Biofilm hydrophobicity in environmental isolates of Bacillus subtilis

Harnessing Microbes to Weather Native Silicates in Agricultural Soils for Scalable Carbon Dioxide Removal

Anthropogenic carbon emissions contribute significantly to the greenhouse effect, resulting in global warming and climate change. Thus, addressing this critical issue requires innovative and comprehensive solutions. Silicate weathering moderates atmospheric CO2 levels over geological time, but it occurs too slowly to counteract anthropogenic emissions effectively. Here, we show that the microorganism Bacillus subtilis strain MP1 promotes silicate weathering across different experimental setups with various levels of complexity. First, we found that MP1 was able to form a robust biofilm in the presence of feldspar and significantly increased (p < 0.05) silicate dissolution rates, pH, and calcium carbonate formation in culture experiments. Second, in mesocosm experiments, we found that MP1 enhanced the silicate weathering rate in soil by more than six times compared to the untreated control. In addition, soil inorganic carbon increased by 20%, and the concentrations of ions, including calcium, magnesium, and iron, were also elevated under the MP1 treatment. More importantly, when applied as a seed treatment on eight soybean fields, we found that MP1 significantly (p < 0.05) boosted soil inorganic carbon, leading to a gross accrual of 2.02 tonnes of inorganic carbon per hectare annually. Our findings highlight the potential of enhancing native silicate weathering with microorganisms in agricultural fields to increase soil inorganic carbon, contributing to climate change mitigation.

Large scale identification of pellicle and cell-free liquid phase associated proteins in Bacillus amyloliquefaciens L-17

Bacillus amyloliquefaciens is a soil-associated and plant growth-promoting bacterium. It is the focus of numerous studies due to its ability to sporulate, form biofilms, produce antimicrobial peptides and commercial enzymes. The ability of B. amyloliquefaciensl-17 to form floating biofilm at the air-liquid interface "pellicle" was previously demonstrated. This pellicle exhibits a highly structured architecture which is provided by loosely and tightly matrix bound polysaccharides and proteins. In this study, a first large scale proteomic investigation of both the pellicle and the cell-free liquid phase of l-17 strain was performed. An approach based on physical and chemical extraction of the pellicular matrix combined with protein analysis by mass spectrometry identified 87 weakly matrix-bound proteins and 62 tightly bound proteins. A total of 131 pellicle-associated proteins were identified, including (i) the conserved proteins TasA and TapA, involved in biofilm formation and cohesion (ii) BslA, important for biofilm hydrophobicity (iii) several enzymes that make nutrients available and protect the biofilm from competitors (iv) flagellin and (v) proteins involved in the sporulation process. Proteomic characterization of the cell-free liquid phase underlying the analyzed pellicle allowed the identification of 423 proteins including 118 proteins yet identified in the matrix of the pellicle. The proteins identified specifically in the liquid phase include enzymes involved in the biosynthesis process of non-ribosomal peptides and a variety of commercial enzymes such as proteases, lipases, aminotransferases, peroxidases and phytases. This provides valuable clues to promote the industrial and agricultural application of the cell-free liquid phase of B. amyloliquefaciensl-17.

Inhibitory effects of garlic, cinnamon, and rosemary on viability, heat resistance, and biofilm formation of Bacillus cereus spores in the broth of a fermented soybean paste stew, Cheonggukjang jjigae

Foods prepared through heating, including broths, have the potential and risk of survival of Bacillus cereus, which has the ability to form spores and biofilms. This study evaluated the efficacy of various natural products (particularly spices) in mitigating B. cereus contamination in Cheonggukjang jjigae (CJ) broth. The following characteristics of B. cereus were examined: viability of vegetative cells (including other pathogenic bacteria) and planktonic spores, heat resistance of planktonic spores and spores in intact biofilms, and biofilm formation and persistence. In an antimicrobial test to evaluate the inhibitory effects of spice and cruciferous vegetable extracts on B. cereus CH3 vegetative cells, cinnamon, garlic, and rosemary extracts were selected as they have shown significant inhibitory effects, with inhibition zones of 20-29 mm in diameter at the highest concentration tested (160 mg/mL, unless otherwise stated). These spice extracts also exhibited antimicrobial activity against other foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7. Garlic extract showed the greatest inhibitory effect on the viability and heat resistance of planktonic spores of B. cereus CH3, and cinnamon and rosemary extracts exhibited similar effects. Garlic extract reduced B. cereus CH3 spore counts in phosphate buffer solution (PBS) and CJ broth by 20.22 % and 14.08 %, respectively, compared to control (treated with the same ethanol amount instead of the extract), and effectively weakened spore heat resistance, reducing the D100°C-values of planktonic spores of B. cereus CH3 in PBS and CJ broth by 32.89 % and 23.08 %, respectively, compared to control. As for the characteristics related to biofilm, garlic extract showed the highest inhibitory effect on biofilm formation and persistence and heat resistance of spores in intact biofilms, followed by rosemary and cinnamon extracts. All three spice extracts completely inhibited biofilm formation even at the lowest concentration (20 mg/mL) at the early stage of biofilm formation. They completely eradicated biofilm persistence formed in brain heart infusion (BHI) and CJ broth at the highest concentration. A high garlic extract concentration (80 mg/mL) also reduced the D100°C-values of spores in biofilms formed in BHI and CJ broth by 16.34 % and 9.00 %, respectively, compared to control. Taken together, garlic extract was most effective in mitigating B. cereus contamination in a concentration-dependent manner in in vitro-menstrua and CJ broth. This study may provide one of the promising strategies to reduce the risk of B. cereus in soybean stews such as CJ.

Defining early steps in Bacillus subtilis biofilm biosynthesis

IMPORTANCE

Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here, we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide (EPS) synthesis pathway. Together, our studies and approaches provide the foundation for the sequential characterization of the steps in EPS biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenyl diphosphate-linked glycan substrates.

Bacillus subtilis extracellular protease production incurs a context-dependent cost

Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.

The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition

Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.

Founder cell configuration drives competitive outcome within colony biofilms

Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells' potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.