Involvement of the flagellar assembly pathway in Vibrio alginolyticus adhesion under environmental stresses

Molecular insights into cobalt homeostasis in estuarine microphytobenthos: A meta-transcriptomics and biogeochemical approach

Meta-transcriptomics data supported by biofilm physico-chemical parameters unravelled the molecular and biochemical processes utilized by multicomponent intertidal biofilms to endure cobalt toxicity. Findings indicated activation of influx (BtuB, ABC-type transporters) and efflux pumps (RND, CZC) to maintain metal ion homeostasis. Enhanced specific activity of antioxidant enzymes namely catalases and peroxidases (KatG, SodA) mitigated oxidative damage. Heightened synthesis of capsular polysaccharide components, specifically uronic acid and carbohydrate via PEP-CTERM sorting system, wzy pathway and glycosyltransferases protected biofilms against cobalt exposure. Despite chlorophyll biosynthesis genes being upregulated, metal toxicity impeded chlorophyll replenishment. Principal pathways associated with iron acquisition (AfuA), energy metabolism (AtpG), general metabolic activities (FruK, NifD, coABC) and central dogma regulation (DPS, AsrR, RRM) were activated to combat cobalt toxicity. This investigation offered novel insights into the regulatory network employed by intertidal microphytobenthic communities for maintaining cobalt homeostasis and underlined the basis for their application as biomarkers for estuarine cobalt pollution.

Screening and functional characterization of isocitrate lyase AceA in the biofilm formation of Vibrio alginolyticus

Biofilm is a well-known sessile lifestyle for bacterial pathogens, but a little is known about the mechanism on biofilm formation in Vibrio alginolyticus. In this study, we screened V. alginolyticus strains with strong biofilm formation ability from coastal seawater. The antibiotic resistance of the biofilm cells (BFs) was higher than that of the planktonic cells (PTs). To study the genes and pathways involved in biofilm formation, we performed transcriptome analysis of the BFs and PTs of V. alginolyticus R9. A total of 685 differentially expressed genes (DEGs) were upregulated, and 517 DEGs were downregulated in the BFs. The upregulated DEGs were significantly enriched in several pathways including glyoxylate and dicarboxylate metabolism, while the downregulated genes were significantly enriched in the flagellar assembly pathways. The key gene involved in glyoxylate shunt, aceA, was cloned, and ΔaceA mutant was constructed to determine the function of AceA in carbon source utilization, biofilm formation, and virulence. Real-time reverse transcription PCR showed that the expression of aceA was higher at the mature stage but lower at the disperse stage of biofilm formation, and the expression of the flagellar related genes was upregulated in ΔaceA. This is the first study to illustrate the global gene expression profile during the biofilm formation of V. alginolyticus, and isocitrate lyase AceA, the key enzyme involved in glyoxylate shunt, was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the late stage.IMPORTANCEBiofilms pose serious public problems, not only protecting the cells in it from environmental hazard but also affecting the composition and abundance of bacteria, algae, fungi, and protozoa. The important opportunistic pathogen Vibrio alginolyticus is extremely ubiquitously present in seawater, and it also exhibited a strong ability to form biofilm; thus, investigation on the biofilm formation of V. alginolyticus at molecular level is fundamental for the deeper exploration of the environmental concerns arose by biofilm. In this study, transcriptome analysis of biofilm cells (BFs) and planktonic cells (PTs) from V. alginolyticus was performed and AceA was screened to play an important role in biofilm formation. AceA was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the disperse stage. This method was helpful to further understand the ability and mechanism of V. alginolyticus biofilm formation and provide clues for prevention of V. alginolyticus infection.

Optimizing the placement of medical wastewater outlets in sewer systems to reduce chemical consumption at wastewater treatment plants

The severely low influent chemical oxygen demand (COD) concentration at wastewater treatment plants (WWTPs) has become a critical issue. A key factor is the excessive biodegradation of organic matter by microbial communities within sewer systems. Intense disinfection commonly adopted for medical wastewater leads to abundant residual chlorine entering sewers, likely causing significant changes in microbial communities and sewage quality in sewers, yet our understanding is limited. Through long-term sewer simulation batch tests, this study revealed the response mechanism of microbial communities to residual chlorine and its impact on organic matter concentration in sewage. Under residual chlorine stress, microbial community structure rapidly changed, and more complex microbial interactions were observed. Besides, pathways related to stress response such as two-component system were significantly enriched; pathways related to energy metabolism (such as carbon fixation in prokaryotes and citrate cycle) in microbial communities were inhibited, and carbon metabolism shifted from the Embden-Meyerhof pathway to the pentose phosphate pathway to enhance cellular reducing power, reduce oxidative stress, and consequently decrease organic matter degradation. Therefore, compared to sewers with normal disinfection, concentrations of COD and dissolved organic carbon in sewage under chlorine stress increased by 12.6 % and 7.4 %, respectively. Besides, the decay and transformation of residual chlorine in sewers were explored. These findings suggest a new approach to medical wastewater discharge management: placing the medical wastewater outlet at the upstream in sewer systems, which ensures that residual chlorine consumption reaches maximum during long-distance transportation, mitigating its harmful effects on WWTPs, and increases the influent organic matter concentration, thereby reducing the need for additional carbon sources.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Responses of the gut microbiota to environmental heavy metal pollution in tree sparrow (Passer montanus) nestlings

