Biofilm Development in Bacteria

Benefits of Immobilized Bacteria in Bioremediation of Sites Contaminated with Toxic Organic Compounds

Although bioremediation is considered the most environmentally friendly and sustainable technique for remediating contaminated soil and water, it is most effective when combined with physicochemical methods, which allow for the preliminary removal of large quantities of pollutants. This allows microorganisms to efficiently eliminate the remaining contaminants. In addition to requiring the necessary genes and degradation pathways for specific substrates, as well as tolerance to adverse environmental conditions, microorganisms may perform below expectations. One typical reason for this is the high toxicity of xenobiotics present in large concentrations, stemming from the vulnerability of bacteria introduced to a contaminated site. This is especially true for planktonic bacteria, whereas bacteria within biofilms or microcolonies have significant advantages over their planktonic counterparts. A physical matrix is essential for the formation, maintenance, and survival of bacterial biofilms. By providing such a matrix for bacterial immobilization, the formation of biofilms can be facilitated and accelerated. Therefore, bioremediation combined with bacterial immobilization offers a comprehensive solution for environmental cleanup by harnessing the specialized metabolic activities of microorganisms while ensuring their retention and efficacy at target sites. In many cases, such bioremediation can also eliminate the need for physicochemical methods that are otherwise required to initially reduce contaminant concentrations. Then, it will be possible to use microorganisms for the remediation of higher concentrations of xenobiotics, significantly reducing costs while maintaining a rapid rate of remediation processes. This review explores the benefits of bacterial immobilization, highlighting materials and processes for developing an optimal immobilization matrix. It focuses on the following four key areas: (i) the types of organic pollutants impacting environmental and human health, (ii) the bacterial strains used in bioremediation processes, (iii) the types and benefits of immobilization, and (iv) the immobilization of bacterial cells on various carriers for targeted pollutant degradation.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level

Bacteria live in complex polymicrobial communities and are constantly competing for resources. The type VI secretion system (T6SS) is a widespread antagonistic mechanism used by Gram-negative bacteria to gain an advantage over competitors. T6SSs translocate toxic effector proteins inside target prokaryotic cells in a contact-dependent manner. In addition, some T6SS effectors can be secreted extracellularly and contribute to the scavenging scarce metal ions. Bacteria deploy their T6SSs in different situations, categorizing these systems into offensive, defensive and exploitative. The great variety of bacterial species and environments occupied by such species reflect the complexity of regulatory signals and networks that control the expression and activation of the T6SSs. Such regulation is tightly controlled at the transcriptional, posttranscriptional and posttranslational level by abiotic (e.g. pH, iron) or biotic (e.g. quorum-sensing) cues. In this review, we provide an update on the current knowledge about the regulatory networks that modulate the expression and activity of T6SSs across several species, focusing on systems used for interbacterial competition.

Immobilization of Microbes for Biodegradation of Microcystins: A Mini Review

Harmful cyanobacterial blooms (HCBs) frequently occur in eutrophic freshwater ecosystems worldwide. Microcystins (MCs) are considered to be the most prominent and toxic metabolites during HCBs. MCs may be harmful to human and animal health through drinking water and recreational water. Biodegradation is eco-friendly, cost-effective and one of the most effective methods to remove MCs. Many novel MC-degrading bacteria and their potential for MCs degradation have been documented. However, it is a challenge to apply the free MC-degrading bacterial cells in natural environments due to the long-term operational instability and difficult recycling. Immobilization is the process of restricting the mobility of bacteria using carriers, which has several advantages as biocatalysts compared to free bacterial cells. Biological water treatment systems with microbial immobilization technology can potentially be utilized to treat MC-polluted wastewater. In this review article, various types of supporting materials and methods for microbial immobilization and the application of bacterial immobilization technology for the treatment of MCs-contaminated water are discussed. This article may further broaden the application of microbial immobilization technology to the bioremediation of MC-polluted environments.

Biofilm Inhibition and Antiviral Response of Cold Sprayed and Shot Peened Copper Surfaces: Effect of Surface Morphology and Microstructure

Antibacterial properties of copper against planktonic bacteria population are affected by surface microstructure and topography. However, copper interactions with bacteria in a biofilm state are less studied. This work aims at better understanding the difference in biofilm inhibition of bulk, cold-sprayed, and shot-peened copper surfaces and gaining further insights on the underlying mechanisms using optical and scanning electron microscopy to investigate the topography and microstructure of the surfaces. The biofilm inhibition ability is reported for all surfaces. Results show that the biofilm inhibition performance of cold sprayed copper, while initially better, decreases with time and results in an almost identical performance than as-received copper after 18h incubation time. The shot-peened samples with a rough and ultrafine microstructure demonstrated an enhanced biofilm control, especially at 18 hr. The biofilm control mechanisms were explained by the diffusion rates and concentration of copper ions and the interaction between these ions and the biofilm, while surface topography plays a role in the bacteria attachment at the early planktonic state. Furthermore, the data suggest that surface topography plays a key role in antiviral activity of the materials tested, with a smooth surface being the most efficient.

