Comparative Proteome Analysis of Shewanella putrefaciens WS13 Mature Biofilm Under Cold Stress

Antibiofilm efficacies and mechanism of perillaldehyde against Shewanella putrefaciens

Shewanella putrefaciens is Gram-negative bacterium and important spoilage organism in aquatic products, negatively impacting the organoleptic properties of aquatic products. S. putrefaciens could form biofilm, which increases persistence and contamination in food system. Efficient antibiofilm strategies are urgently needed to reduce its presence in food environment. This study aimed to explore the impact of perillaldehyde on S. putrefaciens biofilm and the underlying mechanisms using transcriptomic analysis. Perillaldehyde remarkably reduced extracellular polymeric substance contents, inhibited metabolic activity of biofilm cells, disrupted bacterial motility, loose biofilm structure and decreased biofilm formation in food juice and on various surfaces (stainless steel, silicone, glass, razon clam and shrimp). Transcriptome analysis revealed that 553 differentially expressed genes were identified, among which 254 were down-regulated and 299 were up-regulated. The differentially expressed genes included ATP-binding cassette transporters, ribosome, two-component systems, resistance/nodulation/division efflux systems, quorum sensing, amino acid metabolism, biosynthesis and degradation pathways. The findings demonstrate antibiofilm properties of perillaldehyde against S. putrefaciens and indicate that perillaldehyde could be developed as an antibiofilm agent to mitigate existence and contamination of S. putrefaciens and to reduce associated food loss caused by this spoilage bacteria.

Research Progress Regarding Psychrotrophic Pseudomonas in Aquatic Products: Psychrophilic Characteristics, Spoilage Mechanisms, Detection Methods, and Control Strategies

Aquatic products are an important part of the human diet, but they are easily contaminated by Pseudomonas spp., which leads to food deterioration and economic loss. In this paper, the main characteristics of psychrotrophic Pseudomonas in aquatic products are reviewed, including its growth adaptation mechanism and biofilm formation ability at low temperatures, and the key role of psychrotrophic Pseudomonas in aquatic product spoilage is emphasized. Studies have shown that psychrotrophic Pseudomonas can produce a variety of volatile compounds by decomposing proteins and amino acids, affecting the sensory quality and safety of aquatic products. A variety of control strategies to extend the shelf life of aquatic products have been explored, including physical, chemical, and biological methods, particularly biofilm-specific inhibition techniques such as inhibition of quorum sensing and the application of natural antimicrobials. Future research should prioritize the development of novel anti-biofilm products to address the growing problem of psychrotrophic Pseudomonas contamination in the aquatic product industry to ensure food safety and public health.

Mechanisms underlying the low-temperature adaptation of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9: insights from physiological and transcriptomic analyses

The 17β-estradiol (E2)-degrading bacterium Rhodococcus sp.RCBS9 previously showed remarkable resistance to the combined stresses of low temperature and E2. In this study, physiological experiments and transcriptomic analysis were performed to investigate the mechanisms underlying the strain's low-temperature adaptation and briefly analyze how it maintains its ability to degrade E2 at low temperature. The results showed that the strain's signal transduction functions, adaptive changes in cell membrane and cell wall structure, gene repair functions, and synthesis of antioxidants and compatible solutes are key to its ability to adapt to low temperature. In addition, its stress proteins in response to low temperature were not typical cold shock proteins, but rather universal stress proteins (USPs) and heat shock proteins (HSPs), among others. The strain also upregulated biofilm production, transporter proteins for carbon source uptake, and proteins for fatty acid degradation to ensure energy generation. The strain's multiple stress responses work synergistically to resist low-temperature stress, ensuring its adaptability to low-temperature environments and ability to degrade E2. Finally, six genes related to survival at low temperature (identified in the transcriptome analysis) were expressed in E. coli BL21, and they were found to contribute to recombinant E. coli growth at low temperature.

Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout

BACKGROUND

Recirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.

RESULTS

The moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.

CONCLUSION

Our study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.

Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria

This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.