Gut microbiota plays a critical role in regulating the health and adaptation of wildlife. However, our understanding of how exposure to environmental heavy metals influences the gut microbiota of wild birds, particularly during the vulnerable and sensitive nestling stage, remains limited. In order to investigate the relationship between heavy metals and the gut microbiota, we analyzed the characteristics of gut microbiota and heavy metals levels in tree sparrow nestlings at different ages (6, 9 and 12-day-old). The study was conducted in two distinct areas: Baiyin (BY), which is heavily contaminated with heavy metals, and Liujiaxia (LJX), a relatively unpolluted area. Our result reveled a decrease in gut microbiota diversity and increased inter-individual variation among nestlings in BY. However, we also observed an increase in the abundance of bacterial groups and an up-regulation of bacterial metabolic functions associated with resistance to heavy metals toxicity in BY. Furthermore, we identified a metal-associated shift in the relative abundance of microbial taxa in 12-day-old tree sparrow nestlings in BY, particularly involving Aeromonadaceae, Ruminococcaceae and Pseudomonadaceae. Moreover, a significant positive correlation was found between the body condition of tree sparrow nestlings and the abundance of Bifidobacteriaceae in BY. Collectively, our findings indicate that the gut microbiota of tree sparrow nestlings is susceptible to heavy metals during early development. However, the results also highlight the presence of adaptive responses that enable them to effectively cope with environmental heavy metal pollution.

Response characteristics of indigenous microbial community in polycyclic aromatic hydrocarbons (PAHs) contaminated aquifers under polyethylene microplastics stress: A microcosmic experimental study

To understand the response characteristics of indigenous microbial community in PAH-contaminated aquifers to the coexistence of microplastics. In this paper, we constructed a groundwater microecosystem using lithologic media collected from the field and subjected it to the stress of a polyethylene microplastics (PE-MPs) concentration gradient. By conducting adsorption experiments and 16S rRNA sequencing, we revealed the growth, structure, metabolism, and resistance mechanisms of the indigenous microbial community in the aquifer lithologic media exposed to varying levels of co-stress from PE-MPs and phenanthrene. Our findings suggest that the adsorption capacity of aquifer lithologic media for phenanthrene is significantly weaker than that of PE-MPs. Additionally, our observations indicated that small particle lithologic media had a greater adsorption capacity for phenanthrene than large particle lithologic media. The presence of PE-MPs was found to increase both the abundance and diversity of microbial communities, although the relationship was not linear with the content of PE-MPs. When exposed to the combined stress of PE-MPs and phenanthrene, the relative abundance of Proteobacteria decreased while that of Bacteroidetes increased. Several genera belonging to Proteobacteria (Aeromonas, Desulfovibrio, Klebsiella, Pantoea, and Microvirgula) and Bacteroidetes (Macellibacteroides and Bacteroides) occupied a central position in the microbial community interaction network and showed significant correlations with other genera. Furthermore, an increase in the proportion of genera capable of degrading various refractory organics was observed. The presence of PE-MPs increased the phenanthrene content in the aquifer lithologic media, thereby intensifying the inhibitory effect on indigenous microbial community in this environment. Despite an increase in the phenanthrene content of aquifer lithologic media due to the presence of PE-MPs, indigenous microbial community in this environment exhibited resistance to the combined inhibition of PE-MPs and phenanthrene through a series of resistance mechanisms. These mechanisms included strengthening the N-cycle process, enhancing metabolic capacity for phenanthrene, improving perception, response, and adaptation to changes in the external environment or intracellular state, modifying the transmembrane transport of the cell membrane to the substrate, and regulating life processes.

Functional response of Acinetobacter guillouiae SFC 500-1A to tannery wastewater as revealed by a complementary proteomic approach

Acinetobacter guillouiae SFC 500-1 A is a promising candidate for the bioremediation of tannery wastewater. In this study, we applied shotgun proteomic technology in conjunction with a gel-based assay (Gel-LC) to explore the strain's intracellular protein profile when grown in tannery wastewater as opposed to normal culture conditions. A total of 1775 proteins were identified, 52 of which were unique to the tannery wastewater treatment. Many of them were connected to the degradation of aromatic compounds and siderophore biosynthesis. On the other hand, 1598 proteins overlapped both conditions but were differentially expressed in each. Those that were upregulated in wastewater (109) were involved in the processes mentioned above, as well as in oxidative stress mitigation and intracellular redox state regulation. Particularly interesting were the downregulated proteins under the same treatment (318), which were diverse but mainly linked to the regulation of basic cellular functions (replication, transcription, translation, cell cycle, and wall biogenesis); metabolism (amino acids, lipids, sulphate, energetic processes); and other more complex responses (cell motility, exopolysaccharide production, biofilm formation, and quorum sensing). The findings suggest that SFC 500-1 A engages in survival and stress management strategies to cope with the toxic effects of tannery wastewater, and that such strategies may be mostly oriented at keeping metabolic processes to a minimum. Altogether, the results might be useful in the near future to improve the strain's effectiveness if it will be applied for bioremediation.

Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of pathogenic Enterobacter cloacae from Macrobrachium rosenbergii

Enterobacter cloacae is widely distributed in the aquatic environment, and has been determined as a novel pathogen of various aquatic animals recently. Our previous studies have indicated E. cloacae caused repeated infections in Macrobrachium rosenbergii, suggesting a high survival ability of the bacteria, and rpoS gene has been known to regulate stress response and virulence of many bacteria. In this study, the E. cloacae-rpoS RNAi strain was constructed by RNAi technology, and the regulation role of rpoS in stress resistance and virulence of E. cloacae was explored by transcriptomic and phenotype analysis. The transcriptome analysis showed a total of 488 differentially expressed genes (DEGs) were identified between rpoS-RNAi and wild-type strains, including 30 up-regulated genes and 458 down-regulated genes, and these down-regulated DEGs were mainly related to environmental response, biofilm formation, bacterial type II secretory system, flagellin, fimbrillin, and chemotactic protein which associated with bacterial survival and virulence. The phenotype changes also showed the E. cloacae-rpoS RNAi strain exhibited significantly decreasing abilities of survival in environmental stresses (starvation, salinity, low pH, and oxidative stress), biofilm production, movement, adhesion to cells, pathogenicity, and colonization to M. rosenbergii. These results reveal that rpoS plays an important regulatory role in environmental stress adaptation and virulence of E. cloacae.

