Biofilms: an emergent form of bacterial life

Role of nutrient limitation in the competition between uropathogenic strains of Klebsiella pneumoniae and Escherichia coli in mixed biofilms

Klebsiella pneumoniae and Escherichia coli form mixed species biofilms in catheter-associated urinary tract infections. Recently, a detrimental effect of K. pneumoniae over E. coli was observed in mixed species biofilms grown in an artificial urine medium. The mechanism behind this competitive interaction was studied. K. pneumoniae partially outcompeted E. coli in early-stage batch-fed biofilms, whereas both microorganisms co-exist at longer times (K. pneumoniae:E. coli ratio, 55:1), as shown by cell counts and confocal microscopy. E. coli cells were scattered along the K. pneumoniae biofilm. Biofilm supernatants did not appear to contain either antimicrobial or anti-biofilm activities against E. coli. Biofilms grown under continuous flow prevented interspecies competition. K. pneumoniae showed both increased siderophore production and better growth in iron-limited media compared to E. coli. In summary, these results indicate the importance of nutrient (particularly iron) competition in the modulation of the bacterial composition of mixed species biofilms formed by uropathogenic K. pneumoniae and E. coli.

Bacterial autoaggregation

Many bacteria, both environmental and pathogenic, exhibit the property of autoaggregation. In autoaggregation (sometimes also called autoagglutination or flocculation), bacteria of the same type form multicellular clumps that eventually settle at the bottom of culture tubes. Autoaggregation is generally mediated by self-recognising surface structures, such as proteins and exopolysaccharides, which we term collectively as autoagglutinins. Although a widespread phenomenon, in most cases the function of autoaggregation is poorly understood, though there is evidence to show that aggregating bacteria are protected from environmental stresses or host responses. Autoaggregation is also often among the first steps in forming biofilms. Here, we review the current knowledge on autoaggregation, the role of autoaggregation in biofilm formation and pathogenesis, and molecular mechanisms leading to aggregation using specific examples.

Bone and joint infection

Bone and joint infections include septic arthritis, prosthetic joint infections, osteomyelitis, spinal infections (discitis, vertebral osteomyelitis and epidural abscess) and diabetic foot osteomyelitis. All of these may present through the acute medical take. This article discusses the pathogenesis of infection and highlights the importance of taking a careful history and fully examining the patient. It also emphasises the importance of early surgical intervention in many cases. Consideration of alternative diagnoses, appropriate imaging and high-quality microbiological sampling is important to allow appropriate and targeted antimicrobial therapy. This article makes some suggestions as to empiric antibiotic choice; however, therapy should be guided by local antimicrobial policies and infection specialists. Involvement of a multidisciplinary team is essential for optimal outcomes.

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments

Biofilms are microbial communities embedded within an extracellular matrix, forming a highly organized structure that causes many human infections. Dental caries (tooth decay) is a polymicrobial biofilm disease driven by the diet and microbiota-matrix interactions that occur on a solid surface. Sugars fuel the emergence of pathogens, the assembly of the matrix, and the acidification of the biofilm microenvironment, promoting ecological changes and concerted multispecies efforts that are conducive to acid damage of the mineralized tooth tissue. Here, we discuss recent advances in the role of the biofilm matrix and interactions between opportunistic pathogens and commensals in the pathogenesis of dental caries. In addition, we highlight the importance of matrix-producing organisms in fostering a pathogenic habitat where interspecies competition and synergies occur to drive the disease process, which could have implications to other infections associated with polymicrobial biofilms.

Emerging Nanomedicine Therapies to Counter the Rise of Methicillin-Resistant Staphylococcus aureus

In a recent report, the World Health Organisation (WHO) classified antibiotic resistance as one of the greatest threats to global health, food security, and development. Methicillin-resistant Staphylococcus aureus (MRSA) remains at the core of this threat, with persistent and resilient strains detectable in up to 90% of S. aureus infections. Unfortunately, there is a lack of novel antibiotics reaching the clinic to address the significant morbidity and mortality that MRSA is responsible for. Recently, nanomedicine strategies have emerged as a promising therapy to combat the rise of MRSA. However, these approaches have been wide-ranging in design, with few attempts to compare studies across scientific and clinical disciplines. This review seeks to reconcile this discrepancy in the literature, with specific focus on the mechanisms of MRSA infection and how they can be exploited by bioactive molecules that are delivered by nanomedicines, in addition to utilisation of the nanomaterials themselves as antibacterial agents. Finally, we discuss targeting MRSA biofilms using nano-patterning technologies and comment on future opportunities and challenges for MRSA treatment using nanomedicine.

Bacteria-Derived Carbon Dots Inhibit Biofilm Formation of Escherichia coli without Affecting Cell Growth

Biofilms are deleterious in many biomedical and industrial applications and prevention of their formation has been a pressing challenge. Here, carbon dots, CDs-LP that were easily synthesized from the biomass of Lactobacillus plantarum by one-step hydrothermal carbonization, were demonstrated to prevent biofilm formation of E. coli. CDs-LP did not thwart the growth of E. coli, indicating the anti-biofilm effect was not due to the bactericidal effect. Moreover, CDs-LP did not affect the growth of the animal cell AT II, showing low cytotoxicity, good safety and excellent biocompatibility. Therefore, CDs-LP could overcome the cytotoxicity issue found in many current antibiofilm agents. CDs-LP represent a new type of anti-biofilm materials, opening up a novel avenue to the development of biofilm treatment.

Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis

Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the “White Queen” here. The existence of DGs leads to the view of evolution as a more “intelligent” and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life.

Extracellular matrix influence in Streptococcus mutans gene expression in a cariogenic biofilm

Caries etiology is biofilm-diet-dependent. Biofilms are highly dynamic and structured microbial communities enmeshed in a three-dimensional extracellular matrix. The study evaluated the expression dynamics of Streptococcus mutans genes associated with exopolysaccharides (EPS) (gtfBCD, gbpB, dexA), lipoteichoic acids (LTA) (dltABCD, SMU_775c) and extracellular DNA (eDNA) (lytST, lrgAB, ccpA) during matrix development within a mixed-species biofilm of S. mutans, Actinomyces naeslundii and Streptococcus gordonii. Mixed-species biofilms using S. mutans strains UA159 or ΔgtfB formed on saliva-coated hydroxyapatite discs were submitted to a nutritional challenge (providing an abundance of sucrose and starch). Biofilms were removed at eight developmental stages for gene expression analysis by quantitative polymerase chain reaction. The pH of spent culture media remained acidic throughout the experimental periods, being lower after sucrose and starch exposure. All genes were expressed at all biofilm developmental phases. EPS- and LTA-associated genes had a similar expression profile for both biofilms, presenting lower levels of expression at 67, 91 and 115 hours and a peak of expression at 55 hours, but having distinct expression magnitudes, with lower values for ΔgtfB (eg, fold-difference of ~382 for gtfC and ~16 for dltB at 43 hours). The eDNA-associated genes presented different dynamics of expression between both strains. In UA159 biofilms lrgA and lrgB genes were highly expressed at 29 hours (which were ~13 and ~5.4 times vs ΔgtfB, respectively), whereas in ΔgtfB biofilms an inverse relationship between lytS and lrgA and lrgB expression was detected. Therefore, the deletion of gtfB influences dynamics and magnitude of expression of genes associated with matrix main components.

New Perspectives in Biofilm Eradication

Microbial biofilms, which are elaborate and highly resistant microbial aggregates formed on surfaces or medical devices, cause two-thirds of infections and constitute a serious threat to public health. Immunocompromised patients, individuals who require implanted devices, artificial limbs, organ transplants, or external life support and those with major injuries or burns, are particularly prone to become infected. Antibiotics, the mainstay treatments of bacterial infections, have often proven ineffective in the fight against microbes when growing as biofilms, and to date, no antibiotic has been developed for use against biofilm infections. Antibiotic resistance is rising, but biofilm-mediated multidrug resistance transcends this in being adaptive and broad spectrum and dependent on the biofilm growth state of organisms. Therefore, the treatment of biofilms requires drug developers to start thinking outside the constricted "antibiotics" box and to find alternative ways to target biofilm infections. Here, we highlight recent approaches for combating biofilms focusing on the eradication of preformed biofilms, including electrochemical methods, promising antibiofilm compounds and the recent progress in drug delivery strategies to enhance the bioavailability and potency of antibiofilm agents.

Broad impact of extracellular DNA on biofilm formation by clinically isolated Methicillin-resistant and -sensitive strains of Staphylococcus aureus

Staphylococcus aureus is a major causative agent for biofilm-associated infections. Inside biofilms, S. aureus cells are embedded in an extracellular matrix (ECM) composed of polysaccharide-intercellular adhesins (PIA), proteins, and/or extracellular DNA (eDNA). However, the importance of each component and the relationship among them in biofilms of diverse strains are largely unclear. Here, we characterised biofilms formed by 47 S. aureus clinical isolates. In most (42/47) of the strains, biofilm formation was augmented by glucose supplementation. Sodium chloride (NaCl)-triggered biofilm formation was more prevalent in methicillin-sensitive S. aureus (15/24) than in methicillin-resistant strain (1/23). DNase I most effectively inhibited and disrupted massive biofilms, and Proteinase K was also effective. Anti-biofilm effects of Dispersin B, which cleaves PIA, were restricted to PIA-dependent biofilms formed by specific strains and showed significant negative correlations with those of Proteinase K, suggesting independent roles of PIA and proteins in each biofilm. ECM profiling demonstrated that eDNA was present in all strains, although its level differed among strains and culture conditions. These results indicate that eDNA is the most common component in S. aureus biofilms, whereas PIA is important for a small number of isolates. Therefore, eDNA can be a primary target for developing eradication strategies against S. aureus biofilms.