Graphical Abstract

Bioballs carrying a syntrophic Rhodococcus and Mycolicibacterium consortium for simultaneous sorption and biodegradation of fuel oil in contaminated freshwater

Nonpathogenic effective bacterial hydrocarbon degraders, Rhodococcus ruber S103, Mycolicibacterium parafortuitum J101 and Mycolicibacterium austroafricanum Y502, were isolated from mixed polycyclic aromatic hydrocarbon (PAH)-enriched river sediments. They possessed broad substrate specificities toward various PAHs and aliphatic compounds as sole carbon sources. These strains exhibited promising characteristics, including biosurfactant production, high cell hydrophobicity, biofilm formation and no antagonistic interactions, and contained genes encoding hydrocarbon-degrading enzymes. The mixed bacterial consortium combining S103, J101 and Y502, showed more effective syntrophic degradation of two types of refined petroleum products, diesel and fuel oils, than monocultures. The defined consortium immobilized on plastic balls achieved over 50% removal efficiency of high fuel oil concentration (3000 mg L^-1) in a synthetic medium and contaminated freshwater. Furthermore, the immobilized cells simultaneously degraded more than 46% of total fuel oil adsorbed on plastic balls in both culture systems. SEM imaging confirmed that the immobilized consortium exhibited biofilm formation with the bacterial community covering most of the bioball surface, resulting in high bacterial survival against toxic contaminants. The results of this study showed the potential use of the cooperative interaction between Rhodococcus and Mycolicibacterium as immobilized bioballs for the bioremediation of fuel oil-contaminated environments. Additionally, this research has motivated further investigations into the development of bioremediation products for fuel oil degradation.

Marano M, Vojnov AA. The histone-like protein HupB influences biofilm formation and virulence in Xanthomonas citri ssp. citri through the regulation of flagellar biosynthesis

Citrus canker is an important disease of citrus, whose causal agent is the bacterium Xanthomonas citri ssp. citri (Xcc). In previous studies, we found a group of Xcc mutants, generated by the insertion of the Tn5 transposon, which showed impaired ability to attach to an abiotic substrate. One of these mutants carries the Tn5 insertion in hupB, a gene encoding a bacterial histone-like protein, homologue to the β-subunit of the Heat-Unstable (HU) nucleoid protein of Escherichia coli. These types of protein are necessary to maintain the bacterial nucleoid organization and the global regulation of gene expression. Here, we characterized the influence of the mutation in hupB regarding Xcc biofilm formation and virulence. The mutant strain hupB was incapable of swimming in soft agar, whereas its complemented strain partially recovered this phenotype. Electron microscope imaging revealed that impaired motility of hupB was a consequence of the absence of the flagellum. Comparison of the expression of flagellar genes between the wild-type strain and hupB showed that the mutant exhibited decreased expression of fliC (encoding flagellin). The hupB mutant also displayed reduced virulence compared with the wild-type strain when they were used to infect Citrus lemon plants using different infection methods. Our results therefore show that the histone-like protein HupB plays an essential role in the pathogenesis of Xcc through the regulation of biofilm formation and biosynthesis of the flagellum.

Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli FORC_035 Reveals the Essential Role of Iron Acquisition for Survival in Canola Sprouts and Water Dropwort

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that poses a serious threat to humans. Although EHEC is problematic mainly in food products containing meat, recent studies have revealed that many EHEC-associated foodborne outbreaks were attributable to spoiled produce such as sprouts and green leafy vegetables. To understand how EHEC adapts to the environment in fresh produce, we exposed the EHEC isolate FORC_035 to canola spouts (Brassica napus) and water dropwort (Oenanthe javanica) and profiled the transcriptome of this pathogen at 1 and 3 h after incubation with the plant materials. Transcriptome analysis revealed that the expression of genes associated with iron uptake were down-regulated during adaptation to plant tissues. A mutant strain lacking entB, presumably defective in enterobactin biosynthesis, had growth defects in co-culture with water dropwort, and the defective phenotype was complemented by the addition of ferric ion. Furthermore, gallium treatment to block iron uptake inhibited bacterial growth on water dropwort and also hampered biofilm formation. Taken together, these results indicate that iron uptake is essential for the fitness of EHEC in plants and that gallium can be used to prevent the growth of this pathogen in fresh produce.

Innovative Solutions to Sticky Situations: Antiadhesive Strategies for Treating Bacterial Infections

Bacterial adherence to host tissue is an essential process in pathogenesis, necessary for invasion and colonization and often required for the efficient delivery of toxins and other bacterial effectors. As existing treatment options for common bacterial infections dwindle, we find ourselves rapidly approaching a tipping point in our confrontation with antibiotic-resistant strains and in desperate need of new treatment options. Bacterial strains defective in adherence are typically avirulent and unable to cause infection in animal models. The importance of this initial binding event in the pathogenic cascade highlights its potential as a novel therapeutic target. This article seeks to highlight a variety of strategies being employed to treat and prevent infection by targeting the mechanisms of bacterial adhesion. Advancements in this area include the development of novel antivirulence therapies using small molecules, vaccines, and peptides to target a variety of bacterial infections. These therapies target bacterial adhesion through a number of mechanisms, including inhibition of pathogen receptor biogenesis, competition-based strategies with receptor and adhesin analogs, and the inhibition of binding through neutralizing antibodies. While this article is not an exhaustive description of every advancement in the field, we hope it will highlight several promising examples of the therapeutic potential of antiadhesive strategies.

