Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens
© Zhao et al. 2015
Received: 14 July 2015
Accepted: 22 December 2015
Published: 5 January 2016
The probiotic bacterium Phaeobacter inhibens strain S4Sm, isolated from the inner shell surface of a healthy oyster, secretes the antibiotic tropodithietic acid (TDA), is an excellent biofilm former, and increases oyster larvae survival when challenged with bacterial pathogens. In this study, we investigated the specific roles of TDA secretion and biofilm formation in the probiotic activity of S4Sm.
Mutations in clpX (ATP-dependent ATPase) and exoP (an exopolysaccharide biosynthesis gene) were created by insertional mutagenesis using homologous recombination. Mutation of clpX resulted in the loss of TDA production, no decline in biofilm formation, and loss of the ability to inhibit the growth of Vibrio tubiashii and Vibrio anguillarum in co-colonization experiments. Mutation of exoP resulted in a ~60 % decline in biofilm formation, no decline in TDA production, and delayed inhibitory activity towards Vibrio pathogens in co-colonization experiments. Both clpX and exoP mutants exhibited reduced ability to protect oyster larvae from death when challenged by Vibrio tubiashii. Complementation of the clpX and exoP mutations restored the wild type phenotype. We also found that pre-colonization of surfaces by S4Sm was critical for this bacterium to inhibit pathogen colonization and growth.
Our observations demonstrate that probiotic activity by P. inhibens S4Sm involves contributions from both biofilm formation and the production of the antibiotic TDA. Further, probiotic activity also requires colonization of surfaces by S4Sm prior to the introduction of the pathogen.
KeywordsPhaeobacter inhibens Tropodithietic acid Biofilm formation Probiotic Marine pathogens Vibrio tubiashii Vibrio anguillarum Oyster disease ClpX ExoP
Infections by pathogenic marine bacteria are a major problem for both the shellfish and finfish aquaculture industries, causing severe disease and high mortality, which seriously affect aquaculture production and cause significant economic loss . This problem particularly affects the survival and growth of fish and shellfish during the larval and juvenile stages [1, 2]. Opportunistic pathogens from the Vibrionaceae and at least one member of the Roseobacter clade cause disease in a variety of shellfish [3, 4]. For example, Vibrio tubiashii, a reemerging pathogen of larval bivalve mollusks that causes invasive and toxigenic disease, has been responsible for massive mortalities among larval Pacific oysters (Crassostrea gigas) in hatcheries on the west coast of the United States . Additionally, Roseovarius crassostreae, a member of the Roseobacter clade and the causative agent of juvenile or Roseovarius oyster disease (JOD or ROD), can cause high mortalities in juvenile eastern oysters (Crassostrea virginica) in the northeastern United States during the summer when water temperatures are ≥20 °C . Although antibiotics and vaccines can be used to control some infectious diseases in aquaculture, they have some distinct disadvantages and limitations. Use of antibiotics increases the risk of development and transfer of antibiotic resistance . Vaccines, which rely on an adaptive immune response, are only effective for vertebrate organisms and cannot be used to protect shellfish .
Probiotics represent a promising alternative strategy to control infection and some probiotic strains are already used commonly in aquaculture as biological control agents in finfish and shellfish [8, 9]. For example, the probionts Bacillus subtilis and Bacillus licheniformis are widely used in shrimp aquaculture to provide beneficial effects potentially including improved health and water quality, control of pathogenic bacteria and their virulence, stimulation of the immune system and improved growth . Several Phaeobacter species have been shown to be effective probiotics for both finfish and shellfish. For example, D’Alvise et al.  demonstrated that Phaeobacter can be used as a probiotic treatment to reduce the density of the fish pathogen Vibrio anguillarum in cultures of cod larvae, resulting in the reduction of mortality by vibriosis. The probiotic activity was dependent upon the production of tropodithietic acid (TDA) by P. gallaeciensis. Further, D’Alvise et al.  demonstrated that a different TDA-producing strain of Phaeobacter was able to reduce or eliminate V. anguillarum from a combined liquid-surface system. These and other studies strongly suggest that antagonistic interactions by probiotic bacteria against marine pathogens may be useful in protecting commercially important species of shellfish and finfish from infectious disease.
