furthermore, macrogenomic analysis demonstrated that SCH increased beneficial gut microbes and decreased pro-inflammatory bacteria. Furthermore, metabolomic analysis of colonic tissues identified elevated levels of anti-inflammatory metabolites, such as Phenyllactate, 2-Hydroxyglutarate, and L-Aspartic acid, in colitis mice after oral administration of SCH. In conclusion, SCH represents a promising candidate for the treatment of colitis. Full article

As the mobile cassette carrier of the methicillin resistance gene mecA that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome mec (SCCmec)—and in particular, the composition of mecA and SCCmec—have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCCmec. Herein, the cassette chromosome recombinase genes ccrAB/C, as essential components of SCCmec, were employed to explore the evolution of SCCmec. This work established the basic taxonomy of 33 staphylococci species. The CUB of mecA, ccrAB/C of 12 SCCmec types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of ccrAB/C was observed via SCCmec typing on a temporal and geographical scale; and the duplicate appearance of ccrAB/C was illustrated by comparing SCCmec compositions. The results highlighted a deviation in the CUB of mecA and ccrAB/C, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of ccrAB/C as representative of SCCmec. Importantly, the phylogenetic relationship of ccrAB/C did not exhibit centralization over time; instead, similarly to mecA, ccrAB/C with similar identities had close clades across decades and geographical limits and different SCCmec types, which enabled us to discriminate SCCmec based on the sequence identity of ccrAB/C. In addition, the duplicate appearance of ccrAB/C and fixed composition of the ccrAB/C complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCCmec. Full article

Genetic studies of haematological cancers have pointed out the heterogeneity of leukaemia in its different subpopulations, with distinct mutations and characteristics, impacting the treatment response. Next-generation sequencing (NGS) and genome-wide analyses, as well as single-cell technologies, have offered unprecedented insights into the clonal heterogeneity within the same tumour. A key component of this heterogeneity that remains unexplored is the intracellular metabolome, a dynamic network that determines cell functions, signalling, epigenome regulation, immunity and inflammation. Understanding the metabolic diversities among cancer cells and their surrounding environments is therefore essential in unravelling the complexities of leukaemia and improving therapeutic strategies. Here, we describe the currently available methodologies and approaches to addressing the dynamic heterogeneity of leukaemia progression. In the second section, we focus on metabolic leukaemic vulnerabilities in acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL). Lastly, we provide a comprehensive overview of the most interesting clinical trials designed to target these metabolic dependencies, highlighting their potential to advance therapeutic strategies in leukaemia treatment. The integration of multi-omics data for cancer identification with the metabolic states of tumour cells will enable a comprehensive “micro-to-macro” approach for the refinement of clinical practices and delivery of personalised therapies. Full article

A field experiment was conducted on sunflowers in a mild-to-moderate saline–alkaline area in the Tumochuan Plain irrigation region in China. The experimental design included using surface drip irrigation as a control (CK) and four subsurface drip irrigation treatments at burial depths of 10 cm (D10), 15 cm (D15), 20 cm (D20), and 25 cm (D25) to analyze the effect of the drip irrigation belt burial depth on soil physicochemical properties and soil desalination in the main root zone of saline–alkaline sunflower farmland. Based on macro-genome sequencing technology, the diversity, composition, and structure of soil fungal communities in the main root zone were revealed in response to the depth of drip irrigation. The results show that subsurface drip irrigation treatments improved soil desalination with rates ranging from 15.33% to 26.96%. The D25 treatment achieved an 82.01% higher desalination rate than CK and outperformed D10, D15, and D20 by 43.35%, 13.43%, and 24.89%, respectively, demonstrating the most effective desalination with a 25 cm burial depth under the same water and fertilizer management conditions. Additionally, subsurface drip irrigation enhanced the diversity and abundance of soil fungal communities; the Shannon indices for D15 and D20 were 8.1% and 12.3% higher than that of CK, respectively, whereas the Chao1 indices increased by 21.2% and 17.4%, respectively. During the budding stage, the fungal community in the main root zone (20–40 cm) was dominated by Ascomycetes and Tephritobacterium, with Alternaria being the predominant genus. Notably, the relative abundance of Ascomycetes was 118.8% higher in D25 than in CK. Structural equation modeling quantified the relationships between soil physicochemical properties, with an SMC of 0.94, indicating a model fit within an acceptable range. An SEM analysis revealed that the soil water content (SWC), soil EC, and soil NO₃⁻-N exerted the most significant combined effect on soil fungal composition and diversity. This study examined the effects of the drip irrigation tape burial depth on soil physicochemical characteristics, the fungal community structure, and diversity in the main root zone (20–40 cm) of saline–alkaline sunflower fields under subsurface drip irrigation. This study aims to provide theoretical support for water-saving agricultural practices in saline–alkaline soils. We developed a subsurface drip irrigation method for sunflowers in the lightly to moderately saline–alkaline land in the irrigation area of China’s Tumochuan Plain, and the suitable depth of burial of the drip irrigation belt was 25 cm. Full article