Environmental Pollution, Toxicity Profile and Treatment Approaches for Tannery Wastewater and Its Chemical Pollutants

Leather industries are key contributors in the economy of many developing countries, but unfortunately they are facing serious challenges from the public and governments due to the associated environmental pollution. There is a public outcry against the industry due to the discharge of potentially toxic wastewater having alkaline pH, dark brown colour, unpleasant odour, high biological and chemical oxygen demand, total dissolved solids and a mixture of organic and inorganic pollutants. Various environment protection agencies have prioritized several chemicals as hazardous and restricted their use in leather processing however; many of these chemicals are used and discharged in wastewater. Therefore, it is imperative to adequately treat/detoxify the tannery wastewater for environmental safety. This paper provides a detail review on the environmental pollution and toxicity profile of tannery wastewater and chemicals. Furthermore, the status and advances in the existing treatment approaches used for the treatment and/or detoxification of tannery wastewater at both laboratory and pilot/industrial scale have been reviewed. In addition, the emerging treatment approaches alone or in combination with biological treatment approaches have also been considered. Moreover, the limitations of existing and emerging treatment approaches have been summarized and potential areas for further investigations have been discussed. In addition, the clean technologies for waste minimization, control and management are also discussed. Finally, the international legislation scenario on discharge limits for tannery wastewater and chemicals has also been discussed country wise with discharge standards for pollution prevention due to tannery wastewater.

Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm

BACKGROUND

Engineering of single-species biofilms for enzymatic generation of fine chemicals is attractive. We have recently demonstrated the utility of an engineered Escherichia coli biofilm as a platform for synthesis of 5-halotryptophan. E. coli PHL644, expressing a recombinant tryptophan synthase, was employed to generate a biofilm. Its rapid deposition, and instigation of biofilm formation, was enforced by employing a spin-down method. The biofilm presents a large three-dimensional surface area, excellent for biocatalysis. The catalytic longevity of the engineered biofilm is striking, and we had postulated that this was likely to largely result from protection conferred to recombinant enzymes by biofilm's extracellular matrix. SILAC (stable isotopic labelled amino acids in cell cultures), and in particular dynamic SILAC, in which pulses of different isotopically labelled amino acids are administered to cells over a time course, has been used to follow the fate of proteins. To explore within our spin coated biofilm, whether the recombinant enzyme's longevity might be in part due to its regeneration, we introduced pulses of isotopically labelled lysine and phenylalanine into medium overlaying the biofilm and followed their incorporation over the course of biofilm development.

RESULTS

Through SILAC analysis, we reveal that constant and complete regeneration of recombinant enzymes occurs within spin coated biofilms. The striking catalytic longevity within the biofilm results from more than just simple protection of active enzyme by the biofilm and its associated extracellular matrix. The replenishment of recombinant enzyme is likely to contribute significantly to the catalytic longevity observed for the engineered biofilm system.

CONCLUSIONS

Here we provide the first evidence of a recombinant enzyme's regeneration in an engineered biofilm. The recombinant enzyme was constantly replenished over time as evidenced by dynamic SILAC, which suggests that the engineered E. coli biofilms are highly metabolically active, having a not inconsiderable energetic demand. The constant renewal of recombinant enzyme highlights the attractive possibility of utilising this biofilm system as a dynamic platform into which enzymes of interest can be introduced in a "plug-and-play" fashion and potentially be controlled through promoter switching for production of a series of desired fine chemicals.

Production of valuable compounds by molds and yeasts

We are pleased to dedicate this paper to Dr Julian E Davies. Julian is a giant among microbial biochemists. He began his professional career as an organic chemistry PhD student at Nottingham University, moved on to a postdoctoral fellowship at Columbia University, then became a lecturer at the University of Manchester, followed by a fellowship in microbial biochemistry at Harvard Medical School. In 1965, he studied genetics at the Pasteur Institute, and 2 years later joined the University of Wisconsin in the Department of Biochemistry. He later became part of Biogen as Research Director and then President. After Biogen, Julian became Chair of the Department of Microbiology at the University of British Columbia in Vancouver, Canada, where he has contributed in a major way to the reputation of this department for many years. He also served as an Adjunct Professor at the University of Geneva. Among Julian’s areas of study and accomplishment are fungal toxins including α-sarcin, chemical synthesis of triterpenes, mode of action of streptomycin and other aminoglycoside antibiotics, biochemical mechanisms of antibiotic resistance in clinical isolates of bacteria harboring resistance plasmids, their origins and evolution, secondary metabolism of microorganisms, structure and function of bacterial ribosomes, antibiotic resistance mutations in yeast ribosomes, cloning of resistance genes from an antibiotic-producing microbe, gene cloning for industrial purposes, engineering of herbicide resistance in useful crops, bleomycin-resistance gene in clinical isolates of Staphylococcus aureus and many other topics. He has been an excellent teacher, lecturing in both English and French around the world, and has organized international courses. Julian has also served on the NIH study sections, as Editor for several international journals, and was one of the founders of the journal Plasmid. We expect the impact of Julian’s accomplishments to continue into the future.

Antibacterial, antibiofilm and cytotoxic effects of Nigella sativa essential oil coated gold nanoparticles

This study reports the biological synthesis of gold nanoparticles using essential oil of Nigella sativa (NsEO-AuNPs). The synthesized NsEO-AuNPs were characterized by UV-visible spectra, X-ray diffraction (XRD), FTIR and Transmission electron microscopy (TEM). UV-vis spectra of NsEO-AuNPs showed strong absorption peak at 540 nm. The X-ray diffraction analysis revealed crystalline nature of nanoparticle with distinctive facets (111, 200, 220 and 311 planes) of NsEO-AuNPs. The FTIR spectra recorded peaks at 3388, 2842, 1685, 1607, 1391 and 1018 cm(-1). TEM studies showed the spherical shape of nanoparticles and the particle size ranges between 15.6 and 28.4 nm. The antibacterial activity of NsEO-AuNPs was greater against Gram positive Staphylococcus aureus MTCC 9542 (16 mm) than Gram negative Vibrio harveyi MTCC 7771 (5 mm) at the concentration of 10 μg ml(-1). NsEO-AuNPs effectively inhibited the biofilm formation of S. aureus and V. harveyi by decreasing the hydrophobicity index (78% and 46% respectively). The in-vitro anti-lung cancer activity confirmed by MTT assay on the cell line of A549 carcinoma cells showed IC50 values of bulk Au at 87.2 μg ml(-1), N. sativa essential oil at 64.15 μg ml(-1) and NsEO-AuNPs at 28.37 μg ml(-1). The IC50 value showed that NsEO-AuNPs was highly effective in inhibiting the A549 lung cancer cells compared to bulk Au and N. sativa essential oil.

Immobilization of Microbes for Bioremediation of Crude Oil Polluted Environments: A Mini Review

Petroleum hydrocarbons are the most common environmental pollutants in the world and oil spills pose a great hazard to terrestrial and marine ecosystems. Oil pollution may arise either accidentally or operationally whenever oil is produced, transported, stored and processed or used at sea or on land. Oil spills are a major menace to the environment as they severely damage the surrounding ecosystems. To improve the survival and retention of the bioremediation agents in the contaminated sites, bacterial cells must be immobilized. Immobilized cells are widely tested for a variety of applications. There are many types of support and immobilization techniques that can be selected based on the sort of application. In this review article, we have discussed the potential of immobilized microbial cells to degrade petroleum hydrocarbons. In some studies, enhanced degradation with immobilized cells as compared to free living bacterial cells for the treatment of oil contaminated areas have been shown. It was demonstrated that immobilized cell to be effective and is better, faster, and can be occurred for a longer period.

Influence of biofilms on heavy metal immobilization in sustainable urban drainage systems (SuDS)

This paper physically and numerically models the influence of biofilms on heavy metal removal in a gravel filter. Experimental flow columns were constructed to determine the removal of Cu, Pb and Zn by gabbro and dolomite gravel lithologies with and without natural biofilm from sustainable urban drainage systems (SuDS). Breakthrough experiments showed that, whilst abiotic gravel filters removed up to 51% of metals, those with biofilms enhanced heavy metal removal by up to a further 29%, with Cu removal illustrating the greatest response to biofilm growth. An advection-diffusion equation successfully modelled metal tracer transport within biofilm columns. This model yielded a permanent loss term (k) for metal tracers of between 0.01 and 1.05, correlating well with measured data from breakthrough experiments. Additional 16S rRNA clone library analysis of the biofilm indicated strong sensitivity of bacterial community composition to the lithology of the filter medium, with gabbro filters displaying Proteobacteria dominance (54%) and dolomite columns showing Cyanobacteria dominance (47%).

Reactive oxygen species mediated bacterial biofilm inhibition via zinc oxide nanoparticles and their statistical determination

The formation of bacterial biofilm is a major challenge in clinical applications. The main aim of this study is to describe the synthesis, characterization and biocidal potential of zinc oxide nanoparticles (NPs) against bacterial strain Pseudomonas aeruginosa. These nanoparticles were synthesized via soft chemical solution process in a very short time and their structural properties have been investigated in detail by using X-ray diffraction and transmission electron microscopy measurements. In this work, the potential of synthesized ZnO-NPs (∼10–15 nm) has been assessed in-vitro inhibition of bacteria and the formation of their biofilms was observed using the tissue culture plate assays. The crystal violet staining on biofilm formation and its optical density revealed the effect on biofilm inhibition. The NPs at a concentration of 100 µg/mL significantly inhibited the growth of bacteria and biofilm formation. The biofilm inhibition by ZnO-NPs was also confirmed via bio-transmission electron microscopy (Bio-TEM). The Bio-TEM analysis of ZnO-NPs treated bacteria confirmed the deformation and damage of cells. The bacterial growth in presence of NPs concluded the bactericidal ability of NPs in a concentration dependent manner. It has been speculated that the antibacterial activity of NPs as a surface coating material, could be a feasible approach for controlling the pathogens. Additionally, the obtained bacterial solution data is also in agreement with the results from statistical analytical methods.

Host intestinal signal-promoted biofilm dispersal induces Vibrio cholerae colonization

Vibrio cholerae causes human infection through ingestion of contaminated food and water, leading to the devastating diarrheal disease cholera. V. cholerae forms matrix-encased aggregates, known as biofilms, in the native aquatic environment. While the formation of V. cholerae biofilms has been well studied, little is known about the dispersal from biofilms, particularly upon entry into the host. In this study, we found that the exposure of mature biofilms to physiologic levels of the bile salt taurocholate, a host signal for the virulence gene induction of V. cholerae, induces an increase in the number of detached cells with a concomitant decrease in biofilm mass. Scanning electron microscopy micrographs of biofilms exposed to taurocholate revealed an altered, perhaps degraded, appearance of the biofilm matrix. The inhibition of protein synthesis did not alter rates of detachment, suggesting that V. cholerae undergoes a passive dispersal. Cell-free media from taurocholate-exposed biofilms contains a larger amount of free polysaccharide, suggesting an abiotic degradation of biofilm matrix by taurocholate. Furthermore, we found that V. cholerae is only able to induce virulence in response to taurocholate after exit from the biofilm. Thus, we propose a model in which V. cholerae ingested as a biofilm has coopted the host-derived bile salt signal to detach from the biofilm and go on to activate virulence.