Effects of lead, cadmium, chromium, and arsenic on the sorption of lindane and norfloxacin by river biofilms, particles, and sediments

The sorption of both classic and emerging organic contaminants onto aquatic solids is a critical process that controls their fate in natural waters. Sorption is affected by numerous factors, including coexisting heavy metals. The mechanisms of the influence of heavy metals, especially those occurring in acid radical anions, are still unclear. Here, the effects of Pb, Cd, Cr, and As on the sorption of lindane and norfloxacin (NOR) onto natural biofilms, suspended particles, and sediments from one river were investigated following batch equilibration methods. In addition, changes in representative components that have important roles in sorption from these solids in the presence and absence of metals were characterized by spectrum analyses. The results indicated that sorption of lindane and NOR on the three solids in the absence of heavy metals was highly linear and nonlinear, respectively. Pb and Cd promoted and Cr and As suppressed hydrophobic lindane sorption on the three solids. This was because Pb and Cd enhanced but Cr and As weakened the hydrophobicity of these solids. Pb, Cd, Cr, and As decreased NOR sorption on sediments and suspended particles at pH 5.7~6.3. This was due to electrostatic competition between cationic Pb/Cd and NORH₂⁺, and the combination of Cr/As acid radicals with NORH₂⁺, which suppressed its ion-exchange adsorption. Pb, Cd, Cr, and As generally increased the sorption of NOR onto the biofilms at pH 5.7~6.3. Pb and Cd strengthened the flocculation of dissolved organic matter combined with NORH₂⁺ onto the biofilms. Cr and As enhanced the hydrophilicity of biofilms, and then increased their sorption of NOR with active hydrophilic groups. The mechanisms of how different heavy metals affect NOR sorption by biofilms were more complicated than the mechanisms affecting lindane sorption, as well as by sediments and particles.

High tolerance of and removal of cefazolin sodium in single-chamber microbial fuel cells operation

Single-chamber microbial fuel cells (MFCs) have been shown to be a promising approach for cefazolin sodium (CFZS)-contaminated wastewater treatment, in terms of electricity production, high CFZS tolerance and effective CFZS removal. MFCs exposed to CFZS loadings up to 100 mg L^-1, produced stable power of 18.2 ± 1.1 W m^-3 and a maximum power of 30.4 ± 2.1 W m^-3, similar to that of CFZS-free MFCs (stable power 19.4 ± 0.8 W m^-3 and maximum power 32.5 ± 1.6 W m^-3), notwithstanding a longer acclimitisation MFC activation. More anodophilic genera (i.e. Acinetobacter, Stenotrophomonas, Lysinibacillus) and antibiotic-resisting genera (i.e. Dysgonomonas) were enriched in CFZS acclimitised anodes. Both the thickness of biofilms and the duration of CFZS acclimitisation were essential for the development of high CFZS tolerance (e.g. 450 mg L^-1). The inhibition of MFCs by CFZS was reversible. The present MFCs generated a CFZS removal rate of 1.2-6.8 mg L^-1 h^-1 without any apparent inhibition of electricity production.

Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8

A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.

The physical boundaries of public goods cooperation between surface-attached bacterial cells

Bacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa Using single-cell fluorescence microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 µm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections.

Cyclic-di-GMP and oprF Are Involved in the Response of Pseudomonas aeruginosa to Substrate Material Stiffness during Attachment on Polydimethylsiloxane (PDMS)

Recently, we reported that the stiffness of poly(dimethylsiloxane) (PDMS) affects the attachment of Pseudomonas aeruginosa, and the morphology and antibiotic susceptibility of attached cells. To further understand how P. aeruginosa responses to material stiffness during attachment, the wild-type P. aeruginosa PAO1 and several isogenic mutants were characterized for their attachment on soft and stiff PDMS. Compared to the wild-type strain, mutation of the oprF gene abolished the differences in attachment, growth, and size of attached cells between soft and stiff PDMS surfaces. These defects were rescued by genetic complementation of oprF. We also found that the wild-type P. aeruginosa PAO1 cells attached on soft (40:1) PDMS have higher level of intracellular cyclic dimeric guanosine monophosphate (c-di-GMP), a key regulator of biofilm formation, compared to those on stiff (5:1) PDMS surfaces. Consistently, the mutants of fleQ and wspF, which have similar high-level c-di-GMP as the oprF mutant, exhibited defects in response to PDMS stiffness during attachment. Collectively, the results from this study suggest that P. aeruginosa can sense the stiffness of substrate material during attachment and respond to such mechanical cues by adjusting c-di-GMP level and thus the following biofilm formation. Further understanding of the related genes and pathways will provide new insights into bacterial mechanosensing and help develop better antifouling materials.

On-line biofilm strength detection in cross-flow membrane filtration systems

A fluid dynamic gauging (FDG) technique was used for on-line and in situ measurements of Pseudomonas aeruginosa PAO1 biofilm thickness and strength on flat sheet polyethersulphone membranes. The measurements are the first to be successfully conducted in a membrane cross-flow filtration system under constant permeation. In addition, FDG was used to demonstrate the removal behaviour of biofilms through local biofilm strength and removal energy estimation, which other conventional measurements such as flux and TMP cannot provide. The findings suggest that FDG can provide valuable additional information related to biofilm properties that have not been measured by other monitoring methods.

