https://www.zora.uzh.ch/id/eprint/194894/1/24_OA_1_2020_Karygianni_TrendsMicrobiol.pdf

Biofilm Matrixome: Extracellular Components in Structured Microbial Communities

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

/pdf/bacillus-subtilis-biofilm-formation-and-social-interactions-3shyj0u5pg.pdf

Bacillus subtilis biofilm formation and social interactions.

1. Structure and Function of Biofilms 2. Physico-Chemical Properties of Biofilms 3. Structural Determinants in Biofilm Formation 4. Microscopy Methods for Studying Biofilms 5. Gene Expression of Cells Attached to Surfaces 6. Plasmid Transfer in Biofilms 7. Bacterial Interactions with Marine Fouling Organisms 8. Biofilm Infections on Implant Surfaces 9. Animal Models for the Study of Bacterial Biofilms 10. Antimicrobial Resistance of Biofilms 11. Biofilms in the Oral Cavity: Impact of Surface Characteristics 12. Algal Biofilms 13. Food Industry Biofilms 14. The Role of Biosurfactants in Affecting Initial Microbial Adhesion Mechanisms 15. Monitoring Biofilms by Fourier Transform Infrared Spectroscopy 16. Surface Catalysed Hygiene and Biofilm Control 17. legionella Biofilms: Their Implications, Study and Control 18. Biofilms in Drinking Water Treatment and Distribution 19. Biofilm Control in Industrial Water Systems: Approaching an Old Problem in New Ways 20. Environmentally Acceptable Control of Microbial Biofilms 21. Towards Environmentally Acceptable Control of Biofilms in the Pulp and Paper Industry 22. Study of Biofouling Control with Fluorescent Probes and Image Analysis 23. Microbially Influenced Corrosion in the Context of Metal Microbe Interactions 24. Biofilms Without a Substratum: Flocs and Microbial Communities

Biofilms : recent advances in their study and control

Biofilms are surface‐associated bacterial aggregates, in which bacteria are enveloped by polymeric substances known as the biofilm matrix. Bacillus subtilis biofilms display persistent resistance to liquid wetting and gas penetration, which probably explains the broad‐spectrum resistance of the bacteria in these biofilms to antimicrobial agents. In this study, BslA (formerly YuaB) was identified as a major contributor to the surface repellency of B. subtilis biofilms. Disruption of bslA resulted in the loss of surface repellency and altered the biofilm surface microstructure. BslA localized to the biofilm matrix in an exopolysaccharide‐dependent manner. Purified BslA exhibited amphiphilic properties and formed polymers in response to increases in the area of the air–water interface in vitro. Genetic and biochemical analyses showed that the self‐polymerization activity of BslA was essential for its ability to localize to the biofilm matrix. Confocal laser scanning microscopy showed that BslA formed a layer on the biofilm surface. Taken together, we propose that BslA, standing for biofilm‐surface layer protein, is responsible for the hydrophobic layer on the surface of biofilms.

BslA (YuaB) forms a hydrophobic layer on the surface of

Biofilm patterns in gram-positive and gram-negative bacteria.

In nature, bacteria communicate via chemical cues and establish complex communities referred to as biofilms, wherein cells are held together by an extracellular matrix. Much research is focusing on small molecules that manipulate and prevent biofilm assembly by modifying cellular signalling pathways. However, the bacterial cell envelope, presenting the interface between bacterial cells and their surroundings, is largely overlooked. In our study, we identified specific targets within the biosynthesis pathways of the different cell wall components (peptidoglycan, wall teichoic acids and teichuronic acids) hampering biofilm formation and the anchoring of the extracellular matrix with a minimal effect on planktonic growth. In addition, we provide convincing evidence that biofilm hampering by transglycosylation inhibitors and D-Leucine triggers a highly specific response without changing the overall protein levels within the biofilm cells or the overall levels of the extracellular matrix components. The presented results emphasize the central role of the Gram-positive cell wall in biofilm development, resistance and sustainment.

Disturbance of the bacterial cell wall specifically interferes with biofilm formation

A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d-leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the β-lactamase PenP. This β-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to β-lactam resistance under different conditions. To test whether β-lactam resistance and β-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five β-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental β-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of β-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between β-lactams and β-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.

An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.

/pdf/methodologies-for-studying-b-subtilis-biofilms-as-a-model-ok6uwn3ira.pdf

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria.IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.

https://aem.asm.org/content/aem/early/2019/04/15/AEM.00512-19.full-text.pdf

The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers.

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Disturbance of the bacterial cell wall specifically interferes with biofilm formation

An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers.