Biofilms 2007: broadened horizons and new emphases

Investigation of the population dynamics within a Pseudomonas aeruginosa biofilm using a flow based biofilm model system and flow cytometric evaluation of cellular physiology

In this study a flow based biofilm model system was used to simulate the formation of Pseudomonas aeruginosa biofilms on a stainless steel surface. To investigate the complexity of biofilm-associated P. aeruginosa populations a combination of microscopic observations and flow cytometric analysis (FCM) was adopted. Biofilm-associated P. aeruginosa cells were evaluated (1) under optimal vs reduced nutrient-availability at the initial adhesion stage, and (2) irrespective of nutrient-availability within a mature biofilm. Microscopic estimation of the extent of attachment revealed more effective colonization upon optimal vs starvation conditions. FCM allowed an in situ evaluation of P. aeruginosa vitality, using cellular redox potential measurements to discriminate active, mid-active and non-active sub-populations. Samples from recently attached cells and mature biofilms showed significant differences in the percentages of bacterial cells from the defined sub-populations. The approach demonstrated that distribution of individual P. aeruginosa sub-populations was influenced by the stage of the biofilm life-cycle and nutrient availability.

Roles of Extracellular Polysaccharides and Biofilm Formation in Heavy Metal Resistance of Rhizobia

Bacterial surface components and extracellular compounds, particularly flagella, lipopolysaccharides (LPSs), and exopolysaccharides (EPSs), in combination with environmental signals and quorum-sensing signals, play crucial roles in bacterial autoaggregation, biofilm development, survival, and host colonization. The nitrogen-fixing species Sinorhizobium meliloti (S. meliloti) produces two symbiosis-promoting EPSs: succinoglycan (or EPS I) and galactoglucan (or EPS II). Studies of the S.meliloti/alfalfa symbiosis model system have revealed numerous biological functions of EPSs, including host specificity, participation in early stages of host plant infection, signaling molecule during plant development, and (most importantly) protection from environmental stresses. We evaluated functions of EPSs in bacterial resistance to heavy metals and metalloids, which are known to affect various biological processes. Heavy metal resistance, biofilm production, and co-culture were tested in the context of previous studies by our group. A range of mercury (Hg II) and arsenic (As III) concentrations were applied to S. meliloti wild type strain and to mutant strains defective in EPS I and EPS II. The EPS production mutants were generally most sensitive to the metals. Our findings suggest that EPSs are necessary for the protection of bacteria from either Hg (II) or As (III) stress. Previous studies have described a pump in S. meliloti that causes efflux of arsenic from cells to surrounding culture medium, thereby protecting them from this type of chemical stress. The presence of heavy metals or metalloids in culture medium had no apparent effect on formation of biofilm, in contrast to previous reports that biofilm formation helps protect various microorganism species from adverse environmental conditions. In co-culture experiments, EPS-producing heavy metal resistant strains exerted a protective effect on AEPS-non-producing, heavy metal-sensitive strains; a phenomenon termed “rescuing” of the non-resistant strain.

Adherence to abiotic surface induces SOS response in Escherichia coli K-12 strains under aerobic and anaerobic conditions

During the colonization of surfaces, Escherichia coli bacteria often encounter DNA-damaging agents and these agents can induce several defence mechanisms. Base excision repair (BER) is dedicated to the repair of oxidative DNA damage caused by reactive oxygen species (ROS) generated by chemical and physical agents or by metabolism. In this work, we have evaluated whether the interaction with an abiotic surface by mutants derived from E. coli K-12 deficient in some enzymes that are part of BER causes DNA damage and associated filamentation. Moreover, we studied the role of endonuclease V (nfi gene; 1506 mutant strain) in biofilm formation. Endonuclease V is an enzyme that is involved in DNA repair of nitrosative lesions. We verified that endonuclease V is involved in biofilm formation. Our results showed more filamentation in the xthA mutant (BW9091) and triple xthA nfo nth mutant (BW535) than in the wild-type strain (AB1157). By contrast, the mutant nfi did not present filamentation in biofilm, although its wild-type strain (1466) showed rare filaments in biofilm. The filamentation of bacterial cells attaching to a surface was a consequence of SOS induction measured by the SOS chromotest. However, biofilm formation depended on the ability of the bacteria to induce the SOS response since the mutant lexA Ind(-) did not induce the SOS response and did not form any biofilm. Oxygen tension was an important factor for the interaction of the BER mutants, since these mutants exhibited decreased quantitative adherence under anaerobic conditions. However, our results showed that the presence or absence of oxygen did not affect the viability of BW9091 and BW535 strains. The nfi mutant and its wild-type did not exhibit decreased biofilm formation under anaerobic conditions. Scanning electron microscopy was also performed on the E. coli K-12 strains that had adhered to the glass, and we observed the presence of a structure similar to an extracellular matrix that depended on the oxygen tension. In conclusion, it was proven that bacterial interaction with abiotic surfaces can lead to SOS induction and associated filamentation. Moreover, we verified that endonuclease V is involved in biofilm formation.

Pseudomonas aeruginosa biofilms in disease

Pseudomonas aeruginosa is a ubiquitous organism that is the focus of intense research because of its prominent role in disease. Due to its relatively large genome and flexible metabolic capabilities, this organism exploits numerous environmental niches. It is an opportunistic pathogen that sets upon the human host when the normal immune defenses are disabled. Its deadliness is most apparent in cystic fibrosis patients, but it also is a major problem in burn wounds, chronic wounds, chronic obstructive pulmonary disorder, surface growth on implanted biomaterials, and within hospital surface and water supplies, where it poses a host of threats to vulnerable patients (Peleg and Hooper, N Engl J Med 362:1804-1813, 2010; Breathnach et al., J Hosp Infect 82:19-24, 2012). Once established in the patient, P. aeruginosa can be especially difficult to treat. The genome encodes a host of resistance genes, including multidrug efflux pumps (Poole, J Mol Microbiol Biotechnol 3:255-264, 2001) and enzymes conferring resistance to beta-lactam and aminoglycoside antibotics (Vahdani et al., Annal Burns Fire Disast 25:78-81, 2012), making therapy against this gram-negative pathogen particularly challenging due to the lack of novel antimicrobial therapeutics (Lewis, Nature 485: 439-440, 2012). This challenge is compounded by the ability of P. aeruginosa to grow in a biofilm, which may enhance its ability to cause infections by protecting bacteria from host defenses and chemotherapy. Here, we review recent studies of P. aeruginosa biofilms with a focus on how this unique mode of growth contributes to its ability to cause recalcitrant infections.

Salso-sulphide thermal water in the prevention of recurrent respiratory infections in children

Recurrent respiratory infections (RRI) represent a social problem for both the pharmaco-economic impact and the burden on the family. Thermal water is popularly well accepted. However, there is no scientific evidence of its preventive activity on recurrent respiratory tract infections (RRI). Therefore, the purpose of this study was to evaluate the effects of Agnano thermal water nasal irrigation on RRI prevention in children.A total of 107 children (70 males, mean age 4.5 plus minus1.2 years) with RRI were enrolled in the study. At baseline, children were randomly assigned to the treatment with: A) inhaled crenotherapy with salso-sulphide water or B) isotonic saline (NaCl 0.9 percent). Inhaled therapy was performed using nasal washing by Rino-jet (ASEMA srl, Milan, Italy) b.i.d. for 12 days. Nasal washing lasted 2 minutes per nostril. Immediately before washing, children inhaled 1 l of water by stream inhalation per 2 minutes. Crenotherapy was capable of significantly reducing: the number of respiratory infections, nasal symptoms, neutrophil and bacteria count, turbinate and adenoidal hypertrophy, presence of biofilm, and blockage of ostiomeatal complex (OCM). In conclusion, this study provides the first evidence that Agnano crenotherapy may be capable of preventing RRI in children as it exerts some positive effects, such as reduction of nasal obstruction, OCM blockage, biofilm, and inflammatory events.

In Vitro Antibiofilm Efficacies of Different Antibiotic Combinations with Zinc Sulfate against Pseudomonas aeruginosa Recovered from Hospitalized Patients with Urinary Tract Infection

Urinary tract infections (UTIs) are a serious healthcare dilemma influencing millions of patients every year and represent the second most frequent type of body infection. Pseudomonas aeruginosa is a multidrug-resistant pathogen causing numerous chronic biofilm-associated infections including urinary tract, nosocomial, and medical devices-related infections. In the present study, the biofilm of P. aeruginosa CCIN34519, recovered from inpatients with UTIs, was established on polystyrene substratum and scanning electron microscopy (SEM) and was utilized for visualization of the biofilm. A previously described in vitro system for real-time monitoring of biofilm growth/inhibition was utilized to assess the antimicrobial effects of ciprofloxacin, levofloxacin, moxifloxacin, norfloxacin, ertapenem, ceftriaxone, gentamicin, and tobramycin as single antibiotics as well as in combinations with zinc sulfate (2.5 mM) against P.aeruginosa CCIN34519 biofilm. Meanwhile, minimum inhibitory concentrations (MICs) at 24 h and mutant prevention concentrations (MPCs) at 96 h were determined for the aforementioned antibiotics. The real-time monitoring data revealed diverse responses of P.aeruginosa CCIN34519 biofilm to the tested antibiotic-zinc sulfate combinations with potential synergisms in cases of fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin, and norfloxacin) and carbapenem (ertapenem) as demonstrated by reduced MIC and MPC values. Conversely, considerable antagonisms were observed with cephalosporin (ceftriaxone) and aminoglycosides (gentamicin, and tobramycin) as shown by substantially increased MICs and MPCs values. Further deliberate in vivo investigations for the promising synergisms are required to evaluate their therapeutic potentials for treatment of UTIs caused by P. aeruginosa biofilms as well as for developing preventive strategies.

Arabinose induces pellicle formation by Vibrio fischeri

Biofilms are multicellular communities of bacteria attached to a surface and embedded in a protective matrix. In many cases, the signals that induce biofilm formation are unknown. Here, we report that biofilm formation by the marine bacterium Vibrio fischeri can be induced by the addition of arabinose to LBS (Luria-Bertani-salt), a tryptone-based medium. Growth of cells in the presence of 0.2% arabinose, but not other sugars, induced the production of a pellicle at the air/liquid interfaces of static cultures. V. fischeri failed to grow on arabinose as the sole carbon source, suggesting that pellicle production did not occur as a result of increased growth, but experiments using the acid/base indicator phenol red suggested that V. fischeri may partially metabolize arabinose. Pellicle production was independent of the syp polysaccharide locus but was altered upon disruption of the bcs cellulose locus. Through a screen for mutants defective for pellicle production, we found that loss of motility disrupted the formation of the arabinose-induced pellicle. Among the ∼20 mutants that retained motility were strains with insertions in a putative msh pilus locus and a strain with a defect in yidK, which is involved in galactose catabolism. Mutants with the msh gene disrupted grew poorly in the presence of arabinose, while the yidK mutant appeared to be "blind" to the presence of arabinose. Finally, arabinose impaired symbiotic colonization by V. fischeri. This work thus identifies a novel signal and new pathways involved in control of biofilm formation by V. fischeri.

Quorum-sensing and cheating in bacterial biofilms

The idea from human societies that self-interest can lead to a breakdown of cooperation at the group level is sometimes termed the public goods dilemma. We tested this idea in the opportunistic bacterial pathogen, Pseudomonas aeruginosa, by examining the influence of putative cheats that do not cooperate via cell-to-cell signalling (quorum-sensing, QS). We found that: (i) QS cheating occurs in biofilm populations owing to exploitation of QS-regulated public goods; (ii) the thickness and density of biofilms was reduced by the presence of non-cooperative cheats; (iii) population growth was reduced by the presence of cheats, and this reduction was greater in biofilms than in planktonic populations; (iv) the susceptibility of biofilms to antibiotics was increased by the presence of cheats; and (v) coercing cooperator cells to increase their level of cooperation decreases the extent to which the presence of cheats reduces population productivity. Our results provide clear support that conflict over public goods reduces population fitness in bacterial biofilms, and that this effect is greater than in planktonic populations. Finally, we discuss the clinical implications that arise from altering the susceptibility to antibiotics.

Potential of calcium to scaffold an endodontic biofilm, thus protecting the micro-organisms from disinfection

Biofilms in the root canal of a tooth (endodontic biofilm) can induce and sustain apical periodontitis which is an oral inflammatory disease. Still, little is known about the composition of the endodontic biofilm. Studies on biofilms in root canals focus on the identification of the microbial species, but the majority of the biofilm consists of matrix material. Environmental aspects determine the structure of the biofilm and extracellular matrix. Calcium is involved in biofilm formation and activity at three levels. Firstly in cell-environment; calcium may 'condition' the surfaces of support and bacterial cells. Secondly, in cell-cell interaction; calcium plays a role in build up of biofilm structures. Typically, calcium ions act as 'cation bridges' between polysaccharides originating from different cells. Thirdly, within cells, calcium is required for certain biochemical reactions in bacteria and some bacterial physiological activities. Because calcium is present in the root canal, it could play a significant role in the organization of the biofilm. Chelators, already used in endodontics to remove the smear layer by disintegration of the structural cohesion calcium bonds, could weaken the biofilm matrix by removing calcium from the extracellular matrix thus disturbing its coherence. Subsequently, this disruption could increase the efficacy of disinfecting agents.

Nitric oxide regulation of cyclic di-GMP synthesis and hydrolysis in Shewanella woodyi

Although several reports have documented nitric oxide (NO) regulation of biofilm formation, the molecular basis of this phenomenon is unknown. In many bacteria, an H-NOX (heme-nitric oxide/oxygen-binding) gene is found near a diguanylate cyclase (DGC) gene. H-NOX domains are conserved hemoproteins that are known NO sensors. It is widely recognized that cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule that regulates the transition between motility and biofilm. Therefore, NO may influence biofilm formation through H-NOX regulation of DGC, thus providing a molecular-level explanation for NO regulation of biofilm formation. This work demonstrates that, indeed, NO-bound H-NOX negatively affects biofilm formation by directly regulating c-di-GMP turnover in Shewanella woodyi strain MS32. Exposure of wild-type S. woodyi to a nanomolar level of NO resulted in the formation of thinner biofilms, and less intracellular c-di-GMP, than in the absence of NO. Also, a mutant strain in the gene encoding SwH-NOX showed a decreased level of biofilm formation (and a decreased amount of intracellular c-di-GMP) with no change observed upon NO addition. Furthermore, using purified proteins, it was demonstrated that SwH-NOX and SwDGC are binding partners. SwDGC is a dual-functioning DGC; it has diguanylate cyclase and phosphodiesterase activities. These data indicate that NO-bound SwH-NOX enhances c-di-GMP degradation, but not synthesis, by SwDGC. These results support the biofilm growth data and indicate that S. woodyi senses nanomolar NO with an H-NOX domain and that SwH-NOX regulates SwDGC activity, resulting in a reduction in c-di-GMP concentration and a decreased level of biofilm growth in the presence of NO. These data provide a detailed molecular mechanism for NO regulation of c-di-GMP signaling and biofilm formation.

Survey of fungi and yeast in polymicrobial infections in chronic wounds

OBJECTIVE

To assess the incidence, abundance and species diversity of fungi in chronic wounds, as well as to describe the associations of major fungi populations.

METHOD

Comprehensive molecular diagnostic reports were evaluated from a total of 915 chronic wounds in a retrospective study.

RESULTS

Of the 915 clinical specimens, 208 (23%) were positive for fungal species. These samples were further compared in a compiled dataset, and sub-classified among the four major chronic wound types (decubitus ulcer, diabetic foot ulcer, non-healing surgical wound, and venous leg ulcer). The most abundant fungi were yeasts in the genus Candida; however, Curvularia, Malessezia, Aureobasidium, Cladosporium, Ulocladium, Engodontium and Trichtophyton were also found to be prevalent components of these polymicrobial infections. A notable bacterial/fungal negative correlation was found to be apparent between Staphylococcus and Candida. There were also significant relationships between both bacterial and fungal genera and patient metadata including gender, diabetes status and cardiovascular comorbidities.

CONCLUSION

This microbial survey shows that fungi are more important wound pathogens and opportunistic pathogens than previously reported, exemplifying the impact of these under-reported pathogens. With the application of modern cost-effective and comprehensive molecular diagnostics, clinicians can now identify and address this significant component of chronic wound bioburden with targeted therapies, thereby improving healing trajectories.

Microbial metropolis

Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction.

Identification of yeast in chronic wounds using new pathogen-detection technologies

OBJECTIVE

To evaluate the ability of two new diagnostic methods to detect and accurately identify yeast associated with chronic wound infections.

METHOD

Fungal tag-encoded FLX amplicon pyrosequencing (fTEFAP), a universal fungal identification method, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, and a new quantitative polymerase chain reaction (qPCR) wound pathogen panel were used to evaluate three chronic wounds suspected to contain yeast.

RESULTS

Forty wound samples were analysed in addition to the three samples suspected of containing yeast. The qPCR panel, which targets Candida albicans, detected this yeast in two of the three wound samples. In contrast, fTEFAP detected yeast in each of the three samples: two showed Candida albicans and the third Candida parapsilosis. fTEFAP also identified a lower level of Candida tropicalis in one of the wounds that was positive for Candida albicans. The qPCR wound panel results were returned within two hours, while the fTEFAP results were returned within 24 hours.

CONCLUSION

Two new molecular methods have been developed to aid wound pathogen diagnostics. The quantitative PCR wound panel is rapid but is limited to major wound-associated bacteria and yeasts. The universal fTEFAP and bTEFAP methods take 24 hours to return results but are able to detect the relative contribution of any bacteria of yeast in a chronic wound diagnostic sample.

DECLARATION OF INTEREST

Southwest Regional Wound Care Center is a clinical wound-care provider seeking to improve the ability of wound care practitioners to help patients. The Research and Testing Laboratory develops molecular methods including fTEFAP, bTEFAP and the quantitative PCR wound panel.

Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium of Burkholderia sp. NK8 and Pseudomonas aeruginosa PAO1

AIMS

To characterize biofilm formation of a chlorobenzoates (CBs) degrading bacterium, Burkholderia sp. NK8, with another bacterial species, and the biodegradation activity against CBs in the mixed-species biofilm.

METHODS AND RESULTS

Burkholderia sp. NK8 was solely or co-cultured with each of five other representative bacteria in microtitre dishes. Biofilm formation involving the strain NK8 was synergistically promoted by co-culturing with only Pseudomonas aeruginosa PAO1. Epifluorescent microscopy revealed that cells of the bacterial strain NK8 were viable and distributed randomly in the mixed-species biofilms. Enumeration of the attached cells on the surface of wells revealed that cells of the strain NK8 increased approx. 10-fold by the co-culture with the strain PAO1 compared to those by monoculture of the strain NK8, and the degradation activity of 3-chlorobenzoate by the dual-species biofilms was more promoted than that by the strain NK8-monocultured biofilms.

CONCLUSIONS

Enhanced biofilm formation of Burkholderia sp. NK8 by the bacterial consortium occurred, but is determined by the partner bacterial species. The mixed-species biofilms have the advantage to degrade CBs on a solid surface.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a significance of bacterial consortia on the biofilm formation and the degradation activity of Burkholderia sp. NK8, which contribute for complete degradation of chlorinated aromatics.

Capsular polysaccharides of cultured phototrophic biofilms

Phototrophic biofilm samples from an Italian wastewater treatment plant were studied in microcosm experiments under varying irradiances, temperatures and flow regimes to assess the effects of environmental variables and phototrophic biomass on capsular exopolysaccharides (CPS). The results, obtained from circular dichroism spectroscopy and High Performance Liquid Chromatography, suggest that CPS have a stable spatial conformation and a complex monosaccharide composition. The total amount present was positively correlated with the biomass of cyanobacteria and diatoms, and negatively with the biovolume of green algae. The proportion of uronic acids showed the same correlation with these taxon groups, indicating a potential role of cyanobacteria and diatoms in the removal of residual nutrients and noxious cations in wastewater treatment. While overall biofilm growth was limited by low irradiance, high temperature (30 degrees C) and low flow velocity (25 l h(-1)) yielded the highest phototrophic biomass, the largest amount of CPS produced, and the highest proportion of carboxylic acids present.

Endogenous oxidative stress produces diversity and adaptability in biofilm communities

Many bacterial species are capable of biofilm growth, in which cells live and replicate within multicellular community groups. Recent work shows that biofilm growth by a wide variety of bacterial species can generate genetic diversity in microbial populations. This finding is significant because the presence of diverse subpopulations can extend the range of conditions in which communities can thrive. Here, we used biofilms formed by the pathogen Pseudomonas aeruginosa to investigate how this population diversity is produced. We found that some cells within biofilms incur double-stranded DNA breaks caused by endogenous oxidative stress. Genetic variants then result when breaks are repaired by a mutagenic mechanism involving recombinatorial DNA repair genes. We hypothesized that the mutations produced could promote the adaptation of biofilm communities to changing conditions in addition to generating diversity. To test this idea, we exposed biofilms to an antibiotic and found that the oxidative stress-break repair mechanism increased the emergence of antibiotic-resistant bacteria. The diversity and adaptability produced by this mechanism could help biofilm communities survive in harsh environments.

An archaeal bi-species biofilm formed by Pyrococcus furiosus and Methanopyrus kandleri

Recently it was shown that Pyrococcus furiosus uses its flagella not only for swimming, but also for establishment of cell-cell connections, and for adhesion to abiotic surfaces. Therefore, it was asked here if P. furiosus might be able to adhere also to biotic surfaces. Since Methanopyrus kandleri can be found in habitats similar to those of P. furiosus (seawater close to the boiling point and anaerobic conditions) it was tested if interactions between both archaea occur. Using a standard medium and a gas phase reduced in H2 (compared with the optimal gas phase for M. kandleri) we were able to grow both species in a stable coculture. Very interestingly, M. kandleri could adhere to glass under such conditions, but not P. furiosus. This latter archaeum, however, was able to adhere onto M. kandleri cells and onto itself, resulting in structured biofilms on glass. These very often appeared as a bottom layer of M. kandleri cells covered by a multitude of P. furiosus cells. Interactions between P. furiosus and M. kandleri were mediated not only by flagella, but also by direct cell-cell contact.