1. Introduction
Bacteriocins are ribosomally synthesized antimicrobial peptides or proteins produced by lactic acid bacteria (LAB), exhibiting potent activity against foodborne pathogens and spoilage microorganisms. Regarded as safe for human consumption, they are widely recognized as natural food preservatives with broad application potential [
1,
2,
3]. Many LAB strains harbor the genetic capacity to produce bacteriocins [
4,
5,
6,
7,
8]. However, bacteriocin production is influenced by various factors, including culture conditions, expression of biosynthetic genes, and external stimuli. Although strategies have been developed to modulate these factors, challenges related to safety, yield stability, and genetic consistency remain significant hurdles for industrial application [
9].
L. plantarum EL2, isolated from traditionally fermented yak milk in the high-altitude Gannan Tibetan Autonomous Prefecture of the eastern Tibetan Plateau, produces the class IIb bacteriocin PlnJK [
10]. PlnJK exhibits broad-spectrum activity, inhibiting both Gram-positive bacteria and Gram-negative pathogens such as
S. enterica. Having evolved in natural fermentation systems with fluctuating temperatures and pH, EL2 demonstrates robust adaptability to environmental instability—a trait that may lower technical barriers and resource demands in fermentation processes. However, under overly extreme culture conditions, bacteriocin production can still decline or cease entirely. Microbial co-culture has been shown to significantly influence and enhance bacteriocin synthesis in lactic acid bacteria [
11]. For example, when the non-producer
L. plantarum J23 was co-cultured with 45 inducing strains, bacteriocin production was activated in 10 of these pairings [
12]. Co-culture of
Lactococcus lactis with
Enterobacter increased nisin yield by 85% [
13], while optimizing the inoculation ratio and incubation time for
Lactobacillus paracasei HD1.7 with
lacticaseibacillus markedly boosted the production of bacteriocin Paracin 1.7 [
14]. These findings underscore that screening suitable inducing partners and optimizing co-culture conditions can substantially improve bacteriocin titers, highlighting the importance of elucidating the underlying regulatory mechanisms.
Quorum sensing (QS) is a core molecular mechanism that enables microorganisms to achieve intraspecific or interspecific cell-to-cell communication and coordinated regulation of population behaviors through the secretion, recognition, and response to autoinducer signaling molecules. This mechanism can precisely regulate bacteriocin biosynthesis in lactic acid bacteria (LAB) via cascade signaling pathways [
15]. In the QS regulatory pathway governing bacteriocin synthesis in LAB, the core regulatory mechanism is the two-component system (TCS). In this system, microorganisms first synthesize and secrete autoinducer (AI) signaling molecules. Once the extracellular concentration of these signaling molecules reaches a threshold level, they are specifically recognized and bound by the histidine protein kinase (HPK) encoded by the
plnB gene. Upon binding, the HPK undergoes autophosphorylation and subsequently transfers the phosphate group to the response regulator (RR) encoded by either the
plnC or
plnD gene, thereby activating it through phosphorylation [
16]. The activated response regulator subsequently binds to the promoter regions of downstream target genes, specifically inducing the transcription of functional genes involved in bacteriocin synthesis. These include the
plnJ,
plnK,
plnE,
plnF, and
plnN genes, which encode the bacteriocin precursor peptides; the
plnI gene, which encodes the immunity protein; and the
plnGH genes, which encode the secretion and transport proteins. Ultimately, this cascade leads to the successful synthesis, self-immunity, and extracellular transport of bacteriocin [
17]. Autoinducer signals are primarily categorized into two types: the intraspecific signal peptide AIP encoded by
plnA, and interspecific signals, namely AI-2, which is produced via the enzymatic activity of the LuxS protein encoded by
luxS [
18,
19]. It is generally accepted that in microbial co-culture systems, interspecific QS mediated by AI-2/
luxS is the predominant factor influencing bacteriocin yield [
20]. However, Liu et al. demonstrated through the addition of an AI-2 inhibitor that both AI-2 and AIP still play significant and independent regulatory roles in the process of
Bacillus BS15 inducing bacteriocin synthesis in
L. plantarum RX-8 [
21]. This question necessitates further investigation into the QS system. Notably, while research on microbial co-culture in the food sector has largely focused on its impact on food quality, studies specifically investigating the underlying QS mechanisms and intercellular signaling molecules remain limited [
22]. Consequently, the relationship between the AIP/
plnA pathway and the AI-2/
luxS pathway in co-culture systems, as well as their similarities and differences in modulating the two-component system (HPK and RR), remain unclear.
