Integration of transcriptomic and proteomic approaches unveils the molecular mechanism of membrane disintegration in Escherichia coli O157:H7 with ultrasonic treatment

Transcriptomics and proteomics analyses reveal the molecular mechanisms of yeast cells regulated by Phe-Cys against ethanol-oxidation cross-stress

Antioxidant dipeptide Phe-Cys (FC) could dramatically improve yeast cells resistance to ethanol-oxidation cross-stress, but the regulatory mechanisms remain unclear. Therefore, transcriptomic and proteomic analyses were conducted to investigate the effects of FC treatment on yeast under ethanol-oxidation cross-stress. Following FC supplementation, 875 differential expressed genes (DEGs) and 1296 differential expressed proteins (DEPs) were identified. Integrated analysis revealed a substantial enrichment of DEGs and DEPs in the KEGG pathways of carbon metabolism, amino acid biosynthesis, cofactor biosynthesis, and glycolysis/gluconeogenesis. Furthermore, FC improved yeast cell membrane integrity by promoting fatty acids and steroids biosynthesis, and implemented a high-energy strategy by upregulating glycolysis and oxidative phosphorylation. Additionally, alterations in DEGs and DEPs levels associated with amino acids metabolism accelerated protein synthesis and enhanced cell viability. In conclusion, this study elucidated the response mechanisms of yeast to FC treatment under ethanol-oxidation cross-stress, providing a theoretical basis for the application of FC in high-gravity brewing.

Symbiotic virus-bacteria interactions in biological treatment of coking wastewater manipulating bacterial physiological activities

Biological treatment is commonly used in coking wastewater (CWW) treatment. Prokaryotic microbial communities in CWW treatment have been comprehensively studied. However, viruses, as the critical microorganisms affecting microbial processes and thus engineering parameters, still remain poorly understood in CWW treatment context. Employing viromics sequencing, the composition and function of the viral community in CWW treatment were discovered, revealing novel viral communities and key auxiliary metabolic functions. Caudovirales appeared to be the predominant viral order in the oxic-hydrolytic-oxic (OHO) CWW treatment combination, showing relative abundances of 62.47 %, 56.64 % and 92.20 % in bioreactors O1, H and O2, respectively. At the family level, Myoviridae, Podoviridae and Siphoviridae mainly prevailed in bioreactors O1 and H while Phycodnaviridae dominated in O2. A total of 56.23-92.24% of novel viral contigs defied family-level characterization in this distinct CWW habitat. The virus-host prediction results revealed most viruses infecting the specific functional taxa Pseudomonas, Acidovorax and Thauera in the entire OHO combination, demonstrating the viruses affecting bacterial physiology and pollutants removal from CWW. Viral auxiliary metabolic genes (AMGs) were screened, revealing their involvement in the metabolism of contaminants and toxicity tolerance. In the bioreactor O1, AMGs were enriched in detoxification and phosphorus ingestion, where glutathione S-transferase (GSTs) and beta-ketoadipyl CoA thiolase (fadA) participated in biodegradation of polycyclic aromatic hydrocarbons and phenols, respectively. In the bioreactors H and O2, the AMGs focused on cell division and epicyte formation of the hosts, where GDPmannose 4,6-dehydratase (gmd) related to lipopolysaccharides biosynthesis was considered to play an important role in the growth of nitrifiers. The diversities of viruses and AMGs decreased along the CWW treatment process, pointing to a reinforced virus-host adaptive strategy in stressful operation environments. In this study, the symbiotic virus-bacteria interaction patterns were proposed with a theoretical basis for promoting CWW biological treatment efficiency. The findings filled the gaps in the virus-bacteria interactions at the full-scale CWW treatment and provided great value for understanding the mechanism of biological toxicity and sludge activity in industrial wastewater treatment.

Transcriptome analysis reveals the mechanism of antifungal peptide epinecidin-1 against Botrytis cinerea by mitochondrial dysfunction and oxidative stress

The marine antifungal peptide epinecidin-1 (EPI) have been shown to inhibit Botrytis cinerea growth, while the molecular mechanism have not been explored based on omics technology. This study aimed to investigate the molecular mechanism of EPI against B. cinerea by transcriptome technology. Our findings indicated that a total of 1671 differentially expressed genes (DEGs) were detected in the mycelium of B. cinerea treated with 12.5 μmol/L EPI for 3 h, including 773 up-regulated genes and 898 down-regulated genes. Cluster analysis showed that DEGs (including steroid biosynthesis, (unsaturated) fatty acid biosynthesis) related to cell membrane metabolism were significantly down-regulated, and almost all DEGs involved in DNA replication were significantly inhibited. In addition, it also induced the activation of stress-related pathways, such as the antioxidant system, ATP-binding cassette transporter (ABC) and MAPK signaling pathways, and interfered with the tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathways related to mitochondrial function. The decrease of mitochondrial related enzyme activities (succinate dehydrogenase, malate dehydrogenase and adenosine triphosphatase), the decrease of mitochondrial membrane potential and the increase content of hydrogen peroxide further confirmed that EPI treatment may lead to mitochondrial dysfunction and oxidative stress. Based on this, we speculated that EPI may impede the growth of B. cinerea through its influence on gene expression, and may lead to mitochondrial dysfunction and oxidative stress.