Preliminary analysis of pathways and their implications during salinity stress in abalone

Transcriptome sequencing has offered immense opportunities to study non-model organisms. Abalone is an important marine mollusk that encounters harsh environmental conditions in its natural habitat and under aquaculture conditions; hence, research that increases molecular information to understand abalone physiology and stress response is noteworthy. Accordingly, the study used transcriptome sequencing of the gill tissues of abalone exposed to low salinity stress. The aim is to explore some enriched pathways during salinity stress and the crosstalk and functions of the genes involved in the candidate biological processes for future further analysis of their expression patterns. The data suggest that abalone genes such as YAP/TAZ, Myc, Nkd, and Axin (involved in the Hippo signaling pathway) and PI3K/Akt, SHC, and RTK (involved in the Ras signaling pathways) might mediate growth and development. Thus, deregulation of the Hippo and Ras pathways by salinity stress could be a possible mechanism by which unfavorable salinities influence growth in abalone. Furthermore, PEPCK, GYS, and PLC genes (mediating the Glucagon signaling pathway) might be necessary for glucose homeostasis, reproduction, and abalone meat sensory qualities; hence, a need to investigate how they might be influenced by environmental stress. Genes such as MYD88, IRAK1/4, JNK, AP-1, and TRAF6 (mediating the MAPK signaling pathway) could be useful in understanding abalone's innate immune response to environmental stresses. Finally, the aminoacyl-tRNA biosynthesis pathway hints at the mechanism by which new raw materials for protein biosynthesis are mobilized for physiological processes and how abalone might respond to this process during salinity stress. Low salinity clearly regulated genes in these pathways in a time-dependent manner, as hinted by the heat maps. In the future, qRT-PCR verification and in-depth study of the various genes and proteins discussed would provide enormous molecular information resources for the abalone biology.

Coculture of Acinetobacter johnsonii and Shewanella putrefaciens Contributes to the ABC Transporter that Impacts Cold Adaption in the Aquatic Food Storage Environment

Acinetobacter johnsonii and Shewanella putrefaciens were identified as specific spoilage organisms in aquatic food. The interactions among specific spoilage organisms under cold stress have a significant impact on the assembly of microbial communities, which play crucial roles in the spoilage and cold adaptation processes. The limited understanding of A. johnsonii and S. putrefaciens interactions in the cold adaptation mechanism hinders the elucidation of their roles in protein and metabolism levels. 4D quantitative proteomic analysis showed that the coculture of A. johnsonii and S. putrefaciens responds to low temperatures through ABC transporter proteins, resulting in phospholipid transport and inner membrane components. SapA and FtsX proteins were significantly upregulated, while LolC, LolD, LolE, PotD, PotA, PotB, and PotC proteins were significantly downregulated. Metabolome assays revealed that metabolites of glutathione and spermidine/putrescin were significantly upregulated, while metabolites of arginine/lysine/ornithine were significantly downregulated and involved in the ABC transporter metabolism. The results of ultramicroscopic analyses showed that the coculture of A. johnsonii and S. putrefaciens surface combined with the presence of the leakage of intracellular contents, suggesting that the bacteria were severely damaged and wrinkled to absorb metabolic nutrients and adapt to cold temperatures.

Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32

Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.

Antibacterial and Antibiofilm Efficacy and Mechanism of Ginger (Zingiber officinale) Essential Oil against Shewanella putrefaciens

Ginger (Zingiber officinale) has unique medicinal value and can be used to treat colds and cold-related diseases. The chemical composition and antibacterial activity of ginger essential oil (GEO) against Shewanella putrefaciens were determined in the present study. Zingiberene, α-curcumene, and zingerone were the main active compounds of GEO. GEO displayed significant antibacterial activity against S. putrefaciens, with a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 2.0 and 4.0 μL/mL, respectively. Changes in intracellular ATP content, nucleic acid and protein structure, exopolysaccharides (EPS) content, and extracellular protease production indicated that GEO disrupted the membrane integrity of S. putrescens. At the same time, changes in biofilm metabolic activity content and the growth curve of biofilm showed that GEO could destroy the biofilm. Both scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) observations confirmed that GEO destroyed the cell membrane and lead to the leakage of the constituents. The above results indicate that GEO entered the cells via contact with bacterial membranes, and then inhibited the growth of S. putrefaciens and its biofilms by increasing membrane permeability and inhibiting various virulence factors such as EPS. The findings showed that GEO could destroy the structure of cell membrane and biofilm of tested S. putrefaciens, indicating its potential as a natural food preservative.