In this study, three distinct cultivation models—simulating harsh (extreme), sub-optimal, and favorable environments—were established to investigate bacteriocin synthesis. By harnessing the inducing potential of microbial co-culture, the production of bacteriocin PlnJK was significantly enhanced under each condition. This strategy presents a practical and economical alternative to the stringent cultivation requirements typical of fermentation processes and provides a conceptual framework for using co-culture to improve bacteriocin yield in lactic acid bacteria (LAB). Furthermore, this work elucidates the mechanisms underlying co-culture-induced high-efficiency bacteriocin synthesis in strain EL2 through multi-level analysis, identifying key genetic determinants. These insights advance the functional understanding of QS-associated genes and offer a technical foundation for the scalable industrial production of LAB bacteriocins.
2. Materials and Methods
2.1. Experimental Strains
The bacteriocin-producing strain used in this study was Lactiplantibacillus plantarum EL2.
The co-culture inducing strains used were Saccharomyces cerevisiae SD-1, SD-7; Pichia dushanensis BK-11; Bacillus subtilis QSM27, QSM199; Bacillus pumilus CF88; Lactiplantibacillus plantarum EA3, CD11; Lactococcus lactis SL1; Leuconostoc mesenteroides SL2; Enterococcus durans S12; Enterococcus faecalis S84, MH2; Limosilactobacillus fermentum MK12; Lacticaseibacillus paracasei AC13. These strains were originally isolated from distinct ecological niches, including fermented milk, wine, and soil. Preliminary safety assessments, encompassing antibiotic susceptibility and hemolytic activity tests, indicated a favorable safety profile. All strains are currently preserved at the Gansu Provincial Functional Dairy Engineering Laboratory.
The antibacterial indicator strain used in this study was Salmonella enterica ATCC 13076.
The AI-2 autoinducer reporter strain used was Vibrio harveyi BB170.
Hemolytic control strain: Staphylococcus aureus.
2.2. Materials
All culture media, including De Man, Rogosa and Sharpe Broth (MRS) Broth/Agar, Yeast Extract Peptone Dextrose (YPD) Broth/Agar, Tryptone Soy Agar (TSA), Bacteriocin Production Medium (BPM), Lysogeny Broth (LB) Broth/Agar, Potato Dextrose Broth (PDB), Brain Heart Infusion Broth (BHI), and Tryptone Soy Broth (TSB), were purchased from Beijing Coolaber Science and Technology Co., Ltd. (Beijing, China).
All chemicals and kits used in this study were obtained from commercial suppliers. Catalase, Proteinase K, and Phosphate-Buffered Saline (PBS) were purchased from Shanghai Yuanye Bio-Technology Co., Ltd. (Shanghai, China). The RNA Rapid Extraction Kit and dialysis tubing were sourced from Beijing Solarbio Science & Technology Co., Ltd. (Beijing, China). Physiological saline, ammonium sulfate, and sodium hydroxide were supplied by China National Pharmaceutical Group Co., Ltd. (Sinopharm, Beijing, China).
2.3. Design of Culture Systems for Suboptimal, Low, and Favorable Bacteriocin Production
2.3.1. Design of a Gradient of Cultivation Conditions
With the culture medium (MRS) and incubation time (24 h) held constant, three key factors affecting bacteriocin synthesis—cultivation temperature, initial pH, and inoculum concentration—were varied to establish the experimental conditions detailed in
Table 1.
2.3.2. Collection and Preparation of Cell-Free Fermented Supernatant
Under each of the 12 cultivation conditions, activated
L. plantarum EL2 cultures were inoculated into MRS broth and incubated for 24 h. Subsequently, the cultures were centrifuged (10,000×
g, 10 min, 4 °C). The resulting supernatant was aseptically filtered through a 0.22 μm pore-size membrane to obtain cell-free supernatant (CFS), following established protocols [
23].