On the production of glycogen by Pseudomonas fluorescens during biofilm development: an in situ study by attenuated total reflection-infrared with chemometrics

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to monitor Pseudomonas fluorescens biofilms in situ, non-destructively, in real time, and under fully hydrated conditions. Changes accompanying the metabolic evolution of the sessile bacterial cells from the nascent biofilm monolayer to the beginning of the multi-layered structure in the presence of nutrients were identified via the ATR-FTIR fingerprints of the young biofilm on the ATR crystal. The ATR-FTIR spectra were analysed by classical methods (time evolution of integrated intensities and profile evolution of specific bands), and also by a multivariate curve resolution, Bayesian positive source separation, to extract the pure component spectra and their change of concentration over time occurring during biofilm settlement. This work showed clearly the overproduction of glycogen by sessile P. fluorescens, which had not previously been described by other research groups.

The antibacterial and anti-biofouling performance of biogenic silver nanoparticles by Lactobacillus fermentum

Biofouling is a major challenge in the water industry and public health. Silver nanoparticles (AgNPs) have excellent antimicrobial properties and are considered to be a promising anti-biofouling agent. A modified method was used to produce small sized and well-dispersed biogenic silver nanoparticles with a mean size of ~6 nm (Bio-Ag0-6) using Lactobacillus fermentum. The morphology, size distribution, zeta potential and oxidation state of the silver were systematically characterized. Determination of minimal inhibitory and bactericidal concentration results revealed that biogenic silver Bio-Ag(0-6) can effectively suppress the growth of the test bacteria. Additionally, the inhibition effects of Bio-Ag(0-6) on biofilm formation and on established biofilms were evaluated using P. aeruginosa (ATCC 27853) as the model bacterium. The results from microtiter plates and confocal laser scanning microscopy demonstrated that Bio-Ag(0-6) not only exhibited excellent antibacterial performance but also could control biofilm formation and induce detachment of the bulk of P. aeruginosa biofilms leaving a small residual matrix.

Efficacy of N-Acetyl-Cysteine in Combination with Thiamphenicol in Sequential (Intramuscular/Aerosol) Therapy of Upper Respiratory Tract Infections Even When Sustained by Bacterial Biofilms

A total of 102 patients with recurrent upper respiratory tract infections underwent microbiological exploration with appropriate sampling and direct biopsies of the infected sites. Therapy was then started and on day 1 each patient received two intramuscular injections of thiamphenicol glycinate acetylcysteinate (TGA). From day 2 to 10 sequential therapy with the same drug was continued employing TGA administered by aerosol. All putative etiologic agents recovered were susceptible to thiamphenicol and only 24 demonstrated the ability to produce in vitro biofilms. The organisms comprised 10 Staphylococcus aureus, 6 Streptococcus pyogenes, 4 Streptococcus pneumoniae and 3 Haemophilus influenzae. Of the 24 subjects in whom biofilms were demonstrated to be present in vivo by Scanning Electron Microscopy, clinical and bacteriological cure was obtained in 21 cases (87.5%) following sequential therapy with TGA. Failures were considered to be persistent signs and symptoms at day 15 after initiation of treatment and lack of eradication of 3 S. aureus strains, despite their in vitro susceptibility to thiamphenicol. Very few adverse events attributable to TGA were reported in this cohort of patients. In no case was discontinuation of treatment deemed necessary by the attending physician.

Microbial pathogen control in the beef chain: recent research advances

Within a recent EU research project ("ProSafeBeef"), research on foodborne pathogens in the beef chain was conducted by using a longitudinally integrated (fork-to-farm) approach. There is not any "single intervention-single chain point" combination by which the pathogens would be reliably and entirely eliminated from the chain resulting in total prevention of pathogens in beef and products thereof at the consumption time. Rather, a range of control interventions have to be applied at multiple points of the chain, so to achieve an acceptable, ultimate risk reduction. Various novel interventions were developed and evaluated during the project, and are briefly summarized in this paper. They include on-farm measures, risk categorisation of cattle presented for slaughter, hygiene-based measures and antimicrobial treatments applied on hides and/or carcasses during cattle slaughter, those applied during beef processing-storage-distribution, use of Time Temperature Integrator-based indicators of safety, and effective sanitation of surfaces.

Adaptation of the 3H-leucine incorporation technique to measure heterotrophic activity associated with biofilm on the blades of the seaweed Sargassum spp

The ecological interaction between microorganisms and seaweeds depends on the production of secondary compounds that can influence microbial diversity in the water column and the composition of reef environments. We adapted the (3)H-leucine incorporation technique to measure bacterial activity in biofilms associated with the blades of the macroalgae Sargassum spp. We evaluated (1) if the epiphytic bacteria on the blades were more active in detritus or in the biofilm, (2) substrate saturation and linearity of (3)H-leucine incorporation, (3) the influence of specific metabolic inhibitors during (3)H-leucine incorporation under the presence or absence of natural and artificial light, and (4) the efficiency of radiolabeled protein extraction. Scanning electron microscopy showed heterogeneous distribution of bacteria, diatoms, and polymeric extracellular secretions. Active bacteria were present in both biofilm and detritus on the blades. The highest (3)H-leucine incorporation was obtained when incubating blades not colonized by macroepibionts. Incubations done under field conditions reported higher (3)H-leucine incorporation than in the laboratory. Light quality and sampling manipulation seemed to be the main factors behind this difference. The use of specific metabolic inhibitors confirmed that bacteria are the main group incorporating (3)H-leucine but their association with primary production suggested a symbiotic relationship between bacteria, diatoms, and the seaweed.

Biofouling of water treatment membranes: a review of the underlying causes, monitoring techniques and control measures

Biofouling is a critical issue in membrane water and wastewater treatment as it greatly compromises the efficiency of the treatment processes. It is difficult to control, and significant economic resources have been dedicated to the development of effective biofouling monitoring and control strategies. This paper highlights the underlying causes of membrane biofouling and provides a review on recent developments of potential monitoring and control methods in water and wastewater treatment with the aim of identifying the remaining issues and challenges in this area.