Survival Characteristics and Transcriptomic Analyses Reveal the Adaptive Response of the Aquatic Pathogen Non-O1/O139 Vibrio cholerae to Starvation Stress

Non-O1/O139 Vibrio cholerae is a pathogen of various aquatic organisms but requires major self-regulation to overcome environmental stress in the aquatic environment. However, its survival strategies under environmental stress are not well understood. The objective of this study was to describe the survival characteristics and changes in expression of stress resistance-related genes of non-O1/O139 V. cholerae after 6 months of starvation at room temperature. The results demonstrated that starved cells were still viable, exhibited shortened rods and shrinking surface, and maintained virulence to Macrobrachium rosenbergii. To investigate the changes in gene expression in non-O1/O139 V. cholerae under starvation stress, especially those involved in stress resistance, transcriptome profiles of starved and wild-type cells were determined. The differentially expressed genes (DEGs) in starved cells were identified, including 191 upregulated genes and 180 downregulated genes. Among these DEGs, the well-known stress resistance-related genes were upregulated significantly, including rpoS, rpoD, rpoN, rpoE, uspA, uspC, cspD, hslJ, etc. Gene Ontology (GO) analysis of the DEGs demonstrated that environmental adaptation-related categories, such as response to stimulus and signal transduction, were upregulated significantly in the starved cells, while cell motility was downregulated significantly. These DEGs were also enriched into 54 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including biofilm formation, two-component system, quorum sensing, flagellar assembly, bacterial chemotaxis stress resistance-related pathways, etc. The potential existence of long-starved non-O1/O139 V. cholerae bacteria in the aquatic environment may raise new concerns about this devastating pathogen in aquaculture.

IMPORTANCE Non-O1/O139 V. cholerae is a causal agent of vibriosis that can be subject to nutrient insufficiency and cause high rates of mortality in aquatic animals. However, its molecular mechanisms of survival in response to starvation stress have been investigated only partially. Here, we demonstrate that under starvation stress, non-O1/O139 V. cholerae can survive over the long term and cause disease by dwarfing of the cell structure, upregulation of a series of stress resistance-related genes, and downregulation of flagellum assembly-related genes. This knowledge can help the development of intervention strategies to control non-O1/O139 V. cholerae infection in aquaculture.

The role of dctP gene in regulating colonization, adhesion and pathogenicity of Vibrio alginolyticus strain HY9901

Vibriosis caused by Vibrio alginolyticus has severely affected the development of mariculture industry in recent decades. DctP, a tripartite ATP-independent periplasmic transporter solute-binding subunit, is thought to be one of the virulence factors in Vibrio. In this study, the results displayed no difference in morphological characteristics and growth between ΔdctP (dctP mutant strain) and WT (wild-type strain). Nevertheless, the ability of swarming motility, biofilm formation, ECPase formation, cell adhesion and colonized ability of ΔdctP significantly decreased compared to those of WT. The LD₅₀ of ΔdctP significantly increased by 40-fold compared to that of WT. The transcriptome analysis demonstrated the deletion mutation of dctP could regulate the expression levels of 22 genes related to colonization, adhesion and pathogenicity in V. alginolyticus. The analysis of qRT-PCR showed the transcriptome data were reliable. These results reveal the effect of attenuated function of DctP on colonization, adherence and pathogenicity by controlling the expression of related gene.

Intestinal morphology and microflora to Vibrio alginolyticus in pacific white shrimp (Litopenaeus vannamei)

In recent years, the shrimp farming industry encountered significant economic losses induced by Vibrio alginolyticus. In this study, the influence of Vibrio alginolyticus on intestinal histomorphology and microbiome composition in Litopenaeus vannamei were studied. The results showed that the intestinal mucosal epithelial cells of Vibrio group (VA group) injected only with Vibrio alginolyticus showed large area exfoliation at 12 h, and the tissue morphology of intestine recovered at 48 h. Compared with the control group (CK group), the abundance of Proteobacteria was significantly higher (P < 0.05), while the abundance of Actinobacteria was significantly lower after infection with Vibrio alginolyticus. The abundance of Shewanella in intestinal microbiome of Litopenaeus vannamei was significantly higher at 12 h (P < 0.05), but the abundance of Candidatus_Bacilloplasma was significantly lower at 48 h after infection (P < 0.05). In VA group, the diversity of intestinal microbiome was significantly lower at 12 h, which could be caused by the proliferation of Candidatus_Bacilloplasma and Shewanella. All above findings suggested that the stability of the dynamic balance of microbiome in the intestine helped Litopenaeus vannamei to resist pathogen colonization.

