Inhibition of Flavobacterium psychrophilum biofilm formation using a biofilm of the antagonist Pseudomonas fluorescens FF48

Evaluation of the biocontrol activity of Frateuria defendens-derived metabolites against mollicutes

Frateuria defendens is a candidate biocontrol agent that has been shown to reduce phytoplasma-related disease symptoms in grapevines and periwinkle plants. While a crude filtrate prepared from F. defendens can inhibit mollicute growth, the specific growth parameters for this bacterium, necessary to enhance this protective inhibitory response, remain unknown. Moreover, the separation of filtrate preparations from bacterial cells via centrifugation and filtration is laborious and time-consuming. As such, the present study was conducted to define the optimal growth conditions associated with maximal inhibitory activity of F. defendens and to establish a better approach to separating these bacterial cells from their secreted metabolites. To conduct these analyses, F. defendens was cultured in a range of media types, while associated inhibitory effects were tested in vitro using Spiroplasma melliferum as a model mollicute bacterium, and in planta using phytoplasma-infected periwinkle plantlets. These analyses revealed F. defendens growth patterns change based upon media composition, with filtrates prepared from a specific rich medium (S-medium) exhibiting beneficial activities, including the inhibition of S. melliferum and enhanced plant growth. When F. defendens cells were grown within semi-permeable, membrane-coated Small Bioreactor Platform (SBP) capsules, they could be more readily separated from the secreted metabolite fraction, obviating the need for filtration and/or centrifugation. This study is the first to have reported the use of SBP capsules to separate bacterial cells from their secreted metabolites under sterile conditions while retaining the ability of these metabolites to inhibit S. melliferum growth and to benefit the host plant. The results highlight promising new approaches to the effective biocontrol of phytoplasma-driven diseases in grapevines and other economically important plant species.

Control strategies for biofilm control in reclaimed water distribution systems from the perspective of microbial antagonism and electrochemistry

Biofilm formation in reclaimed water (RW) distribution systems presents significant technical challenges to RW utilization. Two main technologies to control biofilm formation, microbial antagonism (MA) and electrochemical oxidation (EO), are not yet widely used in drip irrigation systems (DIS) and their mechanisms of action need further clarification. In this study, we first showed that the MA and EO treatments reduced biofilm formation by about 62% and 68%, respectively, and extracellular polymeric substance (EPS) content by 14% and 49%, respectively, in biofilms compared with raw RW type 1 (R-RW1) in unused pipes, thus effectively improving the performance of DIS. When MA-RW and EO-RW were applied to already clogged systems, the degree of clogging alleviation varied depending on the severity of the original clogging. We recommend adding the antagonist, Bacillus subtilis, to RW at 25% clogging for the maximum effect and to slow the microbial adaptation process. Compared to MA, the recovery effect of EO was slower initially but lasted longer and had a significantly better alleviating effect on severely clogged pipelines. Illumina Mi-SEQ high-throughput sequencing data showed that both MA and EO resulted in a significant decrease in microbial diversity, dynamic changes in bacterial community structure, and disruption of network interaction and network modularity. Meanwhile, both treatments promoted the growth of specific microorganisms, enhanced the interaction between certain microbial components, and improved the efficiency of information, matter, and energy exchange within the modules. In summary, we verified the dredging effect of two strategies on DIS under different water conditions, revealed the differences in their mechanisms of action, and proposed their application scenarios. Our results will help improve the efficiency of RW in agricultural drip irrigation systems and effectively reduce maintenance costs.

Integrative analyses of probiotics, pathogenic infections, and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss)

AIMS

Given the pivotal role played by the gut microbiota in regulating the host immune system, interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, the need for a better understanding of the host-microbiota interactions after disease responses to optimise the use of probiotics to strengthen disease resilience and recovery.

METHODS AND RESULTS

We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric redmouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and on the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.

CONCLUSIONS

We discuss the relevance of these results emphasising the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota and the resulting host immune response.