Evaluation of Antibacterial and Antibiofilm Properties of Kojic Acid against Aeromonas sobria and Staphylococcus saprophyticus

Biofilms composed of microbes and extracellular polymeric substances (EPSs) pose a significant risk to human health and lead to economic loss in the food industry. In this study, the antimicrobial and antibiofilm properties of kojic acid (KA) against Aeromonas sobria (A. sobria) and Staphylococcus saprophyticus (S. saprophyticus) were investigated by determining the leakage of DNA and protein, cell morphology, biofilm formation, the metabolic activity of biofilms, excretion of EPS, and biofilm architecture. The results indicated that the values of minimum inhibitory concentration (MIC) of A. sobria and S. saprophyticus after KA treatment were 0.4 mg/mL and 1.6 mg/mL, respectively. 1 × MIC KA showed unignorable antimicrobial activity against the two bacteria, leading to alterations in the bacterial physicochemical characteristics and cell death. Sub-MICs of KA can inhibit biofilm formation and decrease the metabolic activity and excretion of EPS, and these inhibition effects were in a dose-dependent manner. These results were further confirmed by the visual images obtained from scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Moreover, S. saprophyticus is more susceptible to KA in inhibiting biofilm formation, and for A. sobria, changes in the cell structure and the permeability of the cell membrane were more obvious. This research highlighted the antibacterial and antibiofilm activity of KA against A. sobria and S. saprophyticus.

The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13

Shewanella putrefaciens is a special spoilage bacterium of seafood during cold storage, which is easy to form biofilm and bring serious hazard to the seafood quality. Life cycle of biofilm starts after bacterial adhesion, which is essential for the formation and development of biofilm. As a ubiquitous second messenger in bacteria, c-di-GMP regulates the conversion between bacterial planktonic state and biofilm state. In this study, the adhesion and biofilm formation of S. putrefaciens WS13 under 4°C were compared to those under 30°C. Atom force microscope and scanning electron microscope were used to study the bacterial adhesion. Biofilm was analyzed by Fourier transform infrared spectroscopy, Bradford assay and phenol-sulfuric acid method. High-performance liquid chromatographic-tandem mass spectrometric and quantitative real-time PCR were applied to study c-di-GMP level and genes encoding diguanylate cyclases in cells, respectively. Results showed that the swarming mobility of S. putrefaciens WS13 was weaker under 4°C, however, the adhesive force under 4°C was 4–5 times higher than that under 30°C. Biofilm biomass, extracellular polysaccharides and extracellular proteins were 2.5 times, 3 times, and 1.6 times more than those under 30°C, respectively, but biofilm composition formed under both temperatures were similar. c-di-GMP level in S. putrefaciens WS13 under 30°C was no more than half of that in the corresponding growth stage under 4°C. Quantitative real-time PCR analysis also showed that the expression of genes encoding diguanylate cyclases were significantly enhanced under 4°C than that under 30°C. S. putrefaciens WS13 adapted to the cold stress by enhancing the expression of genes encoding diguanylate cyclases to promote bacterial adhesion and biofilm formation. This study provides a theoretical foundation for the research on the cold adaptation mechanism of specific spoilage bacteria of seafood based on c-di-GMP, and also provides a new idea to control seafood quality from the perspective of microbial molecular biology.