2.3.3. Preparation of Crude Bacteriocin
Bacteriocin was partially purified from the CFS of strain EL2 using ammonium sulfate precipitation. Briefly, the CFS was first adjusted to pH 7.0 with 1 M NaOH. Solid ammonium sulfate was then slowly added with constant stirring at 4 °C to achieve 70% saturation. The mixture was incubated overnight at 4 °C to allow for protein precipitation, followed by centrifugation (10,000×
g, 10 min, 4 °C). The resulting pellet was redissolved in 0.2 mol/L phosphate-buffered saline (PBS, pH 7.0) for subsequent analysis, as described previously [
24].
Based on the reported molecular weight of bacteriocin PlnJK (approximately 3–3.5 kDa), a two-step desalting and concentration procedure was performed. The solution was sequentially dialyzed using membranes with molecular weight cutoffs of 4 kDa and 2.5 kDa, followed by lyophilization for 48 h to obtain semi-purified PlnJK [
25]. Previous purification and activity profiling within our research group confirmed that the antimicrobial activity in extracts prepared by this method is specific to PlnJK. Therefore, in this study, the antibacterial activity of the crude extract was used as a direct indicator of PlnJK production.
2.3.4. Antibacterial Activity Assay of Crude Bacteriocin Extracts Under Varied Culture Conditions
Bacteriocin PlnJK obtained from each of the 12 cultivation conditions was reconstituted to a concentration of 1 mg/mL. Its antibacterial activity against S. enterica ATCC 13076 was assessed using the double-layer agar diffusion assay. Briefly, 100 µL of the bacteriocin solution was loaded into wells punched in agar plates previously seeded with the indicator strain. After incubation, the diameters of the inhibition zones were measured with a digital vernier caliper to a precision of 0.01 mm.
Since the bacteriocin concentration and loading volume were consistent across samples, the diameter of the inhibition zone served as a direct proxy for the bacteriocin production level of strain EL2. Based on the comparative activity results from the 12 culture conditions, three representative sets were selected to establish defined cultivation models, corresponding to non-inducing, weakly inducing, and strongly inducing conditions for bacteriocin synthesis.
2.4. Screening for Optimal Inducing Strains
Fifteen safe strains, phylogenetically distinct from EL2, were selected as candidate inducers for co-culture screening. Each candidate strain was pre-cultured in its appropriate liquid medium through two sequential passages. Third-passage cultures were then used for co-culture experiments under the three predefined cultivation models (non-inducing, weakly inducing, and strongly inducing conditions for bacteriocin production). EL2 and each inducer were inoculated at an equal-volume ratio (1:1) into MRS broth and incubated for 24 h to obtain co-culture broths. For comparison, EL2 was also cultured alone in MRS broth for 24 h under the same three models to generate pure-culture controls. In both pure- and co-culture systems, the total inoculation volume was maintained at 2% (v/v).
CFS was prepared from both the pure-culture and co-culture broths, followed by partial purification of bacteriocin. The antibacterial activity of the resulting extracts (adjusted to 1 mg/mL) was determined against S. enterica ATCC 13076 via the agar diffusion assay, with inhibition zone diameters measured as described previously. For each of the three cultivation models, the difference in zone diameter between the co-culture and its corresponding pure-culture control was calculated. A positive difference served as the indicator of inducing capability, whereas a difference of zero or negative indicated no induction.
2.5. Susceptibility of Inducing Strains to Bacteriocin PlnJK
The inhibitory activity of bacteriocin PlnJK against each of the 15 candidate co-culture strains was assessed by measuring the diameter of the inhibition zones. All assays were conducted in triplicate, and the mean zone diameter was calculated for each strain.
2.6. Characterization of Co-Culture Derived Inducing Substances
CFS was prepared from the fermentation broth of the optimal inducing strain, E. faecalis MH2. To neutralize acidic components, the CFS was adjusted to pH 7.0 using NaOH. Catalase was then added to remove any residual hydrogen peroxide. The antibacterial activity of the treated CFS against S. enterica was subsequently evaluated by the agar diffusion assay, with inhibition zone diameters serving as the readout.
Crude bacteriocin extracts were prepared from eight distinct co-culture fermentation broths, each subjected to a different pre-treatment regimen. The antibacterial activity of each extract was then assessed by measuring the diameter of the corresponding inhibition zone (
Table 2).