Activation of the TCA Cycle to Provide Immune Protection in Zebrafish Immunized by High Magnesium-Prepared Vibrio alginolyticus Vaccine

Vaccines are safe and efficient in controlling bacterial diseases in the aquaculture industry and are in line with green farming. The present study develops a previously unreported approach to prepare a live-attenuated V. alginolyticus vaccine by culturing bacteria in a high concentration of magnesium to attenuate bacterial virulence. Furthermore, metabolomes of zebrafish immunized with the live-attenuated vaccines were compared with those of survival and dying zebrafish infected by V. alginolyticus. The enhanced TCA cycle and increased fumarate were identified as the most key metabolic pathways and the crucial biomarker of vaccine-mediated and survival fish, respectively. Exogenous fumarate promoted expression of il1β, il8, il21, nf-κb, and lysozyme in a dose-dependent manner. Among the five innate immune genes, the elevated il1β, il8, and lysozyme are overlapped in the vaccine-immunized zebrafish and the survival from the infection. These findings highlight a way in development of vaccines and exploration of the underlying mechanisms.

cheA, cheB, cheR, cheV, and cheY Are Involved in Regulating the Adhesion of Vibrio harveyi

Diseases caused by Vibrio harveyi lead to severe economic losses in the aquaculture industry. Adhesion is an important disease-causing factor observed in bacteria with chemotactic activity. In our study, we measured the adhesion of V. harveyi by subjecting the bacteria to stress using Cu²⁺, Pb²⁺, Hg²⁺, and Zn²⁺. The genes responsible for chemotaxis (cheA, cheB, cheR, cheV, and cheY), which are also crucial for adhesion, were identified and silenced via RNAi. We observed that a decrease in chemotactic gene expression reduced the ability of the organism to demonstrate adhesion, motility, chemotaxis, and biofilm formation. Upon comparing the cheA-RNAi bacteria to the wild-type strain, we observed that the transcriptome of V. harveyi was significantly altered. Additionally, the expression of key genes and the adhesion ability were affected by the pH (pH of 5, 6, 7, 8, and 9), salinity (NaCl at concentrations of 0.8, 1.5, 2.5, 3.5, or 4.5%), and temperature (4, 15, 28, 37, and 44°C) of the medium. Based on these results, the following conclusions were made: (1) The chemotactic genes cheA, cheB, cheR, cheV, and cheY may regulate the adhesion ability of V. harveyi by affecting bacterial motility, and participate in the regulation of adhesion at different temperatures, salinities, and pH values; (2) stable silencing of cheA could alter the transcriptional landscape of V. harveyi and regulate the expression of genes associated with its adhesion mechanisms.

Current and future perspectives for controlling Vibrio biofilms in the seafood industry: a comprehensive review

The contamination of seafood with Vibrio species can have severe repercussions in the seafood industry. Vibrio species can form mature biofilms and persist on the surface of several seafoods such as crabs, oysters, mussels, and shrimp, for extended duration. Several conventional approaches have been employed to inhibit the growth of planktonic cells and prevent the formation of Vibrio biofilms. Since Vibrio biofilms are mostly resistant to these control measures, novel alternative methods need to be urgently developed. In this review, we propose environmentally friendly approaches to suppress Vibrio biofilm formation using a hypothesized mechanism of action.

Biological filters regulate water quality, modulate health status, immune indices and gut microbiota of freshwater crayfish, marron (Cherax cainii, Austin, 2002)

Water quality has significant impacts on the health and immune responses of aquaculture species. This study aimed to analyse and compare the effects of two biological filters namely, gravel and, Bio-Ball with a recently developed filter called Water-cleanser on regulation of water quality parameters, health and immune response of marron reared in plastic tanks for 60 days. Results showed that addition of Bio-Ball significantly (P < 0.05) reduced the concentration of ammonia, nitrate and phosphate while Water-cleanser showed the ability to reduce ammonia and nitrate from water in aquaculture tanks. Although the biological filters had no significant effect on marron growth but inclusion of Bio-Ball and Water-cleanser positively influenced the biochemical composition of tail muscle and some haemolymph parameters of marron. The next generation sequence data demonstrated higher bacterial diversity in the hindgut of marron with Water-cleanser, followed by Bio-Ball and gravel, respectively. In addition, the predicted metabolic pathways revealed a significantly higher bacterial activity and gene function correlated to metabolism and biosynthesis of protein, energy and secondary metabolites in Bio-Ball and Water-cleanser. Bio-Ball and Water-cleanser were also associated with up-regulation of innate immune responsive genes of marron gut. Overall, Bio-Ball and Water-cleanser proved to have higher water remediation and immune response modulation capabilities, and therefore could be used as preferred filters for growth of beneficial bacteria in crayfish culture.

A LuxR-type regulator, AcrR, regulates flagellar assembly and contributes to virulence, motility, biofilm formation, and growth ability of Acidovorax citrulli

LuxR-type regulators regulate many bacterial processes and play important roles in bacterial motility and virulence. Acidovorax citrulli is a seedborne bacterial pathogen responsible for bacterial fruit blotch, which causes great losses in melon and watermelon worldwide. We identified a LuxR-type, nonquorum sensing-related regulator, AcrR, in the group II strain Aac-5 of A. citrulli. We found that the acrR mutant lost twitching and swimming motilities, and flagellar formation. It also showed reduced virulence, but increased biofilm formation and growth ability. Transcriptomic analysis revealed that 394 genes were differentially expressed in the acrR mutant of A. citrulli, including 33 genes involved in flagellar assembly. Our results suggest that AcrR may act as a global regulator affecting multiple important biological functions of A. citrulli.