Bacterial Adhesion Is Affected by the Thickness and Stiffness of Poly(ethylene glycol) Hydrogels

Despite lacking visual, auditory, and olfactory perception, bacteria sense and attach to surfaces. Many factors, including the chemistry, topography, and mechanical properties of a surface, are known to alter bacterial attachment, and in this study, using a library of nine protein-resistant poly(ethylene glycol) (PEG) hydrogels immobilized on glass slides, we demonstrate that the thickness or amount of polymer concentration also matters. Hydrated atomic force microscopy and rheological measurements corroborated that thin (15 μm), medium (40 μm), and thick (150 μm) PEG hydrogels possessed Young's moduli in three distinct regimes, soft (20 kPa), intermediate (300 kPa), and stiff (1000 kPa). The attachment of two diverse bacteria, flagellated Gram-negative Escherichia coli and nonmotile Gram-positive Staphylococcus aureus was assessed after a 24 h incubation on the nine PEG hydrogels. On the thickest PEG hydrogels (150 μm), E. coli and S. aureus attachment increased with increasing hydrogel stiffness. However, when the hydrogel's thickness was reduced to 15 μm, a substantially greater adhesion of E. coli and S. aureus was observed. Twelve times fewer S. aureus and eight times fewer E. coli adhered to thin-soft hydrogels than to thick-soft hydrogels. Although a full mechanism to explain this behavior is beyond the scope of this article, we suggest that because the Young's moduli of thin-soft and thick-soft hydrogels were statistically equivalent, potentially, the very stiff underlying glass slide was causing the thin-soft hydrogels to feel stiffer to the bacteria. These findings suggest a key takeaway design rule; to optimize fouling-resistance, hydrogel coatings should be thick and soft.

Active microbial biofilms in deep poor porous continental subsurface rocks

Deep continental subsurface is defined as oligotrophic environments where microorganisms present a very low metabolic rate. To date, due to the energetic cost of production and maintenance of biofilms, their existence has not been considered in poor porous subsurface rocks. We applied fluorescence in situ hybridization techniques and confocal laser scanning microscopy in samples from a continental deep drilling project to analyze the prokaryotic diversity and distribution and the possible existence of biofilms. Our results show the existence of natural microbial biofilms at all checked depths of the Iberian Pyrite Belt (IPB) subsurface and the co-occurrence of bacteria and archaea in this environment. This observation suggests that multi-species biofilms may be a common and widespread lifestyle in subsurface environments.

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.

Optogenetics Manipulation Enables Prevention of Biofilm Formation of Engineered Pseudomonas aeruginosa on Surfaces

Synthetic biologists have attempted to solve real-world problems, such as those of bacterial biofilms, that are involved in the pathogenesis of many clinical infections and difficult to eliminate. To address this, we employed a blue light responding system and integrated it into the chromosomes of Pseudomonas aeruginosa. With making rational adaptions and improvements of the light-activated system, we provided a robust and convenient means to spatiotemporally control gene expression and manipulate biological processes with minimal perturbation in P. aeruginosa. It increased the light-induced gene expression up to 20-fold. Moreover, we deliberately introduced a functional protein gene PA2133 containing an EAL domain to degrade c-di-GMP into the modified system, and showed that the optimally engineered optogenetic tool inhibited the formation of P. aeruginosa biofilms through the induction of blue light, resulting in much sparser and thinner biofilms. Our approach establishes a methodology for leveraging the tools of synthetic biology to guide biofilm formation and engineer biofilm patterns with unprecedented spatiotemporal resolution. Furthermore, the findings suggest that the synthetic optogenetic system may provide a promising strategy that could be applied to control and fight biofilms.

Novel Miniature Membrane Active Lipopeptidomimetics against Planktonic and Biofilm Embedded Methicillin-Resistant Staphylococcus aureus

Escalating multidrug resistance and highly evolved virulence mechanisms have aggravated the clinical menace of methicillin-resistant Staphylococcus aureus (MRSA) infections. Towards development of economically viable staphylocidal agents here we report eight structurally novel tryptophan-arginine template based peptidomimetics. Out of the designed molecules, three lipopeptidomimetics (S-6, S-7 and S-8) containing 12-amino dodecanoic acid exhibited cell selectivity and good to potent activity against clinically relevant pathogens MRSA, methicillin-resistant Staphylococcus epidermidis and vancomycin-resistant Enterococcus faecium (MIC: 1.4–22.7 μg/mL). Mechanistically, the active peptidomimetics dissipated membrane potential and caused massive permeabilization on MRSA concomitant with loss of viability. Against stationary phase MRSA under nutrient-depleted conditions, active peptidomimetics S-7 and S-8 achieved > 6 log reduction in viability upon 24 h incubation while both S-7 (at 226 μg/mL) and S-8 (at 28 μg/mL) also destroyed 48 h mature MRSA biofilm causing significant decrease in viability (p < 0.05). Encouragingly, most active peptidomimetic S-8 maintained efficacy against MRSA in presence of serum/plasma while exhibiting no increase in MIC over 17 serial passages at sub-MIC concentrations implying resistance development to be less likely. Therefore, we envisage that the current template warrants further optimization towards the development of cell selective peptidomimetics for the treatment of device associated MRSA infections.