The Transwell co-culture system prevents direct physical contact between strains, thereby enabling the investigation of intercellular communication mediated by metabolic compounds.
2.7. Monitoring of Bacterial Growth and Bacteriocin Activity Kinetics over 24 h
L. plantarum EL2 and
E. faecalis MH2 were pre-cultured through two sequential passages. They were then co-inoculated at a 1:1 (
v/
v) ratio into fresh MRS broth, achieving a total inoculum of 2% (
v/
v). A pure culture of EL2 alone was prepared in parallel as the control. The optical density at 600 nm (OD
600) of both the pure-culture and co-culture broths was monitored at 2 h intervals over 24 h to generate growth curves [
27].
In parallel, samples were collected from both the pure-culture and co-culture broths at 2 h intervals. Each sample was centrifuged, and crude bacteriocin extracts were prepared. The antibacterial activity of these extracts was assessed by measuring the inhibition zone diameter against S. enterica ATCC 13076.
2.8. Monitoring of AI-2 Autoinducer Concentration During a 24 h Period in Pure- and Co-Culture Systems
Fermentation broth samples were collected from both co-culture and pure-culture systems at 2 h intervals. The AI-2 autoinducer concentration in each sample was quantified using the bioluminescent reporter strain
V. harveyi BB170, following established protocols [
28].
2.9. Co-Culture-Induced Bacteriocin Synthesis: Condition Optimization
To optimize bacteriocin production, a stepwise screening of cultivation parameters was initiated. First, the co-culture performance of EL2 and MH2 was evaluated in five media: Potato Dextrose Broth (PDB), Brain Heart Infusion (BHI), Bacteriocin Production Medium (BPM), Tryptic Soy Broth (TSB), and de Man, Rogosa and Sharpe (MRS) broth. Subsequently, using MRS medium, suitable ranges for incubation time (8–24 h), temperature (34–38 °C), and initial pH (4.0–8.0) were determined. Based on these preliminary results, cell-associated parameters were further optimized. This included assessing the effects of different initial cell densities (104–108 CFU/mL) and the EL2:MH2 inoculation ratio (1:6, 1:3, 1:1, 3:1, 6:1) on bacteriocin yield. All optimization steps were assessed by measuring the inhibition zone diameter of the corresponding crude bacteriocin extract.
2.10. Optimization of Co-Culture Conditions via Response Surface Methodology
Based on preliminary single-factor experiments, three key factors—initial cell density (A), inoculation ratio (B), and initial pH (C)—were selected for response surface optimization. Each factor was assigned three levels, and a Box–Behnken design (BBD) was generated using Design-Expert
® software (v. 8.0.6.1). The inhibition zone diameter served as the response variable to model and identify the optimal cultivation conditions, following the methodology outlined by [
29].
A Box–Behnken design was used to analyze the main and interactive effects of the selected factors on antibacterial activity via multiple regression modeling, with the aim of determining the optimal co-culture conditions. Verification experiments were performed in triplicate under the predicted optimum. Model validity was evaluated by comparing the experimentally measured antibacterial activity with the corresponding values predicted by the regression model (
Table 3).
2.11. Minimum Inhibitory Doses (MIDs) of the Crude Bacteriocin Extract from Strain EL2 Against S. enterica Before and After Response Surface Optimization
2.11.1. MID of the Crude Bacteriocin Extract from Strain EL2 Against S. enterica Under Pure Culture Conditions
A S. enterica suspension was harvested during the logarithmic growth phase and adjusted to 106 CFU/mL. A 1.024 g sample of the crude bacteriocin extract (lyophilized powder obtained by ammonium sulfate precipitation, without further purification) was dissolved in 1 L of PBS to obtain a 1.024 mg/mL stock solution, which was then serially diluted twofold with PBS. Aliquots (100 μL) of the bacterial suspension and of the crude bacteriocin extract at various concentrations were added to the wells of a 96-well plate. After incubation at 37 °C for 16 h, the optical density at 600 nm (OD600) was measured. The lowest dose of the crude extract that completely inhibited the growth of S. enterica was defined as the MID. A mixture of 100 μL of the bacteriocin solution and 100 μL of sterile LB broth served as the negative control, while 200 μL of the bacterial suspension alone served as the positive control.