Protection against Pseudomonas plecoglossicida in Epinephelus coioides immunized with a cspA1-knock-down live attenuated vaccine

Pseudomonas plecoglossicida is well-known as the cause of viscera granulomas disease in fish. In this study, a cspA1 knock-down strain was constructed and tested in Epinephelus coioides to observe the changes in virulence and evaluate its potential as an attenuated live vaccine. The results showed that the cspA1 knock-down strain caused a significant reduction in the ability of biofilm formation, motility, adhesion and virulence. E. coioides vaccinated with cspA1 knock-down strain were more tolerant of the infection by wild-type P. plecoglossicida. The relative percent survival value of E. coioides vaccinated with cspA1 knock-down strain reached 80% after challenging with wild-type P. plecoglossicida. In the meanwhile, the expression level of genes associated with immunity, including IL-1β, IgM, MHC-I and MHC-II, was up-regulated after vaccination, indicating that the cspA1 knock-down strain can induce effective and durable immune response in E. coioides and it may be an effective attenuated live vaccine candidate for the prevention of infections by P. plecoglossicida.

Effect of Baicalin-Aluminum Complexes on Fecal Microbiome in Piglets

The gut microbiome has important effects on gastrointestinal diseases. Diarrhea attenuation functions of baicalin (BA) is not clear. Baicalin-aluminum complexes (BBA) were synthesized from BA, but the BBA's efficacy on the diarrhea of piglets and the gut microbiomes have not been explored and the mechanism remains unclear. This study has explored whether BBA could modulate the composition of the gut microbiomes of piglets during diarrhea. The results showed that the diarrhea rate reduced significantly after treatment with BBA. BBA altered the overall structure of the gut microbiomes. In addition, the Gene Ontology (GO) enrichment analysis indicated that the functional differentially expressed genes, which were involved in the top 30 GO enrichments, were associated with hydrogenase (acceptor) activity, nicotinamide-nucleotide adenylyltransferase activity, and isocitrate lyase activity, belong to the molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that flagellar assembly, bacterial chemotaxis, lipopolysaccharide biosynthesis, ATP-binding cassette transporters (ABC) transporters, biosynthesis of amino acids, and phosphotransferase system (PTS) were the most enriched during BBA treatment process. Taken together, our results first demonstrated that BBA treatment could modulate the gut microbiomes composition of piglets with diarrhea, which may provide new potential insights on the mechanisms of gut microbiomes associated underlying the antimicrobial efficacy of BBA.

The regulation of oxidative phosphorylation pathway on Vibrio alginolyticus adhesion under adversities

Vibrio alginolyticus is one of the most important pathogens in mariculture and leading to heavy losses. After treatment with Cu²⁺, Pb²⁺, and low pH, the expression of oxidative phosphorylation pathway genes, including coxA, coxB, coxC, ccoN, ccoO, and ccoQ, was found commonly downregulated by RNA‐seq as well as quantitative real‐time PCR. RNAi significantly reduced the expression of coxA, coxB, coxC, ccoN, ccoO, and ccoQ in V. alginolyticus. Compared with the wild‐type strain, the adhesion abilities of RNAi strains of V. alginolyticus were significantly impaired, as well as their cytochrome C oxidase activity. ccoQ appeared to be more important in the regulation of bacterial adhesion in these target genes, while ccoO was relatively weak in the regulation of the adhesion. Meanwhile, the changes of temperature, salinity, pH, and starvation affected coxA, coxB, coxC, ccoN, ccoO, and ccoQ expression remarkably. These findings indicated that: the oxidative phosphorylation pathway is a critical regulator of adhesion in V. alginolyticus; coxA, coxB, coxC, ccoN, ccoO, and ccoQ regulate the bacterial adhesion in response to environmental changes such as temperature, salinity, pH, and starvation.

Isolation and characterization of a virulence related Vibrio alginolyticus strain Wz11 pathogenic to cuttlefish, Sepia pharaonis

Vibrio alginolyticus is a ubiquitous marine opportunistic pathogen that can infect various hosts in marine environment. In the present study, V. alginolyticus strain Wz11 was isolated from diseased cuttlefish, Sepia pharaonis, with 20% of promoted death and high survival capacity in skin mucus and tissue liquid. Its growth, siderophore production, and expressions of haemolysin and swarming related genes were characterized under iron limited conditions. The minimal inhibitory concentration (MIC) of 2,2'-dipyridyl (DP) to V. alginolyticus strain Wz11 was 640 μM. While growth of V. alginolyticus strain Wz11 was inhibited by DP, production of iron-seizing substances, haemolytic activity and swarming motility were increased. Moreover, expressions of haemolysin related genes tlh, tdh and vah and flagellar related genes flgH, fliC, fliD and fliS were also characterized using real-time reverse transcriptase PCR. Expression of tdh was up-regulated to 7.7-fold, while expressions of tlh and vah were down-regulated to 0.016-fold and 0.03-fold, respectively. The expression of fliC, flgH, fliD and fliS was up-regulated to 4.9-, 3.8-, 8.6- and 4.5-fold, respectively. Concluded from our results suggested that V. alginolyticus strain Wz11 was considered as a potential pathogen of S. pharaonis, and iron level played an important role in the production of iron-seizing substances, and activities of haemolysin and bacterial swarming as well as their related gene expressions.