Phaeobacter inhibens is gram-negative α-Proteobacteria from the Roseobacter clade. The Roseobacter clade, an important member of the marine microbiota, accounts for ~4 % to as much as ~40 % of bacterial DNA from the ocean and plays an important role in the organic sulfur cycle of the ocean [13–15]. Several species in this clade exhibit inhibitory activity against the growth of marine pathogens, including V. anguillarum, V. tubiashii and R. crassostreae [11, 12, 16]. Additionally, several potentially probiotic species from the Roseobacter clade can be routinely isolated from larval production facilities for turbot . Further, Phaeobacter species are typically excellent biofilm formers, colonizing a variety of surfaces including the walls of rearing tanks, microalgae, the skin of finfish, and the shells of mollusks [12, 18, 19]. Although, biofilm formation is thought to be essential for probiotic activity by a variety of mechanisms including competition for adhesion sites, oxygen, nutrients, and by preventing contact between pathogens and hosts , the role of biofilm formation in the probiotic activity of Phaeobacter species against shellfish pathogens has not been thoroughly investigated.
Previously, we isolated P. inhibens S4 from the inner shell surface of a healthy oyster . This bacterium is a short rod with 1–2 flagella on one or both poles. It has pleiomorphic morphology and will elongate into long rods and filaments under specific conditions (low salt concentration, static incubation, stationary phase). It can form rosettes and is an excellent biofilm former and a dominant colonizer of surfaces in marine environments. P. inhibens S4Sm is a spontaneous streptomycin-resistant mutant of the parental S4. When S4Sm was used as a potential probiotic treatment of oyster larvae, it showed strong anti-pathogen activity and increased host survival , but the actual mechanisms of probiotic activity used by this isolate are not fully understood.
In this study we examined the roles of biofilm formation and TDA production in probiotic activity of P. inhibens S4Sm in oysters challenged by the pathogen, V. tubiashii. In order to determine the contributions of TDA production and biofilm formation to the probiotic activity of S4Sm, mutations in clpX (which blocks TDA biosynthesis ) and an exopolysaccharide biosynthesis gene (exoP) (potentially involved in biofilm formation) were created by insertional mutagenesis. The effects of these mutations upon TDA production, biofilm formation and probiotic activity were determined.
P. inhibens S4Sm secretes the antibiotic tropodithietic acid
Differential sensitivities of marine pathogens to TDA
We examined the relative sensitivities of three pathogens of marine organisms, V. anguillarum NB10Sm, V. tubiashii RE22Sm, and R. crassostreae CV919Sm, to P. inhibens S4Sm by looking at the inhibition of growth around a colony of S4Sm. V. anguillarum NB10Sm was most sensitive to S4Sm with largest zone of inhibition (ZOI) (diameter = 12.5 ± 0.5 mm); R. crassostreae exhibited slightly less sensitivity to S4Sm (ZOI =11.2 ± 0.3 mm); and the least sensitive pathogen to S4Sm was V. tubiashii RE22Sm (ZOI = 9.2 ± 0.6 mm) (Fig. 1b). These data were consistent with the results for minimum inhibitory concentration (MIC) of TDA against each of the three pathogens: the MIC for TDA against NB10Sm was 1.25 μg/ml, against R. crassostreae the MIC was 5 μg/ml, and against RE22Sm the MIC was 6.25 μg/ml.
Biofilm formation by P. inhibens S4Sm
Quantification of biofilm formation by measuring optical density at 580 nm (OD580) of crystal violet dye attached to the cells forming biofilms on glass tubes at 27 °C under static conditions at 60 h
P. inhibens S4Sm
3.89 ± 0.06
P. inhibens WZ10 (clpX-)
3.90 ± 0.12
P. inhibens WZ11 (clpX+)
4.0 ± 0.06
P. inhibens WZ20 (exoP-)
1.60 ± 0.09b
P. inhibens WZ21 (exoP+)
3.90 ± 0.10
V. anguillarum NB10Sm
0.58 ± 0.02b
V. tubiashii RE22Sm
0.54 ± 0.02b
R. crassostreae CV919Sm
0.52 ± 0.08b
Effect of clpX gene mutation on TDA production
Killing ability of culture supernatant of various P. inhibens strains against V. anguillarum NB10Sm cellsa
Surviving V. anguillarum cell density (CFU/ml) after the treatment (±SDb)
NSSc (negative control)
40.7 (±3.8) × 107
S4Sm culture supernatant
WZ10 (clpX-) culture supernatant
41.3 (±1.5) × 107
WZ11 (clpX+) culture supernatant
WZ10 (clpX-) culture supernatant plus TDA
WZ20 (exoP-) culture supernatant
WZ21 (exoP+) culture supernatant
Effect of exoP gene mutation on biofilm formation
In order to develop a strain of S4 defective in biofilm formation but able to produce TDA, the exoP gene, which encodes an exopolysaccharide biosynthesis domain protein (based on Tigrfam classification systems), was identified in P. inhibens S4Sm strain. Mutation of exoP resulted in decreased biofilm formation, with the exoP mutant exhibiting only ~40 % of the wild type level of biofilm formation (Table 1) (P < 0.05). Complementation of exoP gene restored biofilm formation to wild type level (Table 1). Mutation of exoP did not result in defective TDA production (Fig. 1b). The exoP mutant and the exoP complement exhibited the same growth rate and final cell density as the wild type when grown in YP30 under shaking and static conditions (Additional file 5).