2.11.2. MID of the Crude Bacteriocin Extract from Strain EL2 Against S. enterica Under Co-Culture Conditions
The MID of the crude bacteriocin extract obtained from the co-culture of strains EL2 and MH2 was determined against
S. enterica using the method described in
Section 2.11.1.
2.11.3. MID of the Crude Bacteriocin Extract from Optimized Co-Culture (Strains EL2 and MH2) Against S. enterica
The MID of the crude bacteriocin extract obtained under optimized co-culture conditions was determined against
S. enterica using the method described in
Section 2.11.1.
2.12. Quantitative Analysis of Quorum-Sensing-Related Gene Expression
Gene sequences of
L. plantarum were retrieved from the NCBI database. Primers were designed using Primer Premier 5.0 and commercially synthesized (Tsingke Biotechnology Co., Ltd., Beijing, China). The primer sequences are provided in
Table 4.
Cell pellets were harvested from the pure culture (EL2) and co-culture (EL2 and MH2) groups at the late logarithmic phase (12 h and 14 h) and mid-stationary phase (18 h and 20 h), with three biological replicates per group at each time point. Total RNA was extracted from the harvested cell pellets using a commercial RNA extraction kit, and genomic DNA was removed by DNase digestion. Using total RNA as a template, cDNA was synthesized by reverse transcription with the Tsingke SynScript® III RT SuperMix for qPCR. The resulting cDNA was diluted threefold and used as a template for qPCR amplification with the Tsingke ArtiCanCEO SYBR qPCR Mix. Following the manufacturer’s instructions, a 20 μL real-time quantitative PCR reaction mixture was prepared, with three technical replicates for each sample. The thermal cycling conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 40 cycles of 95 °C for 15 s, 60 °C for 20 s, and 72 °C for 20 s.
The relative expression levels of the key QS gene luxS and the bacteriocin synthesis genes plnA, plnB, plnC, plnD, plnJ, and plnK were determined in the co-culture system at different time points using the 2^(−ΔΔCt) method, with 16S rRNA as the reference gene and pure culture of EL2 during the logarithmic phase as the calibrator (expression level = 1).
2.13. Statistical Analysis
All experiments were conducted with at least three independent replicates, and the data are presented as the mean ± standard deviation (SD). Differences between groups were assessed using one-way analysis of variance (ANOVA). Statistical analyses were performed using SPSS software (version 19.0, IBM Corp., Armonk, NY, USA). Graphs were generated using OriginPro software (version 2019b, OriginLab Corporation, Northampton, MA, USA).
4. Discussion
Previous studies indicate that microbial co-cultures can establish stable interactions, enhancing resilience against environmental stressors that otherwise impair growth and metabolism [
30]. Co-cultivation can improve strain adaptability, thereby supporting enhanced metabolic output even under suboptimal cultivation parameters [
15]. In this work, we established defined cultivation models that simulate extreme environments to challenge lactic acid bacteria growth. Microbial co-culture significantly enhanced the tolerance of
L. plantarum EL2 to these stressors. Notably, eight inducing strains enabled bacteriocin synthesis under conditions that completely abolished production in monoculture. The most potent inducer,
E. faecalis MH2, increased the yield of bacteriocin PlnJK by approximately 1.66-fold. Subsequent optimization of the co-culture conditions further increased PlnJK production by approximately 1.97-fold. This aligns with reports such as that of Ye et al., who achieved a substantial increase in bacteriocin Paracin 1.7 yield via co-culture optimization [
14]. This approach thus represents a sustainable and economically favorable strategy for process intensification and high-titer bacteriocin production in industrial lactic acid bacteria fermentations.
The Transwell co-culture system physically separates the strains, eliminating direct cell-to-cell contact and allowing the role of extracellular metabolites in intercellular communication to be specifically investigated [
31,
32]. The bacteriocin produced in the Transwell system was identical to that synthesized in direct co-culture, demonstrating that direct physical contact is not a prerequisite for induction and that informational exchange is primarily mediated by diffusible extracellular metabolites [
33]. The
luxS protein, encoded by the
luxS gene, is a known key mediator in co-culture-induced bacteriocin synthesis and is susceptible to degradation by proteinase K [
34]. However, the CFS of MH2 retained partial inducing activity following heat inactivation or proteinase K treatment. This suggests that a component of the inducing factors produced by MH2 is not proteinaceous in nature.