Biofilm control in water by a UV-based advanced oxidation process

An ultraviolet (UV)-based advanced oxidation process (AOP), with hydrogen peroxide and medium-pressure (MP) UV light (H(2)O(2)/UV), was used as a pretreatment strategy for biofilm control in water. Suspended Pseudomonas aeruginosa cells were exposed to UV-based AOP treatment, and the adherent biofilm formed by the surviving cells was monitored. Control experiments using H(2)O(2) or MP UV irradiation alone could inhibit biofilm formation for only short periods of time (<24 h) post-treatment. In a H(2)O(2)/filtered-UV (>295 nm) system, an additive effect on biofilm control was shown vs filtered-UV irradiation alone, probably due to activity of the added hydroxyl radical (OH•). In a H(2)O(2)/full-UV (ie full UV spectrum, not filtered) system, this result was not obtained, possibly due to the germicidal UV photons overwhelming the AOP system. Generally, however, H(2)O(2)/UV prevented biofilm formation for longer periods (days) only when maintained with residual H(2)O(2). The ratio of surviving bacterial concentration post-treatment to residual H(2)O(2) concentration played an important role in biofilm prevention and bacterial regrowth. H(2)O(2) treatments alone resulted in poorer biofilm control compared to UV-based AOP treatments maintained with similar levels of residual H(2)O(2), indicating a possible advantage of AOP.

Differential gene expression in bacterial symbionts from loliginid squids demonstrates variation between mutualistic and environmental niches

Luminescent bacteria (gamma-Proteobacteria: Vibrionaceae) are found in complex bilobed light organs of both sepiolid and loliginid squids (Mollusca: Cephalopoda). Despite the existence of multiple strain colonization between Vibrio bacteria and loliginid squids, specificity at the genus level still exists and may influence interactions between symbiotic and free-living stages of the symbiont. The environmentally transmitted behaviour of Vibrio symbionts bestows a certain degree of recognition that exists prior and subsequent to the colonization process. Therefore, we identified bacterial genes required for successful colonization of loliginid light organs by examining transcripts solely expressed in either the light organ or free-living stages. Selective capture of transcribed sequences (SCOTS) was used to differentiate genes expressed by the same bacterium when thriving in two different environments (i.e. loliginid light organs and seawater). Genes specific for squid light organs included vulnibactin synthetase, outer membrane protein W and dihydroxy dehydratase, which have been associated with the maintenance of bacterial host associations in other systems. In contrast, genes that were solely expressed in the free-living condition consisted of transcripts recognized as important factors for bacterial survival in the environment. These transcripts included genes for methyl accepting chemotaxis proteins, arginine decarboxylase and chitinase. These results provide valuable information regarding mechanisms determining specificity, establishment, and maintenance of bacteria-squid associations.

Control of biofilm formation in water using molecularly capped silver nanoparticles

Control of biofouling and its negative effects on process performance of water systems is a serious operational challenge in all of the water sectors. Molecularly capped silver nanoparticles (Ag-MCNPs) were used as a pretreatment strategy for controlling biofilm development in aqueous suspensions using the model organism Pseudomonas aeruginosa. Biofilm control was tested in a two-step procedure: planktonic P. aeruginosa was exposed to the Ag-MCNPs and then the adherent biofilm formed by the surviving cells was monitored by applying a model biofilm-formation assay. Under specific conditions, Ag-MCNPs retarded biofilm formation, even when high percentage of planktonic P. aeruginosa cells survived the treatment. For example, Ag-MCNPs (10 microg mL(-1)) retarded biofilm formation (>60%), when 50 percent of the planktonic P. aeruginosa cells survived the treatment. Moreover, stable low value of relative biomass has been formed in the presence of fixed Ag-MCNPs concentrations at various biofilm incubation times. Our results showed that Ag-MCNPs pretreated cells were able to produce EPS although they succeeded to form relatively low adherent biofilm. These pretreated cells appear well preserved and undamaged under TEM HPH/freeze micrographs, yet the intra cellular material seems to be pushed towards the peripheral parts of the cell, possibly indicating a survival strategy to the presence of Ag-MCNPs. The lower value of relative biomass formed in the presence of Ag-MCNPs could be associated with molecular mechanisms related to biofilm formation or continuous release of silver ions in the sample. However, further research is required to examine these factors.

Changes in the bacterial community structure in two-stage constructed wetlands with different plants for industrial wastewater treatment

This study focused on the diversity of bacterial communities from two series of two-stage constructed wetlands (CWs) treating tannery wastewater, under different hydraulic conditions. Series were separately planted with Typha latifolia and Phragmites australis in expanded clay aggregates and operated for 31 months. The effect of plant species, hydraulic loading and unit stage on bacterial communities was addressed through bacterial enumeration and denaturating gradient gel electrophoresis (DGGE). Diverse and distinct bacterial communities were found in each system unit, which was related in part to the type of plant and stage position (first or second unit in the series). Numerical analysis of DGGE profiles showed high diversity in each unit with an even distribution of species. No clear relation was established between the sample collection time, hydraulic loading applied and the bacterial diversity. Isolates retrieved from plant roots and substrates of CWs were affiliated with gamma-Proteobacteria, Firmicutes, alpha-Proteobacteria, Sphingobacteria, Actinobacteria and Bacteroidetes. Both series were effective in removing organic matter from the inlet wastewater, however, based on batch degradation experiments it seems that biodegradation was limited by the recalcitrant properties of the wastewater.

Metabolic diversification of cells during the development of yeast colonies

Microorganisms in nature form organized multicellular structures (colonies, biofilms) possessing properties absent in individual cells. These are often related to the better ability of communities to survive long-lasting starvation and stress and include mechanisms of adaptation and cell specialization. Thus, yeast colonies pass through distinct developmental phases characterized by changes in pH and the production of ammonia-signalling molecules. Here, we show that Saccharomyces cerevisiae colony transition between major developmental phases (first acidic, alkali, second acidic) is accompanied by striking transcription changes, while the development within each particular phase is guided mostly at the post-transcriptional level. First- and second-acidic-phase colonies markedly differ. Second-acidic-phase colonies maintain the adaptive metabolism activated in the ammonia-producing period, supplemented by additional changes, which begin after colonies enter the second acidic phase. Cells with particular properties are not homogenously dispersed throughout the colony population, but localize to specific colony regions. Thus, cells located at the colony margin are able to export higher amounts of ammonium than central cells and to activate an adaptive metabolism. In contrast, central chronologically aged cells are unable to undergo these changes but they maintain higher levels of various stress-defence enzymes. These divergent properties of both cell types determine their consequent dissimilar fate.

Development of Candida-associated denture stomatitis: new insights

Despite therapeutic progress, opportunistic oral fungal infectious diseases have increased in prevalence, especially in denture wearers. The combination of entrapment of yeast cells in irregularities in denture-base and denture-relining materials, poor oral hygiene and several systemic factors is the most probable cause for the onset of this infectious disease. Hence colonization and growth on prostheses by Candida species are of clinical importance. The purpose of this review is to critically discuss several key factors controlling the adhesion of Candida species which are relevant to denture-associated stomatitis. Although there is some consensus on the role of surface properties, studies on several other factors, as the use of denture liners, salivary properties and yeast-bacterial interactions, have shown contradictory findings. A comprehensive fundamental understanding is hampered by conflicting findings due to the large variations in experimental protocols, while other factors have never been thoroughly studied. Surface free energy and surface roughness control the initial adherence, but temporal changes have not been reported. Neither have in vivo studies shown if the substratum type is critical in dictating biofilm accumulation during longer periods in the oral environment. The contribution of saliva is unclear due to factors like variations in its collection and handling. Initial findings have disclosed that also bacteria are crucial for the successful establishment of Candida in biofilms, but the clinical significance of this observation is yet to be confirmed. In conclusion, there is a need to standardize experimental procedures, to bridge the gap between laboratory and in vivo methodologies and findings and – in general – to thoroughly investigate the factors that modulate the initial attachment and subsequent colonization of denture-base materials and the oral mucosa of patients subjected to Candida infections. Information on how these factors can be controlled is required and this may help to prevent the disease. The societal impact of such information is significant given the magnitude of the candidosis problem worldwide.

Different, overlapping mechanisms for colonization of abiotic and plant surfaces by Pseudomonas putida

Mechanisms governing biofilm formation have generated considerable interest in recent years, yet comparative analyses of processes for bacterial establishment on abiotic and biotic surfaces are still limited. In this report we have expanded previous information on the genetic determinants required for colonization of plant surfaces by Pseudomonas putida populations and analyzed their correlation with biofilm formation processes on abiotic surfaces. Insertional mutations affecting flagellar genes or the synthesis and transport of the large adhesin LapA lead to decreased adhesion to seeds and biofilm formation on abiotic surfaces. The latter also causes reduced fitness in the rhizosphere. Decreased seed adhesion and altered biofilm formation kinetics are observed in mutants affected in heme biosynthesis and a gene that might participate in oxidative stress responses, whereas a mutant in a gene involved in cytochrome oxidase assembly is affected in the bacterium-plant interaction but not in bacterial establishment on abiotic surfaces. Finally, a mutant altered in lipopolysaccharide biosynthesis is impaired in seed and root colonization but seems to initiate attachment to plastic faster than the wild type. This variety of phenotypes reflects the complexity of bacterial adaptation to sessile life, and the partial overlap between mechanisms leading to biofilm formation on abiotic and biotic surfaces.

Altering the ratio of phenazines in Pseudomonas chlororaphis (aureofaciens) strain 30-84: effects on biofilm formation and pathogen inhibition

Pseudomonas chlororaphis strain 30-84 is a plant-beneficial bacterium that is able to control take-all disease of wheat caused by the fungal pathogen Gaeumannomyces graminis var. tritici. The production of phenazines (PZs) by strain 30-84 is the primary mechanism of pathogen inhibition and contributes to the persistence of strain 30-84 in the rhizosphere. PZ production is regulated in part by the PhzR/PhzI quorum-sensing (QS) system. Previous flow cell analyses demonstrated that QS and PZs are involved in biofilm formation in P. chlororaphis (V. S. R. K. Maddula, Z. Zhang, E. A. Pierson, and L. S. Pierson III, Microb. Ecol. 52:289-301, 2006). P. chlororaphis produces mainly two PZs, phenazine-1-carboxylic acid (PCA) and 2-hydroxy-PCA (2-OH-PCA). In the present study, we examined the effect of altering the ratio of PZs produced by P. chlororaphis on biofilm formation and pathogen inhibition. As part of this study, we generated derivatives of strain 30-84 that produced only PCA or overproduced 2-OH-PCA. Using flow cell assays, we found that these PZ-altered derivatives of strain 30-84 differed from the wild type in initial attachment, mature biofilm architecture, and dispersal from biofilms. For example, increased 2-OH-PCA production promoted initial attachment and altered the three-dimensional structure of the mature biofilm relative to the wild type. Additionally, both alterations promoted thicker biofilm development and lowered dispersal rates compared to the wild type. The PZ-altered derivatives of strain 30-84 also differed in their ability to inhibit the fungal pathogen G. graminis var. tritici. Loss of 2-OH-PCA resulted in a significant reduction in the inhibition of G. graminis var. tritici. Our findings suggest that alterations in the ratios of antibiotic secondary metabolites synthesized by an organism may have complex and wide-ranging effects on its biology.