Effect of clpX and exoP mutations on the ability of P. inhibens biofilms to antagonize colonization of coverslips by Vibrio species
Effects of exogenous TDA on the antagonistic activity of the clpX mutant
Effects of V. tubiashii on growth of P. inhibens strains in competition assays
Effects of co-incubation with Phaeobacter strains on pathogen growth and biofilm formation
Effect of mutations in clpX and exoP on probiotic activity of P. inhibens against V. tubiashii in oyster larvae
Several Phaeobacter species are known to have probiotic activity and are able to protect fish species against bacterial pathogens . The production of the broad-spectrum antibiotic, tropodithietic acid (TDA), is regarded as one of the major factors contributing to probiotic activity against V.anguillarum infection in turbot and cod . We recently reported that the new isolate P. inhibens S4Sm protects the Eastern oyster (Crassostrea virginica) from infection by two oyster pathogens, V. tubiashii and R. crassostreae . In this report, we dissect the roles of TDA biosynthesis and biofilm formation in promoting probiotic activity by P. inhibens S4Sm, showing that both mechanisms are involved.
Although the TDA biosynthetic pathway has not been fully elucidated, many of the genes required for the formation of TDA and much of the pathway have been discovered [21, 23, 24]. One gene reported to be involved in TDA biosynthesis is clpX (encoding ClpX) . ClpX is an AAA+ ATPase that functions as an unfoldase chaperon for ClpP (ATP-dependent protease) and with ClpP forms the multimeric ClpXP protease . An insertional mutation in the clpX gene specifically blocked the biosynthesis of TDA in S4Sm (Fig. 1a) without affecting biofilm formation (Table 1) or growth (Additional file 4). Further, the effects of mutations to clpX upon cell physiology are subtle and diverse [26–28]. In contrast, mutations in tdaA, tdaB, and tdbD, all block TDA biosynthesis and also affect biofilm formation in S4Sm. The mechanism by which ClpX affects TDA production is still unknown. Additionally, the reasons why mutations in tdaA, tdaB, and tdbD decrease biofilm formation, as well as TDA biosynthesis, are not understood, and are not the focus of this study.
The clpX TDA deficient mutant was unable to inhibit V. tubiashii growth in either liquid or as a biofilm on a glass coverslip (Fig. 2); however, when cultures were supplemented with TDA, the growth of planktonic V. tubiashii growth was inhibited (Fig. 3). It is well known that organisms in biofilms are more resistant to antibiotics than when suspended in liquid . This is consistent with our data showing that TDA antibiotic activity was more potent against planktonic RE22 cells than towards RE22 cells living in a biofilm. These data, in which the effect of the wild type was restored by adding TDA to the clpX antibiotic activity mutant, strongly suggest that the loss of TDA production is responsible for the defect in antagonistic activity in the clpX mutant. Further, 48 h after the addition of TDA into the co-culture the inhibitory effect of TDA disappeared, likely due to instability of TDA over time or metabolism by V. tubiashii. Except for the loss of TDA synthesis, the clpX mutant exhibited no other defects in growth or biofilm formation compared to the S4Sm wild type when grown in pure culture (Additional file 5). The results reported here confirm the role of TDA as an antibiotic promoting probiotic activity of Phaeobacter species described previously by D’Alvise et al.  in another host-pathogen system. It is interesting to note that the growth of the clpX mutant is depressed by RE22 (Fig. 2), suggesting that TDA production allows P. inhibens to compete with faster growing species for available nutrients.