Multiple fouling dynamics, interactions and synergistic effects in brackish surface water distribution systems

Dissolved salts, colloidal particles, and active microorganisms in brackish surface water distribution systems (BSWD) cause multiple fouling, poses potential threat to the environmental pollution, and raising technical and economic issues as well. So far, the co-occurrence and interactions of multiple fouling remains largely unknown. Multiple fouling behaviors were assessed in agriculture BSWD under different nitrogen (N) fertilizers. X-ray diffraction, Rietveld refinement analysis, 16S rRNA, and microbial network analysis were conducted to determine the fouling characteristics. Statistical analysis was applied to reveal the relative contributions and interaction of multiple fouling. Our results demonstrated, multiple fouling of precipitates, particulates and biofoulings were co-occurred. Fouling growth was largely attributed to the strong interactions of different fouling. The binary interactions of precipitates - particulates contributed 51.1%, and ternary interactions of precipitates - particulates - biofouling contributed 25.4% to explain the decline of system performance, while the contribution of each single type fouling was minimal. Thereby indicating the significant role of calcium silica, biomineralization and bio-silicates in fouling. The lower acid N fertilizer broken the interaction of multiple fouling by increasing the precipitate crystal parameters and repulsive forces amongst particulates, as well as destroyed microbial interactions in biofouling. Overall, this study open frontier for multiple fouling in-depth profiling and antifouling guidance for effective utilization of BSWD.

Quantification and comparison of gene expression associated with iron regulation and metabolism in a virulent and attenuated strain of Flavobacterium psychrophilum

Iron is essential for growth and virulence in most pathogenic bacterial strains. In some cases, the hosts for these pathogenic bacteria develop specialized strategies to sequester iron and limit infectivity. This in turn may result in the invading pathogens utilizing high-affinity iron transport mechanisms, such as the use of iron-chelating siderophores, to extend beyond the host defences. Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (BCWD) in salmonids, relies on iron metabolism for infectivity, and the genome of the model CSF-259-93 strain has recently been made available. Further, this strain serves as a parent strain for a live-attenuated vaccine strain, B.17, which has been shown to provide rainbow trout with protection against BCWD. To elucidate specific gene expression responses to iron metabolism and compare strain differences, both F. psychrophilum strains were grown under iron-limiting conditions and 26 genes related to iron metabolism were mapped for 96 hr in culture via qPCR analyses. Results indicate increased production of the ferrous iron transport protein B (FITB; p =.008), and ferric receptor CfrA (FR 1; p =.012) in the wild-type CSF-259-93 strain at 72 hr and 96 hr post-exposure to iron-limiting media. In the B.17 vaccine strain, siderophore synthase (SS) expression was found to be downregulated at 72 hr, in comparison with 0h (p =.018). When strains were compared, FITB (p =.021), FR1 (p =.009) and SS (p =.016) were also elevated in B.17 at 0 hr and TonB outer protein membrane receptor 1 (TBomr1; p =.005) had a lower expression at 96 hr. Overall, this study demonstrated strain-related gene expression changes in only a fraction of the iron metabolism genes tested; however, results provide insight on potential virulence mechanisms and clarification on iron-related gene expression for F. psychrophilum.

Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum

Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947^T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

Electrochemical biofilm control by reconstructing microbial community in agricultural water distribution systems

Biofilm causes considerable technical challenges in agricultural water distribution systems. Electrochemical treatment (ECT) is a potential technique for controlling biofilm in the systems. Given the limited information on how ECT performance changes of irrigation systems and microbial biofilm community shifts. In this study, the effect of anti-biofilm was assessed. Illumina Miseq high-throughput sequencing, combined with molecular ecological network analysis, were applied to detect the effects of ECT on attached biofilm microbial communities. We found that ECT effectively mitigated biofilm formation with the fixed-biofilm biomass reduced by 37.5 %-79.9 %. ECT significantly shifted the bacterial community structures in the biofilm, reduced the communities' diversity, and changed the dominant species. Molecular ecological network analysis showed that the complexity and size of bacterial networks were destabilized under ECT and decreased the interactions among bacterial species. The reconstruction in bacterial community and networks were responsible for the decline in extracellular polymer substances and biofilm biomass. However, chlorine-resistant bacteria were found increased after ECT, and higher relative abundance and low biofilm removal was identified in continuous ECT as compared with intermittent ECT. These results aimed to highlight the opportunity for biofouling mitigation by ECT for irrigation systems, and reveal the potential anti-biofilm microbial mechanisms of ECT.