Estimation of spatial distribution of quorum sensing signaling in sequencing batch biofilm reactor (SBBR) biofilms

Quorum sensing (QS) signaling, plays a significant role in regulating formation of biofilms in the nature; however, little information about the occurrence and distribution of quorum sensing molecular in the biofilm of carriers has been reported. In this study, distribution of QS signaling molecules (the acylated homoserine lactones-AHLs, and AI-2), extracellular polymeric substances (EPS) and the mechanical properties in sequencing batch biofilm reactor (SBBR) biofilms have been investigated. Using increased centrifugal force, the biofilms were detached into different fractions. The AHLs ranged from 5.2ng/g to 98.3ng/g in different fractions of biofilms, and N-decanoyl-dl-homoserine lactone (C10-HSL) and N-dodecanoyl-dl-homoserine lactone (C12-HSL) in the biofilms obtained at various centrifugal forces displayed significant differences (p<0.01). Interspecies communication signal autoinducer-2(AI-2) in the biofilms ranged from 79.2ng/g to 98.3ng/g. Soluble EPS and loosely bound EPS content in the different fractions of biofilms displayed significant positive relationship with the distribution of C12-HSL (r=0.86, p<0.05). Furthermore, 49.62% of bacteria in the biofilms were positively related with AHLs with 22.76% was significantly positively (p<0.05) related with AHLs. Biofilm adhesion and compliance was the strongest in the tightly-bound biofilm, the weakest in the supernatant/surface biofilm, which was in accordance with the distribution of C12 HSL(r=0.77, p<0.05) and C10-HSL(r=0.75, p<0.05), respectively. This study addressed on better understanding of possible methods for the improvement of wastewater bio-treatment through biofilm application.

Impact of Seed Exudates on Growth and Biofilm Formation of Bacillus amyloliquefaciens ALB629 in Common Bean

We aimed to unravel the events which favor the seed-rhizobacterium Bacillus amyloliquefaciens strain ALB629 (hereafter ALB629) interaction and which may interfere with the rhizobacterium colonization and growth on the spermosphere of common bean. Seed exudates from common bean were tested in vitro for ALB629 biofilm formation and bacterial growth. Furthermore, the performance of ALB629 on plant-related variables under drought stress was checked. Seed exudates (1 and 5% v/v) increased ALB629 biofilm formation. Additionally, the colony forming units for ALB629 increased both in culture and on the bean seed surface. The bean seed exudates up-regulated biofilm operons in ALB629 TasA and EpsD by ca. two and sixfold, respectively. The high-performance liquid chromatography (HPLC)-coupled with MS showed that malic acid is present as a major organic acid component in the seed exudates. Seeds treated with ALB629 and amended with malic acid resulted in seedlings with a higher bacterial concentration, induced plant drought tolerance, and promoted plant growth. We showed that seed exudates promote growth of ALB629 and malic acid was identified as a major organic acid component in the bean seed exudates. Our results also show that supplementation of ALB629 induced drought tolerance and growth in plants. The research pertaining to the biological significance of seed exudates in plant–microbe interaction is unexplored field and our work shows the importance of seed exudates in priming both growth and tolerance against abiotic stress.

Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan

Biofilm formation has been shown to confer protection against grazing, but little information is available on the effect of grazing on biofilm formation and protection in multispecies consortia. With most biofilms in nature being composed of multiple bacterial species, the interactions and dynamics of a multispecies bacterial biofilm subject to grazing by a pelagic protozoan predator were investigated. To this end, a mono and multispecies biofilms of four bacterial soil isolates, namely Xanthomonas retroflexus, Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus, were constructed and subjected to grazing by the ciliate Tetrahymena pyriformis. In monocultures, grazing strongly reduced planktonic cell numbers in P. amylolyticus and S. rhizophila and also X. retroflexus. At the same time, cell numbers in the underlying biofilms increased in S. rhizophila and X. retroflexus, but not in P. amylolyticus. This may be due to the fact that while grazing enhanced biofilm formation in the former two species, no biofilm was formed by P. amylolyticus in monoculture, either with or without grazing. In four-species biofilms, biofilm formation was higher than in the best monoculture, a strong biodiversity effect that was even more pronounced in the presence of grazing. While cell numbers of X. retroflexus, S. rhizophila, and P. amylolyticus in the planktonic fraction were greatly reduced in the presence of grazers, cell numbers of all three species strongly increased in the biofilm. Our results show that synergistic interactions between the four-species were important to induce biofilm formation, and suggest that bacterial members that produce more biofilm when exposed to the grazer not only protect themselves but also supported other members which are sensitive to grazing, thereby providing a "shared grazing protection" within the four-species biofilm model. Hence, complex interactions shape the dynamics of the biofilm and enhance overall community fitness under stressful conditions such as grazing. These emerging inter- and intra-species interactions could play a vital role in biofilm dynamics in natural environments like soil or aquatic systems.

Recent developments in smart antibacterial surfaces to inhibit biofilm formation and bacterial infections

Since their development over 70 years, antibiotics are still the most effective strategy to treat bacterial biofilms and infections.