Biological activity and molecular mechanism of inactivation of Microcystis aeruginosa by ultrasound irradiation

Harmful algal blooms (HABs) significantly impact on water quality and ecological balance. Ultrasound irradiation has proven to be an effective method for algal control. Nevertheless, the molecular mechanisms underlying the inactivation of M. aeruginosa by ultrasound are still unknown. In this study, the physiological activity and molecular mechanism of algal cells exposed to different frequencies of ultrasound were studied. The results indicated a pronounced inhibition of algal cell growth by high-frequency, high-dose ultrasound. Moreover, with increasing ultrasound dosage, there was a higher percentage of algal cell membrane ruptures. SEM and TEM observed obvious disruptions in membrane structure and internal matrix. Hydroxyl radicals generated by high-frequency ultrasound inflicted substantial cell membrane damage, while increased antioxidant enzyme activities fortified cells against oxidative stress. Following 2 min of ultrasound irradiation at 740 kHz, significant differential gene expression occurred in various aspects, including energy metabolism, carbohydrate metabolism, and environmental information processing pathways. Moreover, ultrasound irradiation influenced DNA repair and cellular apoptosis, suggesting that the algal cells underwent biological stress to counteract the damage caused by ultrasound. These findings reveal that ultrasound irradiation inactivates algae by destroying their cell structures and metabolic pathways, thereby achieving the purpose of algal suppression.

Molecular and proteomic response of Pseudomonas fluorescens biofilm cultured on lettuce (Lactuca sativa L.) after ultrasound treatment at different intensity levels

Ultrasonic treatment is widely used for surface cleaning of vegetables in the processing of agricultural products. In the present study, the molecular and proteomic response of Pseudomonas fluorescens biofilm cultured on lettuce was investigated after ultrasound treatment at different intensity levels. The results show that the biofilm was efficiently removed after ultrasound treatment with intensity higher than 21.06 W/cm2. However, at an intensity of less than 18.42 W/cm2, P. fluorescens was stimulated by ultrasound leading to promoted bacterial growth, extracellular protease activity, extracellular polysaccharide secretion (EPS), and synthesis of acyl-homoserine lactones (AHLs) as quorum-sensing signaling molecules. The expression of biofilm-related genes, stress response, and dual quorum sensing system was upregulated during post-treatment ultrasound. Proteomic analysis showed that ultrasound activated proteins in the flagellar system, which led to changes in bacterial tendency; meanwhile, a large number of proteins in the dual-component system began to be regulated. ABC transporters accelerated the membrane transport of substances inside and outside the cell membrane and equalized the permeability conditions of the cell membrane. In addition, the expression of proteins related to DNA repair was upregulated, suggesting that bacteria repair damaged DNA after ultrasound exposure.

Invited review: Current perspectives for analyzing the dairy biofilms by integrated multiomics

Biofilms formed by pathogenic or spoilage microorganisms have become serious issues in the dairy industry, as this mode of life renders such microorganisms highly resistant to cleaning-in-place (CIP) procedures, disinfectants, desiccation, and other control strategies. The advent of omics techniques, especially the integration of different omics tools, has greatly improved our understanding of the features of microbial biofilms, and provided in-depth knowledge on developing effective methods that are directly against deleterious biofilms. This review provides novel insights into the single use of each omics tool and the application of multiomics tools to unravel the mechanisms of biofilm formation, specific molecular phenotypes exhibited by biofilms, and biofilm control strategies. Challenges and future perspective on the integration of omics tools for biofilm studies are also addressed.

A multi-omics analysis strategy reveals the molecular mechanism of the inhibition of Escherichia coli O157:H7 by anthocyanins from Aronia melanocarpa and its application

Water pollution causes the propagation of pathogenic microorganisms, which poses a serious threat to human life. Escherichia coli O157:H7, as a representative organism that can directly exhibit molecular response to stress, was selected as the indicator bacteria for the study. Tandem mass tag (TMT) quantitative proteomics and non-targeted metabolomics were used to study the response of Escherichia coli O157:H7 to Aronia melanocarpa anthocyanin (AMA) treatment. The results showed that 628 proteins and 1338 metabolites changed significantly after treatment with AMAs. According to bioinformatics analysis, integrated proteomics and metabolomics analysis differentially expressed proteins (DEPs) and metabolites participate in pyruvate metabolism, glycolysis/gluconeogenesis, alanine, aspartate and glutamate metabolism and the pentose phosphate pathway. This study preliminarily proposed the inhibition mechanism of AMAs on Escherichia coli O157:H7 from the perspective of multi-omics, providing a theoretical basis for the application of natural preservatives in fresh cut vegetables.