Using electromagnetic fields to inhibit biofouling and scaling in biogas slurry drip irrigation emitters

Reusing biogas slurry (BS) in agricultural drip irrigation systems may provide a solution to deal with the adverse environmental impacts of applying BS. Biofouling and scaling are two leading issues in drip irrigation emitters. This study investigated a practice that applied electromagnetic fields (EMFs) to control biofilms and scales. The bacterial communities and mineral precipitations in the clogging substances of emitters were determined. Results showed that EMFs inhibited the growth of microbes, and influenced BS physicochemical parameters. Consequently, EMFs shifted the bacterial communities with reduced diversities. Network analyses revealed that bacterial species under EMFs treatments showed lower average connectivities and simpler interactions, which were responsible for the decreases of extracellular polymers substances (EPS). Moreover, EMFs treatments not only reduced the carbonates in emitters, but also prevented the depositions of phosphates, silicates, and quartzes. EMFs also had impacts on the lattice parameters and crystal volumes of carbonates. In addition, the changes in bacterial communities and EPS contents were associated with the reductions of various minerals. Accordingly, EMFs effectively mitigated biofilms and scales with the fixed clogging substances reduced by 29.1-53.8 %. These findings demonstrated that applying EMFs is an effective anti-biofouling and anti-scaling treatment with potential applications in BS irrigation systems.

Mitigation of biofouling in agricultural water distribution systems with nanobubbles

Biofouling poses considerable technical challenges to agricultural irrigation systems. Controlling biofouling with strong chemical biocides is not only expensive and sometimes ineffective, but also contributes to environmental pollution. This study investigated the application of nanobubbles (NBs) on minimizing biofouling in agricultural irrigation water pipelines. Treatment performances were assessed using low concentration bubbles (LCB) and high concentration bubbles (HCB) together with a negative control (CK: no-NBs). 16 s rRNA gene sequencing and X-ray diffraction were used to characterize the microbial community and mineral compositions of biofilms in water emitters. Results demonstrated that NBs effectively mitigated biofouling through reducing fixed-biomass by 31.3-52.1%. A significantly different microbial composition was found in the biofilm community with reduced biodiversity. Molecular ecological network analysis revealed that NBs were detrimental to the mutualistic interactions among microbial species - destabilizing the network complexity and size, which was expressed as decreasing in extracellular polymers and biofilm biomass. Furthermore, NBs significantly decreased the deposition of carbonate, silicate, phosphate, and quartz on the pipe surfaces, leading to reductions of total content of minerals in biofilms. Therefore, this study demonstrated that NBs treatment could be an effective, and eco-friendly solution for biofouling control in agricultural water distribution systems.

Electromagnetic fields for biofouling mitigation in reclaimed water distribution systems

Biofouling is ubiquitous in reclaimed water distribution systems and causes various industrial, economic, and health issues. This paper investigated the anti-biofouling efficacy of electromagnetic fields (EMFs) for agricultural emitters used for two types of reclaimed water. 16S rRNA gene sequencing and X-ray diffraction were applied to determine the microbial communities and mineral compositions in biofilms. The obtained results revealed that EMF treatment significantly changed the bacterial communities and reduced their diversities in biofilm by affecting water quality parameters. Network analysis results indicated that EMFs were detrimental to the co-occurrence patterns of mutualistic relationships among bacterial species, destroyed the connectivity and complexity of the networks, and inhibited biofilm formation [decreased total biomass and extracellular polymeric substance (EPS) content]. EMF treatment could also decrease the deposition of mineral precipitates, reducing the carbonate and silicate content in biofilm. The decrease of EPS content appeared to reduce biofilm-induced mineral crystallization, while the ion precipitations accelerated by EMFs caused an erosive effect on biofilm. The results demonstrated that EMF treatment is an effective, chemical-free, and anti-biofouling treatment method with great potential for biofouling control in reclaimed water distribution systems.

Inhibition Activity of Compounds and Bacteriophages against Flavobacterium psychrophilum Biofilms In Vitro