Photoreaction of BlrP1: the role of a nonlinear photo-intensity sensor

Blue-light-regulated phosphodiesterase 1 (BlrP1) dimer exhibits a large conformational change, which is assigned to a quaternary structural change. The conformational change requires photoexcitation of both monomer units in the dimer, indicating that BlrP1 plays a role of a nonlinear light intensity sensor.

Extracellular Polymeric Matrix Production and Relaxation under Fluid Shear and Mechanical Pressure in Staphylococcus aureus Biofilms

The viscoelasticity of a biofilm's EPS (extracellular polymeric substance) matrix conveys protection against mechanical challenges, but adaptive responses of biofilm inhabitants to produce EPS are not well known. Here, we compare the responses of a biofilm of an EPS-producing (ATCC 12600) and a non-EPS producing (5298) Staphylococcus aureus strain to fluid shear and mechanical challenge. Confocal laser scanning microscopy confirmed absence of calcofluor-white-stainable EPS in biofilms of S. aureus 5298. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy combined with tribometry indicated that polysaccharide production per bacterium in the initial adhering layer was higher during growth at high shear than at low shear and that this increased EPS production extended to entire biofilms, as indicated by tribometrically measured coefficients of friction (CoF). CoF of biofilms grown under high fluid shear were higher than those when grown under low shear, likely due to wash-off polysaccharides. Measurement of a biofilm's CoF implies application of mechanical pressure that yielded an immediate increase in the polysaccharide band area of S. aureus ATCC 12600 biofilms due to their compression. Compression decreased after relief of pressure to the level observed prior to mechanical pressure. For biofilms grown under high shear, this coincided with a higher percent whiteness in optical coherence tomography-images indicative of water outflow, returning back into the biofilm during stress relaxation. Biofilms grown under low shear, however, were stimulated during tribometry to produce EPS, also after relief of stress. Knowledge of factors that govern EPS production and water flow in biofilms will allow better control of biofilms under mechanical challenge and better understanding of the barrier properties of biofilms against antimicrobial penetration.IMPORTANCE Adaptive responses of biofilm inhabitants in nature to environmental challenges such as fluid shear and mechanical pressure often involve EPS production with the aim of protecting biofilm inhabitants. EPS can assist biofilm bacteria in remaining attached or can impede antimicrobial penetration. The TriboChemist is a recently introduced instrument, allowing the study of initially adhering bacteria to a germanium crystal using ATR-FTIR spectroscopy, while simultaneously allowing measurement of the coefficient of friction of a biofilm, which serves as an indicator of the EPS content of a biofilm. EPS production can be stimulated by both fluid shear during growth and mechanical pressure, while increased EPS production can continue after pressure relaxation of the biofilm. Since EPS is pivotal in the protection of biofilm inhabitants against mechanical and chemical challenges, knowledge of the factors that make biofilm inhabitants decide to produce EPS, as provided in this study, is important for the development of biofilm control measures.

Mixed community biofilms and microbially influenced corrosion

Metals are used in most marine infrastructures for energy extraction and production. Metal corrosion is a serious concern, due to the environmental, safety, and replacement costs associated with it. Microbially influenced corrosion (MIC) contributes to the overall corrosion process, through several chemical, electrochemical and biochemical mechanisms, particularly in the presence of microbial biofilms. In this short article, we discuss briefly recent advances in MIC research, comparing corrosion in single species and mixed species biofilms, and outline possible strategies for biofilm and corrosion control.

Influence of surface modifications of a nanostructured implant on osseointegration capacity – preliminary in vivo study

In response to the need for implant materials characterized by high biocompatibility a new type of nanostructured Ti6Al7Nb implants for osseous tissue regeneration have been fabricated. The nanostructured cylindrical implants were manufactured in accordance with 3D CAD data using the Selective Laser Melting (SLM) method. Implants were subjected to chemical polishing using a mixture of nitric acid and fluoride (test group) as well as cleaned in distilled water and isopropyl alcohol (control group). The structural and morphological properties of the obtained samples were determined by using XRD (X-ray powder diffraction), TEM (transmission electron microscopy) and SEM (scanning electron microscopy) techniques. The particle size was verified and calculated by Rietveld method to be in the range of 25–90 nm. In the present study, experimental in vivo tests concerning implants fabricated from a nanostructured Ti6Al7Nb alloy, which may substitute bone tissue, were discussed in detail. The control group and test group were used in the study. The animal model was New Zealand rabbit. The implants were implanted into skull fornix and observed after 1, 2 and 3 months. The results of macroscopic and microscopic analysis proved better osseointegration of chemically modified implants.

In response to the need for implant materials characterized by high biocompatibility a new type of nanostructured Ti6Al7Nb implants for osseous tissue regeneration have been fabricated.