Antimicrobial Effect of Epigallocatechin Gallate Against Shewanella putrefaciens ATCC 8071: A Study Based on Cell Membrane and Biofilm

The study was to evaluate the antimicrobial impacts and biofilm influences on epigallocatechin gallate (EGCG) against Shewanella putrefaciens ATCC 8071. The minimum inhibitory concentration (MIC) of EGCG on S. putrefaciens was 160 μg mL^-1. The growth curve exhibited that EGCG had a good antimicrobial activity. EGCG caused damages to the bacterial cell wall and membrane based the intracellular component leakage and cell viability analysis. The damage to the membrane integrity by EGCG has been confirmed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). SEM shows deformation of shape, TEM shows cell membrane and wall damage, and the leakage of cytoplasmic material. The treatment with EGCG at 0.25× and 0.5× MIC resulted in decreased motility and elevated levels of oxidative stress, leading to an increase in biofilm formation. These results demonstrated that EGCG may be used as a natural preservative to reduce S. putrefaciens in fish during cold storage.

Chlorophyllin-Based 405 nm Light Photodynamic Improved Fresh-Cut Pakchoi Quality at Postharvest and Inhibited the Formation of Biofilm

The aim of this study was to evaluate the effect of chlorophyllin-based photodynamic inactivation (Chl-PDI) on biofilm formation and fresh-cut pakchoi quality during storage. Firstly, Chl-based PDI reduced the amount of biofilm in an in vivo experiment and inactivated the food spoilage bacteria. Antibacterial mechanism analysis indicated that the bacterial extracellular polysaccharides and extracellular proteins were vulnerable targets for attacks by the Chl-based PDI. Then, the food spoilage microorganisms (Pseudomonas reinekei and Pseudomonas palleroniana) were inoculated onto the surface of fresh-cut pakchoi. We used chlorophyllin (1 × 10⁻⁵ mol/L) and 405 nm light (22.27 J/cm² per day) to investigate the effect of Chl-based PDI treatment on fresh-cut pakchoi quality during storage. The results showed that Chl-based PDI increased the visual quality and the content of chlorophyll, VC, total soluble solids, and SOD activity and decreased the occurrence of leaf yellowing and POD activity. These suggest that Chl-based PDI can be used for the preservation of fresh-cut pakchoi and has the potential to inhibit biofilm formation of food spoilage bacteria. It is of great significance for the effective processing and traditional vegetable preservation.

Response to Cold Adaption in Acinetobacter johnsonii XY27 from Spoiled Bigeye Tuna (Thunnus obesus): Membrane Protein Composition and Protein Biomarker Identification by Proteomics

Acinetobacter johnsonii is one of the major food-spoilage bacteria and can survive under cold stress. In this study, the membrane composition, membrane permeability, and energy transduction of A. johnsonii XY27 cultured at 4 and 30 °C were examined comparatively by flow cytometry combined with liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The Na⁺/K⁺ATPase activity, alkaline phosphatase and ATPase activity, fluorescence intensity, and cell viability in A. johnsonii XY27 increased with the decrease in cultivation temperature. The polyunsaturated fatty acid and monounsaturated fatty acids have a higher content in A. johnsonii XY27 cultured at 4 °C compared to that cultured at 30 °C, in which the contents of methyl palmitoleate, methyl myristoleate, and methyl oleate increased dramatically with decreasing temperature. Comparative proteomics analysis revealed that 31 proteins were downregulated and 4 proteins were upregulated, in which catalase-peroxidase 1 and cold shock proteins as biomarker proteins could effectively control A. johnsonii during cold adaptation.

Comparative Transcriptome Analysis of Shewanella putrefaciens WS13 Biofilms Under Cold Stress