P. inhibens, a member of the abundant marine Roseobacter clade, is known to be an excellent colonizer of environmental surfaces . While no study of the effects of biofilm formation on the probiotic mechanism of Phaeobacter has been reported, it is interesting to note that Prol Garcia et al. (2014) recently reported that biofilm formation is not a prerequisite for TDA formation in P. inhibens. In that study, the authors, using Tn5 transposon mutagenesis, identified 22 TDA-positive mutants with defects in biofilm formation. Among classes of genes identified as contributing to biofilm formation were those involved in exopolysaccharide formation. In our study, the exoP gene was identified in S4Sm (using RAST ) as an exopolysaccharide biosynthesis gene, which is thought to be involved in biofilm formation. Mutation of exoP resulted in a large decrease in biofilm formation (Table 1), and exhibited no other defects in growth or TDA formation (Fig. 1c and Table 2). Thus, our observations correspond to those reported by Prol Garcia et al. (2014) that biofilm formation is not a prerequisite for TDA production and also that mutation of a gene involved with exopolysaccharide production can affect biofilm formation. While the exoP mutant was modestly defective in its ability to inhibit Vibrio species in competition assays (Figs. 2 & 5) it did exhibit significantly decreased probiotic activity in the oyster challenge assay against V. tubiashii (Fig. 6), these declines were less than those seen in the clpX mutant. We suggest that while in the in vitro (glass coverslip) model the exoP mutant forms much less biofilm than the wild type, enough TDA accumulates to inhibit RE22 to levels near those caused by wild type cells. However, in the in vivo oyster challenge model, the reduced biofilm of the exoP mutant results in decreased TDA production that is diluted by the larger volumes of the system and the feeding activity of the oyster larvae causing less inhibition of RE22. These data suggest that biofilm formation contributes to the probiotic activity of S4Sm. Biofilms may contribute to probiotic activity in two ways. First, biofilms would allow P. inhibens to physically occupy potential sites of colonization and prevent the oyster pathogens from gaining access to the oyster. Second, the formation of an extensive biofilm with cells at high density may induce the production of TDA . A more extensive biofilm would produce more TDA and, therefore, more effectively inhibit the ability of pathogens to infect the oyster host.
As a broad spectrum antibiotic TDA inhibits the growth of several marine pathogens . However, in the ocean environment TDA will be rapidly diluted once it is secreted. We suggest that P. inhibens requires both TDA production and biofilm formation for effective probiotic activity. The biofilm matrix creates a microenvironment within which TDA can accumulate to reach concentrations high enough to inhibit pathogens. In the absence of TDA, a P. inhibens biofilm does not eliminate pathogens and provides only modest protection against disease. Further, P. inhibens growing with a diminished biofilm also exhibits significantly reduced probiotic activity probably due to the decreased mass of cells producing TDA and the increase in available sites for pathogens to colonize. Our data indicate that maximum probiotic activity requires both TDA production and biofilm formation.
Karim et al.  reported that oyster larvae were best protected when P. inhibens S4Sm was added 24 h prior to challenge by either of the two oyster pathogens, V. tubiashii and R. crassostreae. The data presented in this report is consistent with those previous observations and reveal that pre-colonization of a surface by S4Sm is more effective than co-incubation at inhibiting V. tubiashii RE22 from either colonizing the glass coverslip surface or from growing planktonically (Figs. 2 and 5). One potential reason for this need for a 24 h pre-treatment is the rapid generation time of Vibrio species in YP30 (at 27 °C, with shaking), which is less than 1 h (V. tubiashii is ~0.53 h, V. anguillarum is ~0.89 h), while the doubling time for P. inhibens S4Sm is ~3.1 h. Successful probiotic activity by S4Sm may be dependent upon growth rate and having enough TDA producing cells in the biofilm to successfully antagonize and out-compete the oyster pathogens. Interestingly, we show in our study that V. anguillarum cells are more sensitive to TDA than are V. tubiashii cells, and that, while pre-colonization of surfaces by S4Sm was required to prevent the colonization of coverslips by V. tubiashii, it was not required to prevent the colonization by V. anguillarum. Consistent with these observations, D’Alvise et al.  showed that it was not necessary for P. gallaeciensis to precolonize the wells containing cod larvae in order to antagonize V. anguillarum and significantly reduce cod larvae mortalities. Our experiments indicate differences between Vibrio species on how they interact with the S4Sm probiotic. Interestingly, precolonization with RE22 reduces the ability of S4 and mutants to grow & colonize glass cover slips and to grow planktonically (Fig. 5), suggesting that RE22 is able to modulate the probiotic activity of S4Sm through negative impacts on the ability to grow and/or colonize surfaces.