Integration of Transcriptomic and Proteomic Approaches Reveals the Temperature-Dependent Virulence of Pseudomonas plecoglossicida

Pseudomonas plecoglossicida is a facultative pathogen that is associated with diseases of multiple fish, mainly at 15–20°C. Although fish disease caused by P. plecoglossicida has led to significant economic losses, the mechanisms of the temperature-dependent virulence are unclear. Here, we identify potential pathogenicity mechanisms and demonstrate the direct regulation of several virulence factors by temperature with transcriptomic and proteomic analyses, quantitative real-time PCR (qRT-PCR), RNAi, pyoverdine (PVD) quantification, the chrome azurol S (CAS) assay, growth curve measurements, a biofilm assay, and artificial infection. The principal component analysis, the heat map generation and hierarchical clustering, together with the functional annotations of the differentially expressed genes (DEGs) demonstrated that, under different growth temperatures, the animation and focus of P. plecoglossicida are quite different, which may be the key to pathogenicity. Genes involved in PVD synthesis and in the type VI secretion system (T6SS) are specifically upregulated at the virulent temperature of 18°C. Silencing of the PVD-synthesis-related genes reduces the iron acquisition, growth, biofilm formation, distribution in host organs and virulence of the bacteria. Silencing of the T6SS genes also leads to the reduction of biofilm formation, distribution in host organs and virulence. These findings reveal that temperature regulates multiple virulence mechanisms in P. plecoglossicida, especially through iron acquisition and T6SS secretion. Meanwhile, integration of transcriptomic and proteomic data provide us with a new perspective into the pathogenesis of P. plecoglossicida, which would not have been easy to catch at either the protein or mRNA differential analyses alone, thus illustrating the power of multi-omics analyses in microbiology.

Regulatory role of the RstB-RstA system in adhesion, biofilm production, motility, and hemolysis

For infection, initial invasion of the host is of great importance, with adhesion playing a critical role. We previously demonstrated rstA and rstB are remarkably downregulated in Vibrio alginolyticus cultured under heavy metal and acidic stresses, with impaired adhesion, suggesting that rstA and rstB might be involved in adhesion regulation. The present study showed that rstA and rstB silencing resulted in impaired adhesion, biofilm production, motility, hemolysis, and virulence. Meanwhile, changes of temperature, starvation, and pH remarkably affected rstA and rstB expression. These findings indicated that (1) rstA and rstB are critical regulators of adhesion in V. alginolyticus; (2) rstA and rstB have remarkable effects on biofilm production, motility, hemolysis, and virulence in V. alginolyticus; (3) rstA and rstB modulate adhesion in response to environmental changes of temperature, pH, and starvation.

Genome Sequence of Pseudomonas plecoglossicida Strain NZBD9

Pseudomonas plecoglossicida NZBD9 is the causative agent of white nodules in cultured large yellow croaker in Fujian Province, China. We sequenced the genome of NZBD9 to gain a better understanding of the etiological agent. The genome sequence of the bacterium consists of 5.44 million bp, with a G+C content of 61.9%.

mcp, aer, cheB, and cheV contribute to the regulation of Vibrio alginolyticus (ND-01) adhesion under gradients of environmental factors

Adhesion is a key virulence factor of pathogens and can be affected by the environment. Our previously research with RNA-seq indicated that mcp, aer, cheB, and cheV might play roles in the regulation of adhesion in Vibrio alginolyticus (ND-01). In order to determine whether and how environmental factors affect adhesion through these genes, gene silencing was performed followed by quantitative real-time PCR (qRT-PCR), RNAi, transmission electron microscopy, and adhesion, capillary, and motility assays to verify how these genes influence adhesion. Silencing these genes led to deficiencies in adhesion, chemotaxis, flagellar assembly, and motility. The expression levels of cheA, cheW, and cheY, which are important genes closely related to the functions of mcp, aer, cheV, and cheB, were significantly downregulated in all of the RNAi groups. The expression of mcp, aer, cheV, and cheB under different gradients of temperature, pH, and salinity and after starvation for various durations was also detected, which showed that these genes were sensitive to certain environmental stresses, particularly pH and starvation. Our results indicated that mcp, aer, cheB, and cheV: (1) are necessary for ND-01 adhesion; (2) play key roles in the bacterial chemotaxis pathway by controlling the expression of downstream genes; (3) might affect adhesion by impacting motility, though motility is not the only route through which adhesion is affected; and (4) contribute to the regulation of ND-01 adhesion in natural environments with different temperatures, pH levels, and salinities as well as after various starvation periods.

AcfA is an essential regulator for pathogenesis of fish pathogen Vibrio alginolyticus

V. alginolyticus is an important opportunistic pathogen which causes vibriosis in aquatic animals. AcfA, as an accessory colonization factor, is hypothesized to be involved in the pathogenesis of infection. In this study, a mutant strain with an in-frame deletion removed nucleotides 86 to 561 of the acfA gene was constructed to reveal the role of AcfA in the physiology and virulence from V. alginolyticus. An acfA mutant showed a similar growth level, an obvious decrease in swarming motility and the activity of ECPase, a higher LD₅₀ value by intraperitoneal injection of grouper fish compared to that of the wild-type. Furthermore, the deletion of acfA could enhance the level of biofilm formation and suppress the polar flagellum forming. The comparative proteomic analysis demonstrated the deletion mutation of acfA could up-regulate the expression of 4 proteins of p4alcd, deoD, phb and DctP, and down-regulate the expression of 8 proteins of Clp, hpV36980, ABCtp, pepD, arA, aggp, fla and ompA compared to that of the wild-type. The analysis of RT-qPCR showed the mRNA levels of DctP and deoD were significantly induced, and the mRNA levels of pepD, arA, fla and ompA were significantly reduced in acfA mutant compared with the wild-type. The results suggest that acfA may contribute to the overall success in the pathogenesis of V. alginolyticus by regulating the expression of some relevant genes.

secA, secD, secF, yajC, and yidC contribute to the adhesion regulation of Vibrio alginolyticus

Vibrio alginolyticus caused great losses to aquaculture. Adhesion is an important virulence factor of V. alginolyticus. In this study, the relationship between V. alginolyticus adhesion and type II secretion system genes (secA, secD, secF, yajC, and yidC) was determined using gene silencing, qRT‐PCR and in vitro adhesion assay. The results showed that the expression of target genes and the bacterial adhesion exhibited significant decreases after transient gene silencing and stable gene silencing, which indicated that secA, secD, secF, yajC, and yidC played roles in the bacterial adhesion of V. alginolyticus. The expression of secA, secD, secF, yajC, and yidC were significantly influenced by temperature, salinity, pH and starvation. The results indicated that the expression of secA, secD, secF, yajC, and yidC were sensitive to different environmental factors, whereas environmental factors can affect V. alginolyticus adhesion via the expression of secA, secD, secF, yajC, and yidC.