Shewanella putrefaciens is a Gram-negative bacterium that can cause seafood spoilage under low-temperature conditions. The bacterium easily forms biofilms to enhance its survival in challenging environments. Our previous research revealed that the biofilm formed by S. putrefaciens WS13 under the low temperature (4 °C) has larger biomass and tighter structure than at an optimum growth temperature (30 °C). In this study, comparative transcriptome analysis was further performed to get insights into the global-level of gene expression in the biofilm formed by S. putrefaciens WS13 under the refrigerating and optimal temperatures using Illumina RNA-Sequencing technique. The results revealed that a total of 761 genes were differentially expressed, of which 497 were significantly up-regulated and 264 were significantly down-regulated (p<0.05). The qRT-PCR results of randomly selected differentially expressed genes (DEGs) confirmed the RNA sequencing results. Comparison of transcriptome data revealed 28 significantly changed metabolic pathways under the cold stress, including the down-regulated chemotaxis, and motility, and up-regulated tryptophan metabolism, histidine biosynthesis, and quorum sensing, which benefited the biofilm formation of S. putrefaciens WS13 under the adverse circumstance. This study provided useful data for better understanding of the biofilm formation of S. putrefaciens, and also laid a theoretical foundation for novel vaccine and drug targets against the severe spoilage bacterium under the cold stress.

Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior

Shewanella putrefaciens can cause the spoilage of seafood and shorten its shelf life. In this study, both strains of S. putrefaciens (YZ08 and YZ-J) isolated from spoiled bigeye tuna were subjected to in-depth phenotypic and genotypic characterization to better understand their roles in seafood spoilage. The complete genome sequences of strains YZ08 and YZ-J were reported. Unique genes of the two S. putrefaciens strains were identified by pan-genomic analysis. In vitro experiments revealed that YZ08 and YZ-J could adapt to various environmental stresses, including cold-shock temperature, pH, NaCl, and nutrient stresses. YZ08 was better at adapting to NaCl stress, and its genome possessed more NaCl stress-related genes compared with the YZ-J strain. YZ-J was a higher biofilm and exopolysaccharide producer than YZ08 at 4 and 30 °C, while YZ08 showed greater motility and enhanced capacity for biogenic amine metabolism, trimethylamine metabolism, and sulfur metabolism compared with YZ-J at both temperatures. That YZ08 produced low biofilm and exopolysaccharide contents and displayed high motility may be associated with the presence of more a greater number of genes encoding chemotaxis-related proteins (cheX) and low expression of the bpfA operon. This study provided novel molecular targets for the development of new antiseptic antisepsis strategies.

The Antimicrobial Effect of Melissa officinalis L. Essential Oil on Vibrio parahaemolyticus: Insights Based on the Cell Membrane and External Structure

The study was to evaluate the antimicrobial impacts on Melissa officinalis L. essential oil (MOEO) against Vibrio parahaemolyticus. The minimum inhibitory concentration (MIC) of MOEO on Vibrio parahaemolyticus was 1 μL⋅mL^–1. The kill-time curve exhibited that MOEO had good antimicrobial activity. The analysis of cellular ingredients leakage and cell viability illustrated that MOEO has destruction to the morphology of the cell membrane. The damage to the membrane integrity by MOEO has been confirmed by transmission and scanning electron microscopy, obvious morphological and ultrastructural changes were observed in the treated bacterial cells. The MOEO at 0.5 μL⋅mL^–1 can inhibit the biofilm formation, biofilm motility, and extracellular polysaccharide production. Meanwhile, the qPCR results exhibited MOEO inhibited the expression of virulence genes. The findings showed that MOEO exerted its antimicrobial effect mainly by destroying the membrane, which indicated its potential as a natural food preservative.

Comparative Proteomics Reveals the Spoilage-Related Factors of Shewanella putrefaciens Under Refrigerated Condition

Shewanella putrefaciens is a microorganism with strong spoilage potential for aquatic products. This study aimed to investigate the potential spoilage factors of S. putrefaciens by comparative proteomic analysis. The spoilage potential of two strains of S. putrefaciens (00A and 00B) isolated from chilled spoiled bigeye tuna was investigated. The results of total volatile basic nitrogen (TVB-N), trimethylamine (TMA) in fish inoculated with S. putrefaciens, extracellular protease activity of S. putrefaciens, and degradation of fish proteins indicated that the spoilage potential of S. putrefaciens 00A was much higher than that of 00B. Fish proteins are usually degraded by spoilage microorganism proteases into small molecular peptides and amino acids, which are subsequently degraded into spoilage metabolites in bacterial cells, leading to deterioration of fish quality. Thus, proteomic analysis of the extracellular and intracellular proteins of 00A vs. 00B was performed. The results indicated that the intracellular differentially expressed protein (IDEP) contained 243 upregulated proteins and 308 downregulated proteins, while 78 upregulated proteins and 4 downregulated proteins were found in the extracellular differentially expressed protein (EDEP). GO annotation revealed that IDEP and EDEP were mainly involved in cellular and metabolic processes. KEGG annotation results showed that the upregulated proteins in IDEP were mainly involved in sulfur metabolism, amino acid metabolism, and aminoacyl-tRNA biosynthesis, while downregulated proteins were related to propanoate metabolism. In contrast, EDEP of KEGG annotation was mainly involved in ribosomes, quorum sensing, and carbohydrate metabolism. Proteins associated with spoilage containing sulfur metabolism (sulfite reductase, sulfate adenylyltransferase, adenylyl-sulfate kinase), amino acid metabolism (biosynthetic arginine decarboxylase, histidine ammonia-lyase), trimethylamine metabolism (trimethylamine-N-oxide reductase), and extracellular proteins (ATP-dependent Clp protease proteolytic subunit) were identified as upregulated. These proteins may play a key role in the spoilage potential of S. putrefaciens. These findings would contribute to the identification of key spoilage factors and understanding of the spoilage mechanism of microorganisms.

Comparison of Physicochemical Changes and Water Migration of Acinetobacter johnsonii, Shewanella putrefaciens, and Cocultures From Spoiled Bigeye Tuna (Thunnus obesus) During Cold Storage

This study investigates the physicochemical changes and water migration of Acinetobacter johnsonii (A), Shewanella putrefaciens (S), and cocultured A. johnsonii and S. putrefaciens (AS) inoculated into bigeye tuna during cold storage. The physicochemical indexes [fluorescence ratio (FR), total volatile base nitrogen (TVB-N), thiobarbituric acid (TBA), trimethylamine (TMA), peroxide value (POV), and pH] of bigeye tuna increased cold storage. A significant decrease in trapped water was found in the AS samples, and direct monitoring of the water dynamics was provided by low-field nuclear magnetic resonance. Samples inoculated with A. johnsonii and S. putrefaciens also induced the degradation of myofibrillar proteins and weakness of some Z-lines and M-lines. Higher values of physicochemical indexes and water dynamics were shown in the coculture of S. putrefaciens and A. johnsonii than in the other groups. Therefore, this paper reveals that the coculture of A. johnsonii and S. putrefaciens resulted in a bigeye tuna that was more easily spoiled when compared to the single culture. This study provides insight into the spoilage potential of A. johnsonii and S. putrefaciens during cold storage, which further assists in the application of appropriate technologies to keep the freshness of aquatic foods.

Optimisation of treatment conditions for reducing Shewanella putrefaciens and Salmonella Typhimurium on grass carp treated by thermoultrasound-assisted plasma functionalized buffer

A novel method of thermoultrasound-assisted plasma functionalized buffer (PFB) for decontaminating grass carp was evaluated using the Box-Behnken design (BBD) with processing variables including PFB generating voltage (PV), ultrasound treatment time (UT) and temperature (TP). The predicted models were found to be significant (p < 0.05) and displayed sufficient fitness with experimental data as indicated by non-significant (p > 0.05) lack of fit and high coefficient of determination (R2≥0.97) values. The optimum decontamination conditions for the responses of S. putrefaciens and S. Typhimurium were PV of 66 V, UT of 14.90 min and TP of 60 ℃, achieving reductions of 4.40 and 3.97 log CFU/g, respectively, with a desirability of 0.998. Among the variables, temperature presented higher significance for inactivating bacteria and the production of volatile basic nitrogen and lipid peroxidation under the optimized conditions were within the limits of freshness for grass carp. Additionally, the effects of PFB and the optimized thermoultrasound-assisted PFB decontamination were mild on the microstructure of grass carp with slight ruptures and loose myofibril structures, indicating the potential of thermoultrasound-assisted PFB for seafood products decontamination with reduced processing time.

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.