The results presented in this study demonstrate that both TDA production and biofilm formation contribute to the probiotic activity of P. inhibens S4Sm. Specifically blocking TDA production by mutation of the clpX gene resulted in a significant decline in probiotic activity as determined by coverslip colonization assay or by survival of oyster larvae challenged by V. tubiashii RE22. While reducing biofilm formation by mutation of the exoP gene also resulted in a significant decline in probiotic activity as determined by survival of oyster larvae challenged by V. tubiashii RE22, but only a modest decline as measured by coverslip colonization assay. It is possible that biofilm formation contributes to probiotic activity in two ways: 1) occupying potential colonization sites and 2) increasing cell density-dependent induction of TDA biosynthesis. Future investigation will examine these possibilities.
TDA purification, identification and detection
TDA was produced and extracted using a modified method of Bruhn et al. . P. inhibens S4Sm was cultured in 7 x 1 L volumes of YP30 culture medium at 27 °C with shaking at 175 rpm. After 96 h, the cells were pelleted by centrifugation at 10,000 rpm for 10 min. The resulting culture supernatants were acidified to pH 3 with formic acid (FA) and extracted with acidified (0.1 % FA) ethyl acetate. The organic fraction was concentrated in vacuo to yield 0.673 g of crude extract. The extract was fractionated using C18 flash chromatography (Redisep Rf high performance gold 30 g hp combiflash column; linear gradient elution 5 % - 100 % CH3OH in H2O, 0.1 % FA, 35 ml/min, 45 min). Fractions containing TDA (tR = 15 min) were further purified by reversed-phased HPLC (Xterra 5 μm C18 100 x 3.0 mm column, 0.5 ml/min, 5 % to 100 % CH3OH in H2O over 24 min). Pure TDA (10 mg) was identified based on comparison of 1H NMR (Varian 500 MHz spectrometer) and mass spectral data in comparison to previously reported values (Additional files 1, 2 and 3) . All assays were conducted with purified TDA from P. inhibens S4Sm.
Culture supernatants from P. inhibens wild type and mutant strains were analyzed by HPLC for the presence of TDA. P. inhibens strains were cultivated in 50 ml YP30 broth until stationary phase (2 × 109 CFU/ml). Cells were pelleted by centrifugation (5000 × g, 10 min) and extracted as described above. The resulting organic extracts were reconstituted as 10 mg/ml solutions in methanol. Chromatography was performed on a Hitachi LaChromUltra UHPLC equipped with a Fortis C18 UHPLC Column (1.7 μm, 2.1 x 50 mm). Method: 0.25 ml/min flow rate, 5 % CH3OH in H2O (both acidified with 0.1 % FA) for 1 min, linear gradient to 100 % CH3OH over 6.2 min, 100 % CH3OH for 2 min.
Minimum inhibitory concentrations of TDA against V. anguillarum, V. tubiashii, and R. crassostreae
The minimal inhibitory concentrations (MIC) of TDA against selected marine pathogens were determined using a broth dilution method in microtiter plates . Overnight bacterial cultures were diluted to 105 CFU/ml in YP30 and treated with serial dilutions of pure TDA. After 24 h incubation at 27 °C, MICs were determined as the lowest concentration where there was no visible growth. Two independent experiments were done and each independent experiment had three replicates.