High-Antifouling Polymer Brush Coatings on Nonpolar Surfaces via Adsorption-Cross-Linking Strategy

A new "adsorption-cross-linking" technology is presented to generate a highly dense polymer brush coating on various nonpolar substrates, including the most inert and low-energy surfaces of poly(dimethylsiloxane) and poly(tetrafluoroethylene). This prospective surface modification strategy is based on a tailored bifunctional amphiphilic block copolymer with benzophenone units as the hydrophobic anchor/chemical cross-linker and terminal azide groups for in situ postmodification. The resulting polymer brushes exhibited long-term and ultralow protein adsorption and cell adhesion benefiting from the high density and high hydration ability of polyglycerol blocks. The presented antifouling brushes provided a highly stable and robust bioinert background for biospecific adsorption of desired proteins and bacteria after secondary modification with bioactive ligands, e.g., mannose for selective ConA and Escherichia coli binding.

Scanning electron microscopy and microbiological approaches for the evaluation of salivary microorganisms behaviour on anatase titanium surfaces: In vitro study

Implantology research framed the implant surface as a key element for a good and sustainable osseointegration of an implant fixture. The aim of this study was to analyze the antibacterial properties of anatase-coated titanium healing screws through microbiological and scanning electron microscopy. The comparison of the bacterial colonies growth between the anatase-coated titanium healing screws and non-coated titanium healing screws showed comparable antibacterial properties, without significant statistical differences. The scanning electron microscopy observations confirmed the microbiological study. These data, also considering previous reports on the positive effects on osteoblasts genetic expressions, might suggest a use of the anatase-coated titanium healing screws to preserve the tissues surrounding implants from microbial attacks.

Corrosive extracellular polysaccharides of the rock-inhabiting model fungus Knufia petricola

Melanised cell walls and extracellular polymeric matrices protect rock-inhabiting microcolonial fungi from hostile environmental conditions. How extracellular polymeric substances (EPS) perform this protective role was investigated by following development of the model microcolonial black fungus Knufia petricola A95 grown as a sub-aerial biofilm. Extracellular substances were extracted with NaOH/formaldehyde and the structures of two excreted polymers studied by methylation as well as NMR analyses. The main polysaccharide (~ 80%) was pullulan, also known as α-1,4-; α-1,6-glucan, with different degrees of polymerisation. Αlpha-(1,4)-linked-Glcp and α-(1,6)-linked-Glcp were present in the molar ratios of 2:1. A branched galactofuromannan with an α-(1,2)-linked Manp main chain and a β-(1,6)-linked Galf side chain formed a minor fraction (~ 20%). To further understand the roles of EPS in the weathering of minerals and rocks, viscosity along with corrosive properties were studied using atomic force microscopy (AFM). The kinetic viscosity of extracellular K. petricola A95 polysaccharides (≈ 0.97 × 10⁻⁶ m² s⁻¹) ranged from the equivalent of 2% (w/v) to 5% glycerine, and could thus profoundly affect diffusion-dominated processes. The corrosive nature of rock-inhabiting fungal EPS was also demonstrated by its effects on the aluminium coating of the AFM cantilever and the silicon layer below.

Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms

Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS matrix is primarily composed of polysaccharides, proteins and extracellular DNA. In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, it shields the bacterial cells inside the biofilm, by preventing antimicrobial agents from getting in contact with them, thereby reducing their killing effect. New strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of existing antimicrobials. Here we examined the mechanism of the known effect of vitamin C (sodium ascorbate) on enhancing the activity of various antibacterial agents. Our quantitative proteomics analysis shows that non-lethal concentrations of vitamin C inhibit bacterial quorum sensing and other regulatory mechanisms underpinning biofilm development. As a result, the EPS biosynthesis in reduced, and especially the polysaccharide component of the matrix is depleted. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antimicrobials or treatments.

Myroides odoratimimus Forms Structurally Complex and Inherently Antibiotic-Resistant Biofilm in a Wound-Like in vitro Model

Myroides odoratimimus is an aerobic, non-fermenting Gram-negative multidrug-resistant bacterium widely distributed in nature that rarely causes infections in immunocompromised patients. We recently described in a diabetic patient a case of recurrent calcaneal ulcer infection caused by a M. odoratimimus strain showing potential for biofilm formation. For the first time, we therefore evaluated the ability of M. odoratimimus to form biofilm under different pH values and glucose concentrations using an in vitro “skin-like” model, and its susceptibility to levofloxacin, meropenem, and tigecycline. The expression of some antibiotic-resistance related genes was also monitored by RT-PCR during planktonic-to-biofilm transition. Our results indicated that M. odoratimimus can produce relevant amounts of biofilm biomass, in a time-dependent manner, especially at acidic pH and regardless of glucose concentration tested. The comparative analysis of MIC and MBC values between planktonic and sessile cells showed that resistance to antibiotics increased during the planktonic-to-biofilm transition. Viable cell count indicated that none of the tested antibiotics were able to completely eradicate preformed biofilms, although meropenem and levofloxacin were the most active causing a significant, dose-independent, reduction of biofilm's viability, as also confirmed by microscopic analysis. RT-PCR showed that antibiotic-resistance related gyrA and acrB genes are over-expressed during the transition from planktonic to sessile (biofilm) lifestyle. Overall, our findings showed that M. odoratimimus can form relevant amounts of inherently antibiotic-resistant biofilm under conditions relevant to wound site, therefore suggesting a role in the pathogenesis of chronic ulcer infections.