Tight modulation of Escherichia coli bacterial biofilm formation through controlled expression of adhesion factors

Despite the economic and sanitary problems caused by harmful biofilms, biofilms are nonetheless used empirically in industrial environmental and bioremediation processes and may be of potential use in medical settings for interfering with pathogen development. Escherichia coli is one of the bacteria with which biofilm formation has been studied in great detail, and it is especially appreciated for biotechnology applications because of its genetic amenability. Here we describe the development of two new genetic tools enabling the constitutive and inducible expression of any gene or operon of interest at its native locus. In addition to providing valuable tools for complementation and overexpression experiments, these two compact genetic cassettes were used to modulate the biofilm formation capacities of E. coli by taking control of two biofilm-promoting factors, autotransported antigen 43 adhesin and the bscABZC cellulose operon. The modulation of the biofilm formation capacities of E. coli or those of other bacteria capable of being genetically manipulated may be of use both for reducing and for improving the impact of biofilms in a number of industrial and medical applications.

The selective value of bacterial shape

Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.

Life within a community: benefit to yeast long-term survival

Traditionally, living organisms have often been classified into two main categories: unicellular and multicellular. In recent years, however, the boundary between these two groups has become less strict and clear than was previously presumed. Studies on the communities formed by unicellular microorganisms have revealed that various properties and processes so far mainly associated with metazoa are also important for the proper development, survival and behaviour of muticellular microbial populations. In this review, we present various examples of this, using a yeast colony as representative of a structured organized microbial community. Among other things, we will show how the differentiation of yeast cells within a colony can be important for the long-term survival of a community under conditions of nutrient shortage, how colony development and physiology can be influenced by the environment, and how a group of colonies can synchronize their developmental changes. In the last section, we introduce examples of molecular mechanisms that can participate in some aspects of the behaviour of yeast populations.

Quorum sensing and phenazines are involved in biofilm formation by Pseudomonas chlororaphis (aureofaciens) strain 30-84

The biological control bacterium Pseudomonas chlororaphis (aureofaciens) strain 30-84 employs two quorum sensing (QS) systems: PhzR/PhzI regulates the production of the antibiotics phenazine-1-carboxylic acid, 2-hydroxy-phenazine-1-carboxylic acid, and 2-hydroxy-phenazine, whereas CsaR/CsaI regulates currently unknown aspects of the cell surface. Previously characterized derivatives of strain 30-84 with mutations in each QS system and in the phenazine biosynthetic genes were screened for their ability to form surface-attached biofilm populations in vitro, using microtiter plate and flow cell biofilm assays, and on seeds and roots. Results from in vitro, seed, and root studies demonstrated that the PhzR/PhzI and the CsaR/CsaI QS regulatory systems contribute to the establishment of biofilms, with mutations in PhzR/PhzI having a significantly greater effect than mutations in CsaR/CsaI. Interestingly, phenazine antibiotic production was necessary for biofilm formation to the same extent as the PhzR/PhzI QS system, suggesting the loss of phenazines was responsible for the majority of the biofilm defect in these mutants. In vitro analysis indicated that genetic complementation or AHL addition to the growth medium restored the ability of the AHL synthase phzI mutant to form biofilms. However, only phenazine addition or genetic complementation of the phenazine biosynthetic mutation in trans restored biofilm formation by mutants defective in the transcriptional activator phzR or the phzB structural mutant. QS and phenazine production were also involved in the establishment of surface-attached populations on wheat seeds and plant roots, and, as observed in vitro, the addition of AHL extracts restored the ability of phzI mutants, but not phzR mutants, to form surface attached populations on seeds. Similarly, the presence of the wild type in mixtures with the mutants restored the ability of the mutants to colonize wheat roots, demonstrating that AHL and/or phenazine production by the wild-type population could complement the AHL- and phenazine-deficient mutants in situ. Together, these data demonstrate that both QS systems are involved in the formation of surface-attached populations required for biofilm formation by P. chlororaphis strain 30-84, and indicate a new role for phenazine antibiotics in rhizosphere community development beyond inhibition of other plant-associated microorganisms.

Insight into Biofilm-Associated Microbial Life

Microbes cohabit our planet and are engaged in a struggle for survival though on a microscopic scale. This endeavor allows them to develop and devise means for survival and proliferation. One such strategy is the formation of biofilms leading to establishment of a protected community. Such multi-communities may consist of harmful and pathogenic microbes, and they may cause economic problems and threats to human health. Biofilms are formed when microorganisms are typically attached to support surfaces. Biofilm-associated cells are sessile and differentiated from their suspended counterparts by generation of an extracellular polymeric substance matrix, reduced growth rates, and the up- and downregulation of specific genes. Biofilm formation is a complex process regulated by diverse characteristics of the growth medium, substratum, and cell surface. Development of strategies to control or prevent biofilms requires a thorough understanding of the biofilm development process. Biofilm research has witnessed exponential growth, and exciting findings have been reported. This has led us to visualize some previously un-thought-of and fascinating events. This article aims to provide an overview of biofilm research and associated challenges.