Contributions of the oligopeptide permeases in multistep of Vibrio alginolyticus pathogenesis

Vibrio alginolyticus has been associated with several diseases of cultivated marine animals, and has led to considerable economic losses. The oligopeptide permease (Opp) has been proven to play a variety of important roles in nutrition and virulence in several bacteria. In our previous research, the opp gene cluster was identified in Vibrio alginolyticus with transcriptome sequence, which also indicated that the Opp system might play roles in the regulation of adhesion. In this study, the relationship between V. alginolyticus virulence and the opp gene cluster was determined using gene silencing followed by RT‐qPCR, in vitro adhesion assay, growth curves detection in the presence of glutathione (GSH) as a toxic substrate, hemolysis assay, biofilm assay, and artificial infection. Silencing these genes led to deficiencies in adhesion, peptide internalization, biofilm production, hemolytic activity, and virulence. The expression levels of hapr, hapa, tlh, and hlya, which are important genes closely related to the hemolytic activity of Vibrio, were significantly downregulated in all of the RNAi groups. Furthermore, the expression of oppA, oppB, oppC, oppD, and oppF was significantly influenced by temperature, starvation, and pH. These results indicate that (1) oppABCDF contributed in multistep of V. alginolyticus pathogenesis, including adhesion, biofilm production, and hemolytic activity; (2) oppABCDF was sensitive to different temperatures, changes in pH, and increased starvation time.

The complete genome sequence of Exiguobacterium arabatum W-01 reveals potential probiotic functions

Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W‐01, a gram‐positive and orange‐pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole‐genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843.98 bp and a mean GC content of 48.11%, accounting for 89.27% of the genome. Among these ORFs, 2,884 (93.5%) genes were classified into Clusters of Orthologous Groups (COG) families comprising 21 functional categories, and 1,650 ORFs were classified into 83 functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 27 rRNA operons and 68 tRNAs were identified, with all 20 amino acids represented. In addition, 91 genomic islands, 68 potential prophages, and 33 tandem repeats, but no clustered regularly interspaced short palindromic repeats (CRISPRs), were found. No resistance genes and only one virulence gene were identified. Among the 150 secreted proteins of E. arabatum W‐01, a variety of transport system substrate‐binding proteins, enzymes, and biosynthetic proteins, which play important roles in the uptake and metabolism of nutrients, were found. Two adherence‐related protein genes and 31 flagellum‐related protein genes were also identified. Taken together, these results indicate potential probiotic functions for E. arabatum W‐01.

Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus

Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium (Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes (flgA and flgP) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance.IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and promote cellular aggregation without inducing cell death. These findings suggest that CLPs hold great promise as potential drug candidates targeting bacterial motility and biofilm formation with a low overall potential for triggering antibiotic resistance.

AcuC, a histone deacetylase, contributes to the pathogenicity of Aeromonas hydrophila

The interactions of pathogens and phagocytes are complex. Our study demonstrated that Aeromonas hydrophila B11 can survive in the macrophagocytes of Tilapia mossambica. To explore the regulatory processes of A. hydrophila survival in the macrophagocytes, we used the mini-Tn10 transposon mutagenesis system to build a mutant library by mixing Escherichia coli Sm10 (pLOFKm) and A. hydrophila B11. In total, 102 mutant colonies were detected, and 11 of them showed reduced survival in macrophagocytes. The mutant with the most severe phenotype, AM73, was chosen for further research. The ORF interrupted by mini-Tn10 in AM73 was approximately 960 bp and was deposited in GenBank with the accession number SRP049226. The 319 amino acid protein encoded by the ORF showed a high degree of identity (89%) with proteins in the histone deacetylase/AcuC/AphA family of A. hydrophila subsp. hydrophila ATCC7966. A strain (AC73) in which the acuC mutation was complemented was constructed by generating the recombinant expression plasmid pACYC184-acuC and introducing it into the AM73 mutant strain. Our experiments revealed that strain AM73 was deficient in biofilm formation, adhesion, survival in macrophagocytes, and virulence compared with A. hydrophila B11, and all of these biological properties were improved in strain AC73. The expression of 10 significant virulence genes was significantly inhibited in strain AM73. The results indicated that AcuC was an important regulatory protein contributing to the pathogenicity of A. hydrophila.