Blue Light Switchable Bacterial Adhesion as a Key Step toward the Design of Biofilms

The control of where and when bacteria adhere to a substrate is a key step toward controlling the formation and organization in biofilms. This study shows how we engineer bacteria to adhere specifically to substrates with high spatial and temporal control under blue light, but not in the dark, by using photoswitchable interaction between nMag and pMag proteins. For this, we express pMag proteins on the surface of E. coli so that the bacteria can adhere to substrates with immobilized nMag protein under blue light. These adhesions are reversible in the dark and can be repeatedly turned on and off. Further, the number of bacteria that can adhere to the substrate as well as the attachment and detachment dynamics are adjustable by using different point mutants of pMag and altering light intensity. Overall, the blue light switchable bacteria adhesions offer reversible, tunable and bioorthogonal control with exceptional spatial and temporal resolution. This enables us to pattern bacteria on substrates with great flexibility.

ciaR impacts biofilm formation by regulating an arginine biosynthesis pathway in Streptococcus sanguinis SK36

Streptococcus sanguinis is an early colonizer of the tooth surface and competes with oral pathogens such as Streptococcus mutans to maintain oral health. However, little is known about its mechanism of biofilm formation. Here, we show that mutation of the ciaR gene, encoding the response regulator of the CiaRH two-component system in S. sanguinis SK36, produced a fragile biofilm. Cell aggregation, gtfP gene expression and water-insoluble glucan production were all reduced, which suggested polysaccharide production was decreased in ΔciaR. RNA sequencing and qRT-PCR revealed that arginine biosynthesis genes (argR, argB, argC, argG, argH and argJ) and two arginine/histidine permease genes (SSA_1568 and SSA_1569) were upregulated in ΔciaR. In contrast to ΔciaR, most of strains constructed to contain deletions in each of these genes produced more biofilm and water-insoluble glucan than SK36. A ΔciaRΔargB double mutant was completely restored for the gtfP gene expression, glucan production and biofilm formation ability that was lost in ΔciaR, indicating that argB was essential for ciaR to regulate biofilm formation. We conclude that by promoting the expression of arginine biosynthetic genes, especially argB gene, the ciaR mutation reduced polysaccharide production, resulting in the formation of a fragile biofilm in Streptococcus sanguinis.

Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation

Cell-cell communication enables bacteria to coordinate their behavior through the production, recognition, and response to chemical signals produced by their microbial neighbors. An important example of coordinated behavior in bacteria is biofilm formation, where individual cells organize into highly complex, matrix-encased communities that differentiate into distinct cell types and divide labor among individual cells. Bacteria rely on environmental cues to influence biofilm development, including chemical cues produced by other microbes. A multitude of recent studies have demonstrated that natural-product antibiotics at subinhibitory concentrations can impact biofilm formation in neighboring microbes, supporting the hypothesis that these compounds may have evolved as signaling molecules that mediate cell-cell interactions. In this review we discuss the role of antibiotics in modulating biofilm formation and interspecies communication in bacteria.

3D printing of bacteria into functional complex materials

Despite recent advances to control the spatial composition and dynamic functionalities of bacteria embedded in materials, bacterial localization into complex three-dimensional (3D) geometries remains a major challenge. We demonstrate a 3D printing approach to create bacteria-derived functional materials by combining the natural diverse metabolism of bacteria with the shape design freedom of additive manufacturing. To achieve this, we embedded bacteria in a biocompatible and functionalized 3D printing ink and printed two types of "living materials" capable of degrading pollutants and of producing medically relevant bacterial cellulose. With this versatile bacteria-printing platform, complex materials displaying spatially specific compositions, geometry, and properties not accessed by standard technologies can be assembled from bottom up for new biotechnological and biomedical applications.

Targeting microbial biofilms: current and prospective therapeutic strategies

Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections. The multifactorial nature of biofilm development and drug tolerance imposes great challenges for the use of conventional antimicrobials and indicates the need for multi-targeted or combinatorial therapies. In this Review, we focus on current therapeutic strategies and those under development that target vital structural and functional traits of microbial biofilms and drug tolerance mechanisms, including the extracellular matrix and dormant cells. We emphasize strategies that are supported by in vivo or ex vivo studies, highlight emerging biofilm-targeting technologies and provide a rationale for multi-targeted therapies aimed at disrupting the complex biofilm microenvironment.

The interaction of soil phototrophs and fungi with pH and their impact on soil CO2, CO18O and OCS exchange

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO2 and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the 'community-integrated' CA activity differently for CO2 and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO2, OCS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and OCS.

Bacterial social interactions and the emergence of community-intrinsic properties

Bacterial communities are dominated and shaped by social interactions, which facilitate the emergence of properties observed only in the community setting. Such community-intrinsic properties impact not only the phenotypes of cells in a community, but also community composition and function, and are thus likely to affect a potential host. Studying community-intrinsic properties is, therefore, important for furthering our understanding of clinical, applied and environmental microbiology. Here, we provide recent examples of research investigating community-intrinsic properties, focusing mainly on community composition and interactions in multispecies biofilms. We hereby wish to emphasize the importance of studying social interactions in settings where community-intrinsic properties are likely to emerge.