The enhanced bacteriocin synthesis observed in the co-culture system is dependent on the AI-2 autoinducer, whose production is mediated by the
luxS gene and which is subject to gradual inactivation and degradation over the cultivation period [
35,
36]. Within co-culture systems, the autoinducing peptide (AIP, mediated by
plnA) and AI-2 (mediated by
luxS) have been shown to independently promote bacteriocin synthesis [
21]. In the EL2 and MH2 co-culture, AI-2 concentration began to decline in the late exponential phase (14 h), whereas bacteriocin production continued to increase. This indicates that residual, active inducing substances persisted in the system beyond 14 h. RT-qPCR analysis revealed distinct temporal expression patterns:
luxS gene expression was significantly elevated during the exponential phase compared to the stationary phase, while
plnA expression exhibited an inverse pattern, being significantly lower during exponential growth. In contrast, the expression levels of genes encoding the three-component regulatory system (
plnB,
plnC,
plnD) and the bacteriocin structural genes (
plnJ,
plnK) remained relatively stable across both growth phases and were consistently and significantly higher than those in the pure-culture group. Collectively, these findings support a model wherein, during the exponential co-culture phase, accumulation of
luxS-mediated AI-2 promotes efficient activation of the quorum-sensing circuitry, initiating a gradual increase in PlnJK synthesis [
37]. In the subsequent stationary phase, the regulatory influence shifts, and AIP encoded by
plnA becomes the predominant factor sustaining bacteriocin yield. This proposed temporal regulatory mechanism provides a theoretical framework for understanding how quorum-sensing systems orchestrate efficient bacteriocin synthesis in lactic acid bacteria [
38].
The AI-2 autoinducer is chemically derived from 4,5-dihydroxy-2,3-pentanedione (DPD) and can be produced synthetically. Exogenously supplied synthetic AI-2 can significantly modulate the QS systems of lactic acid bacteria [
39,
40,
41]. Certain metabolites, such as maltose or acetate, have been reported to stimulate
plnA gene expression [
42,
43]. Exogenous AI-2 can therefore substitute for interspecies QS, inducing increased bacteriocin synthesis during the logarithmic growth phase. However, the signal molecule responsible for this effect during the stationary phase remains unidentified.
The inducing substances produced by MH2 that are independent of the
luxS/AI-2 system only begin to influence EL2 during the stationary phase of co-culture. Consequently, the upregulation of the
plnA gene during the co-culture stationary phase may be attributed to either (i) specific compounds produced by MH2 that promote bacteriocin metabolism in EL2, or (ii) the continuous accumulation of MH2-secreted metabolites, which creates chemical stress on EL2, thereby inducing it to release more bacteriocin as a self-protective response. For instance, He et al. reported that ascorbic acid, N-acetyl-L-glutamic acid, butyryl trihexyl citrate, N-acetyl aspartate, and L-gulonolactone enhanced bacteriocin synthesis in co-culture systems [
32]. Among these, amino acid-type substances promoted the growth of lactic acid bacteria and increased the expression of genes related to bacteriocin metabolism, whereas butyryl trihexyl citrate inhibited the growth of lactic acid bacteria at elevated concentrations [
37]. Therefore, precise control of the co-culture duration is critical to ensure that these metabolites remain at appropriate concentrations, thereby improving the stability of enhanced bacteriocin synthesis.
In this study, preliminary observations indicated that bacteriocin synthesis was induced by the co-culture system; however, the underlying molecular mechanism remains unclear. To further elucidate this regulatory process, our research group plans to employ targeted metabolomics and other approaches to systematically identify the key signaling molecules within the co-culture system, thereby clarifying the chemical nature of the bacteriocin induction. Building on this, we aim to achieve precise regulation of bacteriocin production via the exogenous addition of target inducers. This approach could provide a feasible strategy to mitigate yield fluctuations during fermentation and reduce production costs. These investigations will help elucidate the intrinsic relationship between microbial interactions and secondary metabolite regulation at the molecular level, thereby advancing the design of efficient bacteriocin production processes.