Xiangzao brine is a special flavored food produced by the natural fermentation of Huangjiu lees. To clarify fermentation time on its quality, this study integrated flavoromics analysis, macro-genomics, and polypeptide omics to analyze the volatile flavor components, microbial species, and flavor peptide distributions of four groups of samples (XZ-1Y, XZ-2Y, XZ-3Y, and XZ-4Y) fermented for 1–4 years. The results showed that the samples fermented for 1 year had the highest contents of umami amino acids and umami peptides, and the samples fermented for 4 years had the highest contents of organic acids and fruity components. In addition, 42 volatile flavor components and 532 peptides were identified, including 393 umami taste peptides and only 37 bitter taste peptides. Correlation analysis showed that ethyl lactate and furfural were positively correlated with the abundance of Nocardioides and Stenotrophomonas, respectively. The abundance of Pseudomonas was positively correlated with four previously unreported umami peptides (FATPR, RELER, FNLERP, and RSSFLGQ) screened by molecular docking. This study provides a reference for the flavor metabolism regulation of Xiangzao brine. Full article

The Loess Plateau, with a fragile ecological environment, is one of the most serious water- and soil-eroded regions in the world, which has been improved by large-scale projects involving returning farmland to forest and grassland. This work is mainly aimed at exploring a more reasonable and efficient ecological forest restoration mode and revealing synergistic restoration mechanisms. This study sampled typical Loess Plateau areas and designed the restoration modes for pure forests of Armeniaca sibirica L. (AR), Amygdalus davidiana (Carrière) de Vos ex Henry. (AM), Medicago sativa L. (MS), and mixed forests of apricot–peach–alfalfa (AR&AM&MS), using abandoned land (AL) as a control treatment. The effects of these modes on the physical and chemical properties and enzyme activities of various soils were investigated in detail. Moreover, the soil microbial diversity and community structure, functional gene diversity, and differences in the restoration modes were deeply analyzed by meta-genomic sequencing technology, and the inherent driving correlation and mechanisms among these indicators were discussed. The results showed that the soil water content and porosity of the AR, AM, and AR&AM&MS treatments increased significantly, while the bulk density decreased significantly, compared with AL. Moreover, the total carbon, total nitrogen, nitrate nitrogen, total phosphorus, available phosphorus, total potassium, and available potassium contents of the AR&AM&MS restoration mode increased significantly. Compared to CK, there was no significant change in the catalase content of pure forest and mixed forest; however, the contents of urease, phosphatase, sucrase, B-glycanase, and N-acetylglucosaminidase in the restoration mode of the mixed forest all increased significantly. The species diversity index of the restoration modes is similar, and the dominant bacteria in soil microorganisms include Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. The mixed forest restoration mode had the highest microbial abundance. The functional gene diversity of the different restoration modes was also similar, including kegg genes, eggNOG genes, and carbohydrate enzymes. The functional genes of the mixed forest restoration mode were the most abundant, and their restoration mechanism was related to the coupling effect of soil–forest grass. After evaluation, the restoration mode of mixed forest was superior to that of pure forest or pure grass. This is attributed to the fact that the mode can improve soil structure, retain soil moisture, enhance soil enzyme activity, optimize soil microbial community structure, and improve microbial diversity and functional gene activity. This provides key data for the restoration of fragile ecological areas, and the promotion of sustainable management of forests and grass in hilly areas of the Loess Plateau. Full article

(1) Background: The unique geographical and climatic conditions of the Antarctic Peninsula contribute to distinct regional ecosystems. Microorganisms are crucial for sustaining the local ecological equilibrium. However, the variability in soil microbial community diversity across different regions of the Antarctic Peninsula remains underexplored. (2) Methods: We utilized metagenome sequencing to investigate the composition and functionality of soil microbial communities in four locations: Devil Island, King George Island, Marambio Station, and Seymour Island. (3) Results: In the KGI region, we observed increased abundance of bacteria linked to plant growth promotion and the degradation of pollutants, including PAHs. Conversely, Marambio Station exhibited a significant reduction in bacterial abundance associated with iron and sulfur oxidation/reduction. Notably, we identified 94 antibiotic resistance genes (ARGs) across 15 classes of antibiotics in Antarctic soils, with those related to aminoglycosides, β-lactamase, ribosomal RNA methyltransferase, antibiotic efflux, gene regulatory resistance, and ABC transporters showing a marked influence from anthropogenic activities. (4) Conclusions: This study carries substantial implications for the sustainable use, advancement, and conservation of microbial resources in Antarctic soils. Full article