Ribose operon repressor (RbsR) contributes to the adhesion of Aeromonas hydrophila to Anguilla japonica mucus

The characterization of adhesion between pathogenic bacteria and the host is critical. Pathogenic Aeromonas hydrophila was shown to adhere in vitro to the mucus of Anguilla japonica. To further investigate the adhesion mechanisms of A. hydrophila, a mini-Tn10 transposon mutagenesis system was used to generate an insertion mutant library by cell conjugation. Seven mutants that were impaired in adhesion to mucus were selected out of 332 individual colonies, and mutant M196 was the most severely impaired strain. National Center for Biotechnology Information (NCBI) blast analysis showed that mutant M196 was inserted by mini-Tn10 with an ORF of approximately 1,005 bp (GenBank accession numbers KP280172). This ORF is predicted to encode a protein consist of 334 amino acid, which displays the highest identity (98%) with the RbsR of A. hydrophila ATCC 7966. Random inactivation of rbsR gene affected the pleiotropic phenotypes of A. hydrophila. The adhesion ability and the survival level of the rbsR gene mutant (M196) were attenuated compared with the wild-type and rbsR complementary type. The findings of this study indicated that RbsR plays roles in the bacterial adhesion and intracellular survival of A. hydrophila.

flrA, flrB and flrC regulate adhesion by controlling the expression of critical virulence genes in Vibrio alginolyticus

Adhesion is an important virulence trait of Vibrio alginolyticus. Bacterial adhesion is influenced by environmental conditions; however, the molecular mechanism underlying this effect remains unknown. The expression levels of flrA, flrB and flrC were significantly downregulated in adhesion-deficient V. alginolyticus strains cultured under Cu²⁺, Pb²⁺, Hg²⁺ and low-pH stresses. Silencing these genes led to deficiencies in adhesion, motility, flagellar assembly, biofilm formation and exopolysaccharide (EPS) production. The expression levels of fliA, flgH, fliS, fliD, cheR, cheV and V12G01_22158 (Gene ID) were significantly downregulated in all of the RNAi groups, whereas the expression levels of toxT, ctxB, acfA, hlyA and tlh were upregulated in flrA- and flrC-silenced groups. These genes play a key role in the virulence mechanisms of most pathogenic Vibrio species. Furthermore, the expression of flrA, flrB and flrC was significantly influenced by temperature, salinity, starvation and pH. These results indicate that (1) flrA, flrB and flrC are important for V. alginolyticus adhesion; (2) flrA, flrB and flrC significantly influence bacterial adhesion, motility, biofilm formation and EPS production by controlling expression of key genes involved in those phenotypes; and (3) flrA, flrB and flrC regulate adhesion in the natural environment with different temperatures, pH levels, salinities and starvation time.

The TCA Pathway is an Important Player in the Regulatory Network Governing Vibrio alginolyticus Adhesion Under Adversity

Adhesion is a critical step in the initial stage of Vibrio alginolyticus infection; therefore, it is important to understand the underlying mechanisms governing the adhesion of V. alginolyticus and determine if environmental factors have any effect. A greater understanding of this process may assist in developing preventive measures for reducing infection. In our previous research, we presented the first RNA-seq data from V. alginolyticus cultured under stress conditions that resulted in reduced adhesion. Based on the RNA-seq data, we found that the Tricarboxylic acid cycle (TCA pathway) might be closely related to adhesion. Environmental interactions with the TCA pathway might alter adhesion. To validate this, bioinformatics analysis, quantitative Real-Time PCR (qPCR), RNAi, and in vitro adhesion assays were performed, while V. alginolyticus was treated with various stresses including temperature, pH, salinity, and starvation. The expression of genes involved in the TCA pathway was confirmed by qPCR, which reinforced the reliability of the sequencing data. Silencing of these genes was capable of reducing the adhesion ability of V. alginolyticus. Adhesion of V. alginolyticus is influenced substantially by environmental factors and the TCA pathway is sensitive to some environmental stresses, especially changes in pH and starvation. Our results indicated that (1) the TCA pathway plays a key role in V. alginolyticus adhesion: (2) the TCA pathway is sensitive to environmental stresses.

Comparative Transcriptome Analysis of Vibrio splendidus JZ6 Reveals the Mechanism of Its Pathogenicity at Low Temperatures

Yesso scallop-pathogenic Vibrio splendidus strain JZ6 was found to have the highest virulence at 10°C, while its pathogenicity was significantly reduced with increased temperature and completely incapacitated at 28°C. In the present study, comparative transcriptome analyses of JZ6 and another nonpathogenic V. splendidus strain, TZ19, were conducted at two crucial culture temperatures (10°C and 28°C) in order to determine the possible mechanism of temperature regulation of virulence. Comparisons among four libraries, constructed from JZ6 and TZ19 cultured at 10°C and 28°C (designated JZ6_10, JZ6_28, TZ19_10, and TZ19_28), revealed that 241 genes were possibly related to the increased virulence of JZ6 at 10°C. There were 10 genes, including 2 encoding Flp pilus assembly proteins (FlhG and VS_2437), 6 encoding proteins of the "Vibrio cholerae pathogenic cycle" (ToxS, CqsA, CqsS, RpoS, HapR, and Vsm), and 2 encoding proteins in the Sec-dependent pathway (SecE and FtsY), that were significantly upregulated in JZ6_10 (P < 0.05) compared to those in JZ6_28, TZ19_10, and TZ19_28, which were supposed to be responsible for adhesion, quorum sensing, virulence, and protein secretion of V. splendidus. When cultured at 10°C, JZ6 cells were larger and tended to aggregate more than those cultured at 28°C. The virulence factor (extracellular metalloprotease) was also found to be highly expressed in the extracellular product (ECP) of JZ6 at 10°C, and this ECP exhibited obvious cytotoxicity to oyster primary hemocytes, A549 cells, and L929 cells. These results indicated that low temperatures (10°C) could enhance adhesion, activate the quorum sensing systems, upregulate virulence factor synthesis and secretion, and, lastly, increase the pathogenicity of JZ6.