Super Antibacterial Capacity and Cell Envelope-Disruptive Mechanism of Ultrasonically Grafted N-Halamine PBAT/PBF Films against Escherichia coli

Antibacterial materials are urgently needed to combat bacterial contamination, growth, or attachment on contact surfaces, as bacterial infections remain a public health crisis worldwide. Here, a novel ultrasound-assisted method is utilized for the first time to fabricate oxidative chlorine-loaded AH@PBAT/PBF-Cl films with more superior grafting efficiency and rechargeable antibacterial effect than those from conventional techniques. The films remarkably inactivate 99.9999% Escherichia coli and Staphylococcus aureus cells, inducing noticeable cell deformations and mechanical instability. The specific antibacterial mechanism against E. coli used as a model organism is unveiled using several cell envelope structural and functional analyses combined with proteomics, peptidoglycomics, and fluorescence probe techniques. Film treatment partially neutralizes the bacterial surface charge, induces oxidative stress and cytoskeleton deformity, alters membrane properties, and disrupts the expression of key proteins involved in the synthesis and transport of the lipopolysaccharide and peptidoglycan, indicating the cell envelope as the primary target. The films specifically target lipopolysaccharides, resulting in structural impairment of the polysaccharide and lipid A components, and inhibit peptidoglycan precursor synthesis. Together, these lead to metabolic disorders, membrane dysfunction, structural collapse, and eventual death. Given the films' antibacterial effects via the disruption of key cell envelope components, they can potentially combat a wide range of bacteria. These findings lay a theoretical basis for developing efficient antibacterial materials for food safety or biomedical applications.

Ultrasound promotes germination of aging Pinus tabuliformis seeds is associated with altered lipid metabolism

Seed germination is an essential biological process for establishing new organisms of higher plants, it is especially significant for those aged seeds stored in gene banks for years. In this study, we investigated ultrasound treatment induced germination for aged Pinus tabuliformis seeds, which has been used in large scale aircraft sowing based afforestation in North China over 30 years' ago without knowing possible mechanisms. We showed certain strength of ultrasound could increase the germination rate of aged seeds for about 3 times compare with control. Interestingly, although our transcriptome and lipidome analysis showed the differences between control and ultrasound treatments can be observed 1 day after germination by partial least squares discriminant analysis (PLSDA) analysis, majority (75 % or 69 %) of the significantly altered genes or lipids were commonly shared between them. Further analysis for the commonly altered lipids between both treatments showed ultrasound provoked the variations of lipids during germination process. Our investigation also revealed large amount of ultrasound-related genes and lipids that might be involved in germination promotion process. We hypothesis ultrasound provokes seed lipidome which further increases seed germination of Pinus tabuliformis. Our study provides new insides into the role of ultrasound induced lipidome change in seed germination. Moreover, we provide a new method to improve germination of aged seeds which might benefit preservation of seeds in gene banks.

Combating Escherichia coli O157:H7 with Functionalized Chickpea-Derived Antimicrobial Peptides

The rapid dissemination of antibiotic resistance accelerates the desire for new antibacterial agents. Here, a class of antimicrobial peptides (AMPs) is designed by modifying the structural parameters of a natural chickpea-derived AMP-Leg2, termed "functionalized chickpea-derived Leg2 antimicrobial peptides" (FCLAPs). Among the FCLAPs, KTA and KTR show superior antibacterial efficacy against the foodborne pathogen Escherichia coli (E. coli) O157:H7 (with MICs in the range of 2.5-4.7 µmol L-1 ) and demonstrate satisfactory feasibility in alleviating E. coli O157:H7-induced intestinal infection. Additionally, the low cytotoxicity along with insusceptibility to antimicrobial resistance increases the potential of FCLAPs as appealing antimicrobials. Combining the multi-omics profiling andpeptide-membrane interaction assays, a unique dual-targeting mode of action is characterized. To specify the antibacterial mechanism, microscopical observations, membrane-related physicochemical properties studies, and mass spectrometry assays are further performed. Data indicate that KTA and KTR induce membrane damage by initially targeting the lipopolysaccharide (LPS), thus promoting the peptides to traverse the outer membrane. Subsequently, the peptides intercalate into the peptidoglycan (PGN) layer, blocking its synthesis, and causing a collapse of membrane structure. These findings altogether imply the great potential of KTA and KTR as promising antibacterial candidates in combating the growing threat of E. coli O157:H7.

Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6

A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.