Bacterial strains, plasmids, and growth conditions
Bacterial strains and plasmids used in this study
Strains or plasmids
Previously Phaeobacter sp. S4; wild type isolate from the inner shell of oysters
Karim et al., 2013
Spontaneous Smr mutant of S4
clpX insertional mutant of S4Sm
clpX+, clpX in trans complement of WZ10
Smr Cmr Apr
exoP insertional mutant of S4Sm
exoP+, exoP in trans complement of WZ20
Smr Cmr Apr
Smr Cmr Kmr
clpX, WZ10 (pRhokHi-2-ofp)
Smr Cmr Kmr
exoP, WZ20 (pRhokHi-2-ofp)
Smr Cmr Kmr
Wild type isolate from oyster larvae
Estes et al., 2004
Spontaneous Smr mutant of RE22
Wild type, serotype O1, clinical isolate from the Gulf of Bothnia
Norqvist et al., 1989
Spontaneous Smr mutant of NB10
Smr Apr Tetr
Wild type isolate from a JOD-affected oyster
Boettcher et al., 1999
Spontaneous Smr mutant of CV919-312 T
thi thr leu tonA lacY supE recA RP4-2 Tc::Mu::Km (λpir)
Simon et al., 1983
Sm10 harboring pNQ705-1
Sm10 harboring pNQ705-clpX
Sm10 harboring pNQ705-exoP
Sm10 harboring pBBR1MCS4
Sm10 harboring pBBR1MCS4-clpX
Sm10 harboring pBBR1MCS4-exoP
Sm10 harboring pSUP202P-gfp(ORF)
Sm10 harboring pSUP202P-PflaB-gfp
Sm10 harboring pRhokHi-2-FbFP
Sm10 harboring pRhokHi-2-gfp
Sm10 harboring pRhokHi-2-ofp
Sm10 harboring pmOrange
Cmr; suicide vector with R6K origin
Cmr; derivative from pNQ705-1 for clpX insertional mutant
Cmr; derivative from pNQ705-1 for exoP insertional mutant
Apr; derivative from pBBR1MCS (a broad-host-range cloning vector)
Kovach et al., 1995
Apr; derivative from pBBR1MCS4 for clpX in trans complement
Apr; derivative from pBBR1MCS4 for exoP in trans complement
Template for gfp ORF PCR amplification
Eggers et al., 2004
Template for PflaB PCR amplification
Eggers et al., 2004
Apr Cmr Tcr; broad host shuttle vector
Simon et al., 1983
Apr Tcr; derivative from pSUP202 for GFP tagging
Apr Tcr; derivative from pSUP202 for GFP tagging
Cmr Kmr; derivative from pBBR1MCS (a broad-host-range cloning vector) with promoter PaphII
Piekarski et al., 2009
Cmr Kmr; derivative from pRhokHi-2-FbFP with gfp under the control of PaphII
Template for ofp ORF PCR amplification
Clontech Laboratories, Inc.
CmrKmr; derivative from pRhokHi-2-FbFP with ofp under the control of PaphII
Primers used in this study
Sequence (5′ to 3′, underlined sequences are engineered restriction sites)
For tdaA insertional mutation, forward, with SacI site
For tdaA insertional mutation, reverse, with XbaI site
For tdaB insertional mutation, forward, with SacI site
For tdaB insertional mutation, reverse, with XbaI site
For tdbD insertional mutation, forward, with SacI site
For tdbD insertional mutation, reverse, with XbaI site
For clpX insertional mutation, forward, with SacI site
For clpX insertional mutation, reverse, with XbaI site
For exoP insertional mutation, forward, with SacI site
For exoP insertional mutation, reverse, with XbaI site
For clpX in trans complement, forward, with SacI site
For clpX in trans complement, reverse, with XbaI site
For exoP in trans complement, forward, with SacI site
For exoP in trans complement, reverse, with XbaI site
For amplification of gfp ORF, forward, with NdeI site
For amplification of gfp ORF, reverse, with BamHI site
For amplification of PflaB, forward, with KpnI site
For amplification of PflaB, forward, with KpnI site
For amplification of ofp ORF, forward, with NdeI site
For amplification of ofp ORF, reverse, with BamHI site
Complementation of mutants
P. inhibens mutants were complemented by cloning the target gene fragment into the shuttle vector pBBR1MCS4 (GenBank accession No. U25060), using a modification of the method by Rock and Nelson . Primers (Table 4) were designed with a SacI or XbaI site added to the 5′ end of the appropriate primer. The primer pair was used to amplify the entire gene plus ∼ 500 bp of the 5′ and 3′ flanking regions from genomic DNA sequences of P. inhibens 2.10 (GenBank accession No.CP002972.1). The resulting amplicon was ligated into the pBBR1MCS4 plasmid after digestion with SacI and XbaI and the ligation mixture introduced into E. coli Sm10 (λ pir) by electroporation with Bio-Rad Gene Pulser II. Transformants were selected on LB10-Amp100 agar plates and the recombinant plasmids confirmed by both PCR amplification and sequencing. The complementing plasmid, pBBR1MCS4-clpX or pBBR1MCS4-exoP, was transferred from E. coli Sm10 into clpX or exoP mutants by conjugation using the procedures described previously [37, 41]. The transconjugants were confirmed by PCR amplification.