Flavobacterium psychrophilum produces biofilms under laboratory conditions, and it has been inconclusively suggested that F. psychrophilum biofilms can be a potential reservoir for transmission of the pathogen to a fish population under fish farming conditions. Therefore, there is a need for anti-biofilm compounds. The main aim of this study was to determine the anti-biofilm properties of certain compounds and bacteriophages on F. psychrophilum biofilms under static conditions using a standard 96-well microtiter plate biofilm assay in vitro. Eight compounds (A-type proanthocyanidins, D-leucine, EDTA, emodin, fucoidan, L-alliin, parthenolide, and 2-aminoimidazole) at three sub-minimum inhibitory concentrations (sub-MICs), four bacteriophages (Fpv-3, Fpv-9, Fpv-10, and Fpv-21), and a phage combination (Fpv-9 + Fpv-10) were tested for inhibition of biofilm formation and reduction of the biomass of mature biofilms formed by two smooth isolates (P7-9/10 and P1-10B/10) and two rough isolates (P7-9/2R/10 and P1-10B/2R/10) of F. psychrophilum. The crystal violet staining method was used to stain the biofilms. Most of the compounds at sub-MICs inhibited the biofilm formation of mainly smooth isolates, attaining up to 80% inhibition. Additionally, the same reduction trend was also observed for 2-aminoimidazole, emodin, parthenolide, and D-leucine on the biomass of mature biofilms in a concentration-dependent manner. The anti-biofilm properties of the compounds are believed to lie in their ability to disturb the cellular interactions during biofilm formation and probably to cause cell dispersal in already formed biofilms. Lytic bacteriophages efficiently inhibited biofilm formation of F. psychrophilum, while they partially reduced the biomass of mature biofilms. However, the phage combination (Fpv-9 + Fpv-10) showed a successful reduction in the biomass of F. psychrophilum mature biofilms. We conclude that inhibiting compounds together with bacteriophages may supplement the use of disinfectants against bacterial biofilms (e.g., F. psychrophilum biofilms), leading to a reduced occurrence of bacterial coldwater disease outbreaks at fish farms.

Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm

Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease and rainbow trout fry syndrome, and hence this bacterium is placed among the most important salmonid pathogens in the freshwater aquaculture industry. Since bacteria in biofilms differ substantially from free-living counterparts, this study sought to find the main differences in gene expression between sessile and planktonic states of F. psychrophilum LM-02-Fp and NCMB1947^T, with focus on stress-related changes in gene expression occurring during biofilm formation. To this end, biofilm and planktonic samples were analyzed by RNA sequencing to detect differentially expressed candidate genes (DECGs) between the two growth states, and decreasing the effects of interstrain variation by considering only genes with log₂-fold changes ≤ −2 and ≥ 2 at Padj-values ≤ 0.001 as DECGs. Overall, 349 genes accounting for ~15% of total number of genes expressed in transcriptomes of F. psychrophilum LM-02-Fp and NCMB1947^T (n = 2327) were DECGs between biofilm and planktonic states. Approximately 83 and 81% of all up- and down-regulated candidate genes in mature biofilms, respectively, were assigned to at least one gene ontology term; these were primarily associated with the molecular function term “catalytic activity.” We detected a potential stress response in mature biofilms, characterized by a generalized down-regulation of DECGs with roles in the protein synthesis machinery (n = 63, primarily ribosomal proteins) and energy conservation (seven ATP synthase subunit genes), as well as an up-regulation of DECGs involved in DNA repair (ruvC, recO, phrB1, smf, and dnaQ) and oxidative stress response (cytochrome C peroxidase, probable peroxiredoxin, and a probable thioredoxin). These results support the idea of a strategic trade-off between growth-related processes and cell homeostasis to preserve biofilm structure and metabolic functioning. In addition, LDH-based cytotoxicity assays and an intraperitoneal challenge model for rainbow trout fry agreed with the transcriptomic evidence that the ability of F. psychrophilum to form biofilms could contribute to the virulence. Finally, the reported changes in gene expression, as induced by the plankton-to-biofilm transition, represent the first transcriptomic guideline to obtain insights into the F. psychrophilum biofilm lifestyle that could help understand the prevalence of this bacterium in aquaculture settings.

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens)

Characterization of interactions within a host-associated microbiome can help elucidate the mechanisms of microbial community formation on hosts and can be used to identify potential probiotics that protect hosts from pathogens. Microbes employ various modes of antagonism when interacting with other members of the community. The formation of biofilm by some strains can be a defense against antimicrobial compounds produced by other taxa. We characterized the magnitude of antagonistic interactions and biofilm formation of 25 phylogenetically diverse taxa that are representative of isolates obtained from egg surfaces of the threatened fish species lake sturgeon (Acipenser fulvescens) at two ecologically relevant temperature regimes. Eight isolates exhibited aggression to at least one other isolate. Pseudomonas sp. C22 was found to be the most aggressive strain, while Flavobacterium spp. were found to be one of the least aggressive and the most susceptible genera. Temperature affected the prevalence and intensity of antagonism. The aggressive strains identified also inhibited growth of known fish pathogens. Biofilm formations were observed for nine isolates and were dependent on temperature and growth medium. The most aggressive of the isolates disrupted biofilm formation of two well-characterized isolates but enhanced biofilm formation of a fish pathogen. Our results revealed the complex nature of interactions among members of an egg associated microbial community yet underscored the potential of specific microbial populations as host probiotics.

Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State

Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease and the rainbow trout fry syndrome in salmonid aquaculture worldwide. However, there have been few studies into the capacity of F. psychrophilum to form biofilms and how these cellular accretions differ from planktonic cells or how they affect potential virulence. We evaluated the biofilm formation by three Chilean isolates of F. psychrophilum (LM-02-Fp, LM-06-Fp, and LM-13-Fp) and two non-Chilean strains (JIP02/86 and NCMB1947^T), and compared biofilm and planktonic states to obtain insights into expression differences of virulence- and biofilm-related genes (VBRGs). Our findings are based on scanning confocal laser microscopy (SCLM) and LIVE/DEAD staining, enzymatic reactions, reverse transcription-quantitative PCR (RT-qPCR) of genes encoding putative virulence factors, and transcriptomes (RNA-Seq). The LM-02-Fp and NCMB1947^T strains were the strongest and weakest biofilm producers, respectively. The strong-biofilm producer showed different physiological cell states distributed in different layers of mature biofilms, whereas the NCMB1947^T biofilms consisted of cells arranged in a monolayer. WGA-binding exopolysaccharides would be the main components of their corresponding extracellular matrices. Transcriptomes of F. psychrophilum NCMB1947^T and LM-02-Fp were clustered by state (biofilm vs. planktonic) rather than by strain, indicating important state-dependent differences in gene expression. Analysis of differentially expressed genes between states identified putative VBRGs involved in polysaccharide biosynthesis, lateral gene transfer, membrane transport (e.g., for drugs and Fe³⁺), sensory mechanisms, and adhesion, and indicated that about 60-100% of VBRGs involved in these processes was significantly upregulated in the biofilm state. Conversely, upregulated motility-related genes in the biofilm state were not identified, whereas a lower fraction of proteolysis-related genes (33%) was upregulated in biofilms. In summary, F. psychrophilum strains that produce different biofilm phenotypes show global transcriptional activity in the mature biofilm state that differs significantly from their planktonic counterparts. Also, different biofilm phenotypes share a genetic potential for virulence that is transcriptionally enhanced with respect to free-living cells. Our results suggest that the F. psychrophilum biofilm lifestyle acts as a reservoir for a given set of putative virulence factors, and recommend a deeper understanding of which could help prevent recurring infections in salmonid farms.

Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?

Almost one‐third of crop yields are lost every year due to microbial alterations and diseases. The main control strategy to limit these losses is the use of an array of chemicals active against spoilage and unwanted pathogenic microorganisms. Their massive use has led to extensive environmental pollution, human poisoning and a variety of diseases. An emerging alternative to this chemical approach is the use of microbial biocontrol agents. Biopesticides have been used with success in several fields, but a better understanding of their mode of action is necessary to better control their activity and increase their use. Very few studies have considered that biofilms are the preferred mode of life of microorganisms in the target agricultural biotopes. Increasing evidence shows that the spatial organization of microbial communities on crop surfaces may drive important bioprotection mechanisms. The aim of this review is to summarize the evidence of biofilm formation by biocontrol agents on crops and discuss how this surface‐associated mode of life may influence their biology and interactions with other microorganisms and the host and, finally, their overall beneficial activity.

Growth inhibition of bacterial fish pathogens and quorum-sensing blocking by bacteria recovered from chilean salmonid farms

The main goal of this study was to find bacterial isolates with the ability to inhibit the growth of the fish pathogens Aeromonas hydrophila, Vibrio anguillarum, and Flavobacterium psychrophilum and to inhibit the blockage of the quorum-sensing (QS) system. A total of 80 gram-negative strains isolated from various freshwater Chilean salmonid farms were studied. We determined that 10 strains belonging to the genus Pseudomonas inhibited at least one of the assayed fish pathogens. Of these, nine strains were able to produce siderophores and two strains were able to inhibit the growth of all assayed pathogenic species. When the 80 strains were examined for QS-blocking activity, only the strains Pseudomonas sp. FF16 and Raoultella planticola R5B1 were identified as QS blockers. When the QS-blocker strains were analyzed for their ability to produce homoserine lactone (HSL) molecules, thin-layer chromatography analysis showed that both strains were able to produce C6-HSL- and C8-HSL-type molecules. Strain R5B1 did not show growth inhibition properties, but strain FF16 also led to inhibition of growth in A. hydrophila and F. psychrophilum as well as to siderophore production. Pseudomonas sp. FF16 exhibited potentially useful antagonistic properties and could be a probiotic candidate for the salmon farming industry.