Fluorescence tagging of P. inhibens strains and Vibrio species
P. inhibens strains were tagged by pRhokHi-2-OFP and V. tubiashii was tagged by pRhokHi-2-GFP. The orange fluorescence protein gene (ofp) and the green fluorescence protein gene (gfp) were PCR amplified by using the appropriate primer pair (Table 4) designed according to the sequence of pmOrange vector (Clontech) and pSUP202p/PflaB-gfp vector. The PCR product was digested with NdeI and BamHI restriction enzymes and the DNA fragments separated on a 1 % agarose gel. Subsequently, the gel-purified ofp or gfp PCR fragment was ligated into pRhokHi-2 after digestion with NdeI and BamHI and the ligation mixture was introduced into E. coli Sm10 (λpir) by electroporation with Bio-Rad Gene Pulser II. Transformants were selected on LB10-Cm20 agar plates. All plasmids were transferred from E. coli SM10 to recipient strains of P. inhibens S4Sm, V. tubiashii RE22Sm, R. crassostreae CV919Sm, and V. anguillarum NB10Sm using the method described previously by Mou et al. . The transconjugants were confirmed by fluorescence microscopy.
Biofilm formation was assessed using a modification of the crystal violet (CV) staining method . Bacteria were grown for 2 days in YP30 (27 °C with shaking) to stationary phase (2 × 109 CFU/ml). Cells (2 μl) were transferred into 2 ml of fresh YP30 broth in 30 mm × 100 mm borosilicate (Pyrex) glass culture tubes containing 2 ml YP30 broth and allowed to grow at 27 °C without shaking. When sampling, the liquid culture was discarded and each tube rinsed twice with NSS to remove loosely attached cells. The biofilm attached to the test tube wall was stained with 2 ml of CV solution (0.2 %) for 20 min at room temperature. Unbound dye was removed with two washes of NSS. The bound dye was eluted with 95 % (vol/vol) ethanol for 30 min and then the amount of eluted crystal violet was measured by spectroscopy at 580 nm using a VERSA-MAX microplate reader.
Inhibition zone assay
Anti-bacterial activity of P. inhibens strains was measured by a growth inhibition assay using V. anguillarum, V. tubiashii, and R. crassostreae as the target organisms. An aliquot (100 μl) from a stationary phase overnight culture of the appropriate Vibrio or R. crassostreae culture (2 × 109 CFU/ml) was spread onto YP30 agar plates, then 10 μl of a 2-day-old culture (2 × 109 CFU/ml) of a P. inhibens strain was spotted in triplicate onto the pathogen cell lawn. After incubation at 27 °C for 24 h, the level of antibacterial activity was determined by the diameter of the inhibition zone around the P. inhibens colonies.
P. inhibens culture supernatant killing assay
In order to determine the bactericidal activity of culture supernatants, P. inhibens strains were grown for 2 days in YP30 (27 °C with shaking). Cultures were centrifuged (8000 × g, 10 min) and filtered through 0.2 μm pore membrane filters to collect filter sterilized cell-free supernatants. Overnight cultures of V. anguillarum (NB10Sm) cells (2 × 109 CFU/ml) were then serially diluted in filter sterilized, cell-free P. inhibens culture supernatant obtained from the various strains of P. inhibens or NSS, and then spotted (10 μl/spot of diluted V. anguillarum cells) in triplicate onto YP30 plates. All experiments were repeated twice. Killing percentage was calculated as follows: Killing % = [(no. of colonies in NSS control) – (no. of colonies in S4 supernatant treated)/(no. of colonies in NSS control)] × 100.
Glass coverslip colonization competition assay between P. inhibens strains and V. tubiashii WZ103 or V. anguillarum WZ203
This assay was performed using a modification of establishment and invasion of pre-established biofilms method . For all competition experiments, P. inhibens strains (S4Sm, clpX mutant and exoP mutant) were grown for 2 days in YP30 (27 °C with shaking) to stationary phase. Cells were harvested by centrifugation, washed twice in NSS, resuspended in fresh YP30, and then transferred into 6-well plates (Costar, Tewksbury MA). Each well contained a glass coverslip, 4 ml YP30 broth supplemented with streptomycin, and was inoculated with the appropriate P. inhibens strain (WZ02, WZ12, or WZ22) tagged with orange fluorescence protein (OFP) (final concentration ~1 × 104 CFU/ml). For experiments examining the effects of pretreatment with P. inhibens, after 24 h incubation at 27 °C with no shaking (pretreatment with P. inhibens) all coverslips were washed twice with NSS. Each coverslip was transferred into a fresh well containing 4 ml of YP30 broth supplemented with streptomycin plus the green fluorescence protein (GFP)-tagged V. tubiashii WZ103 or GFP-tagged V. anguillarum WZ203 (final concentration ~1 × 105 CFU/ml). After another 24 h incubation at 27 °C with no shaking, all coverslips were removed, washed twice on a rotary shaker (LAB-LINE instrument, Inc.) for 2 min (200 rpm) with NSS, and then transferred into clean wells with fresh YP30 broth and allowed to incubate as before. Two coverslips were removed at each sampling time (24, 48, 72 h). One was used for determination of the cell density of the strains on the coverslip; the second one was used for confocal imaging. Glass coverslips were washed with NSS twice on a rotary shaker for 2 min. After draining excess water, coverslips used for confocal imaging were placed on depression slides and cells on the upside of coverslip were wiped off with Kimwipes™. Coverslips used for CFU determinations were immersed in 50 ml plastic tubes containing 10 ml NSS and glass beads (0.5 g, 1 mm), then vortexed for 1 min. Cell densities (CFU/ml) in the wells or suspended from the coverslip were determined by serial dilution and spot plating. Appropriate antibiotics were used for selection of bacteria (see Table 3 for antibiotic resistances for each strain). For experiments without pretreatment with P. inhibens, all procedures were identical to those described above except that GFP-tagged V. tubiashii WZ103 or V. anguillarum WZ203 were added at the same time as OFP-tagged P. inhibens. In the V. anguillarum competition experiments, both P. inhibens and V. anguillarum were inoculated at ~106 CFU/ml.
Effects of TDA supplementation on pathogen growth in a co-culture system containing the clpX mutant and a Vibrio species
OFP-tagged P. inhibens strains (S4Sm, clpX mutant) grown for 2 days in YP30 (27 °C with shaking) to stationary phase, cells were transferred into 6-well plates. Each well was inoculated with the appropriate OFP-tagged P. inhibens strain (initial concentration at ~ 104 CFU/ml) in 4 ml of YP30 broth supplemented with the appropriate antibiotic and one glass coverslip. After 24 h incubation (pre-treatment with P. inhibens), all coverslips were washed twice in NSS. Each coverslip was transferred into a clean well containing 4 ml YP30 broth and either GFP-tagged V. anguillarum WZ203 or V. tubiashii WZ103 at a concentration of ~ 105 CFU/ml plus TDA (5 μg/ml for V. anguillarum WZ203 or 10 μg/ml for V. tubiashii WZ103; based on calculated MIC). The biofilms on the coverslips were imaged as described below and cell densities were determined as described above.
Laser confocal scanning microscopy
Laser confocal scanning microscopy was performed in the Rhode Island Genomic Sequencing Center using a Zeiss AxioImager 2 microscope equipped for digital image acquisition with a Zeiss AxioCam HRc high-resolution camera and for laser scanning microscopy with a Zeiss LSM 700 confocal module. The confocal module is equipped with four diode lasers with excitation lines at 405, 488, 555, and 639 nm and utilizes the Zeiss ZEN 2011 software.
Oyster larvae (n = 21–28 per well, veliger stage, ~0.060–0.150 mm in diameter) were placed in wells of a 6-well plate containing 5 ml of sterile filtered seawater (28 psu). Overnight cultures of P. inhibens strains grown in YP30 (~109 CFU/ml) were added to a final concentration of ~104 CFU/ml. Plates were incubated at 20 °C for 24 h with shaking. Water was changed and V. tubiashii RE22 was added at a concentration of ~105 CFU/ml in seawater and incubated for an additional 24 h before counting living and dead oysters. Oyster larvae treated only by artificial seawater served as control. The survival rate was calculated by using the formula: Survival rate (%) = 100 x (number of live larvae/total number of larvae). These experiments were run at least 2 times in triplicate . As invertebrates, oysters are exempt from approval from the University of Rhode Island Institutional Animal Care and Use Committee.
Data are expressed as means ± standard deviation (SD). Two-tailed, unpaired Student’s t tests were used for statistical analyses for all experiments, and P values of <0.05 were considered statistically significant.
We thank the personnel at the Blount Shellfish Hatchery at Roger Williams University for providing larval oysters. We also thank Petra Tielen (Institute of Microbiology, Universität Braunschweig) for the gift of the plasmids pRhokHi-2FbFP, pRhokHi-2, and pBBR1MCS4. Ralph Elston provided RE22 and Katherine Boettcher for providing CV919-312.
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