Colanic acid is an exopolysaccharide common to many enterobacteria isolated from paper-machine slimes

Research progress on the functions, preparation and detection methods of l-fucose

l-fucose is a six-carbon sugar that has potential applications in many fields. It exerts antitumor effects and could relieve intestinal disease. It exhibits potential as an emulsifier in the food industry. It is also used as a functional food and in anti-aging skincare products. However, at present, it is not possible to prepare high-purity l-fucose on a large scale, and its preparation needs further development. This review summarizes the preparation methods of l-fucose including chemical synthesis, enzymatic synthesis, microbial fermentation, and separation and purification from algae. The detection methods of l-fucose are also introduced in detail, such as l-fucose-specific lectin, detection l-fucose dehydrogenase, cysteine-sulfuric acid method, high-performance liquid chromatography, gas chromatography, and biosensors. In this review, the properties and pharmacological effects of l-fucose; preparation methods, and the commonly used detection methods of l-fucose are reviewed to serve as a reference material.

Evolutionary and co-evolutionary phage training approaches enhance bacterial suppression and delay the emergence of phage resistance

The development of phage resistance by bacteria is a major barrier that impedes the therapeutic use of phages. Phage training has been proposed as a novel tool that harnesses the evolutionary potential of phages to improve phage infectivity. Both evolutionary and co-evolutionary phage training models have been previously reported to train phages. However, both of these phage training models have been reported able to effectively suppress the emergence of phage-resistant bacteria mutants, thus presenting a contradictory phenomenon. Therefore, in this study, we set out to systematically compare the effectiveness of both evolutionary and co-evolutionary phage training models with regard to phage physiology, infectivity, and genotype. To this end, a natural lytic phage capable of infecting a Klebsiella pneumonia strain was isolated from wastewater and subjected to evolutionary and co-evolutionary phage training for 30 days. After the phage training, the physiology and genomic characteristics of evolved and co-evolved phages were assessed. Our results demonstrated that both evolved and co-evolved phages exhibit improved bacterial suppression activity and are able to delay the emergence of phage resistance. Furthermore, both phages harbored unique genome mutational changes in different functionally associated phage proteins. Similarly, evolved and co-evolved phage-resistant bacteria mutants that arose post phage infection displayed varying phage resistance sensitivities, which may be correlated to the unique genome mutational change identified in cell membrane structure. In particular, co-evolved phage-resistant bacteria mutants exhibited less phage resistance compared to evolved phage-resistant bacteria mutants. These results highlighted the finding that the co-evolutionary phage training model serves as a better phage training model as it endows phage with improved infectivity, but also selects for phage-resistant bacteria with a lower phage resistance when compared to evolutionary phage training.

Surface-Enhanced Raman Scattering-Based Surface Chemotaxonomy: Combining Bacteria Extracellular Matrices and Machine Learning for Rapid and Universal Species Identification

Rapid, universal, and accurate identification of bacteria in their natural states is necessary for on-site environmental monitoring and fundamental microbial research. Surface-enhanced Raman scattering (SERS) spectroscopy emerges as an attractive tool due to its molecule-specific spectral fingerprinting and multiplexing capabilities, as well as portability and speed of readout. Here, we develop a SERS-based surface chemotaxonomy that uses bacterial extracellular matrices (ECMs) as proxy biosignatures to hierarchically classify bacteria based on their shared surface biochemical characteristics to eventually identify six distinct bacterial species at >98% classification accuracy. Corroborating with in silico simulations, we establish a three-way inter-relation between the bacteria identity, their ECM surface characteristics, and their SERS spectral fingerprints. The SERS spectra effectively capture multitiered surface biochemical insights including ensemble surface characteristics, e.g., charge and biochemical profiles, and molecular-level information, e.g., types and numbers of functional groups. Our surface chemotaxonomy thus offers an orthogonal taxonomic definition to traditional classification methods and is achieved without gene amplification, biochemical testing, or specific biomarker recognition, which holds great promise for point-of-need applications and microbial research.

Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R

Phytoremediation, a cost-effective, eco-friendly alternative to conventional remediation, could expand efforts to remediate arsenic-contaminated soils. As with other pollutants, the plant microbiome may improve phytoremediation outcomes for arsenic-contaminated sites. We used in vitro and in silico methods to compare the arsenic resistance mechanisms, synthesis of extracellular polymeric substances (EPS), biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas sp. PD9R and Rahnella laticis PD12R. PD12R, which tolerates arsenate (As(V)) and arsenite (As(III)) to concentrations fivefold greater than PD9R, synthesizes high volumes of EPS in response to arsenic, and sequesters arsenic in the capsular EPS and cells. While arsenic exposure induced EPS synthesis in both strains, only PD12R continued to form biofilms at high As(III) and As(V) concentrations. The effects of endophyte inoculation on Arabidopsis growth varied by strain and As(V) concentration, and PD9R had positive effect on plants exposed to low levels of arsenic. Comparative genomic analyses exploring the EPS synthesis and arsenic resistance mechanisms against other Pseudomonas and Rahnella strains suggest that both strains possess atypical arsenic resistance mechanisms from other plant-associated strains, while the configuration of the EPS synthesis systems appeared to be more broadly distributed among plant- and non-plant-associated strains.

Collective protection against the type VI secretion system in bacteria

Bacteria commonly face attacks from other strains using the type VI secretion system (T6SS), which acts like a molecular speargun to stab and intoxicate competitors. Here we show how bacteria can work together to collectively defend themselves against these attacks. This project began with an outreach activity: while developing an online computer game of bacterial warfare, we noticed that one strategist ("Slimy") that made extracellular polymeric substances (EPS) was able to resist attacks from another strategist that employed the T6SS ("Stabby"). This observation motivated us to model this scenario more formally, using dedicated agent-based simulations. The model predicts that EPS production can serve as a collective defence mechanism, which protects both producing cells and neighbouring cells that do not make EPS. We then tested our model with a synthetic community that contains a T6SS-wielding attacker (Acinetobacter baylyi), and two T6SS-sensitive target strains (Escherichia coli) that either secrete EPS, or not. As predicted by our modelling, we find that the production of EPS leads to collective protection against T6SS attacks, where EPS producers protect each other and nearby non-producers. We identify two processes that explain this protection: EPS sharing between cells and a second general mechanism whereby groups of resistant cells shield susceptible cells, which we call "flank protection". Our work shows how EPS-producing bacteria can work together to defend themselves from the type VI secretion system.

Chemical Synthesis of a Colanic Acid Hexasaccharide

Chemical synthesis of a hexasaccharide relevant to colanic acid, which bears a high prevalence of polyanionic and acetyl decoration, has been achieved, highlighting stereoselective glycosylation and effective installation of O-acetyl and pyruvate residues.

Metabolic Engineering for Overproduction of Colanic Acid in Escherichia coli Mutant with Short Lipopolysaccharide

Colanic acid is a major exopolysaccharide existing in most Enterobacteriaceae when exposed to an extreme environment. Colanic acid possesses excellent physical properties and biological activities, which makes it a candidate in the food and healthcare market. Previous strategies for colanic acid overproduction in E. coli mainly focus on removing the negative regulator on colanic acid biosynthesis or overexpressing the rcsA gene to up-regulate the cps operon. In this study, modifications in metabolic pathways were implemented in E. coli mutant strains with shortened lipopolysaccharides to improve colanic acid production. First, ackA was deleted to remove the byproduct acetate and the effect of accumulated acetyl-phosphate on colanic acid production was investigated. Second, 11 genes responsible for O-antigen synthesis were deleted to reduce its competition for glucose-1-phosphate and UDP-galactose with colanic acid production. Third, uppS was overexpressed to supply lipid carriers for synthesizing a colanic acid repeat unit. Colanic acid production in the final engineered strain WZM008/pTrcS reached 11.68 g/L in a 2.0 L bioreactor, 3.54 times the colanic acid production by the WQM001 strain. The results provide insights for further engineering E. coli to maximize CA production.

A novel glucofucobiose with potential prebiotic activity prepared from the exopolysaccharides of Clavibacter michiganensis M1

Fucose and fucosylated oligosaccharides have important applications in various industries owing to their prebiotic, anti-inflammatory, anticoagulant, and antiviral activities. Here, we aimed to obtain fucosylated oligosaccharides using the acidolysis method to depolymerize exopolysaccharides extracted from Clavibacter michiganensis M1. Based on structural analysis, the prepared glucofucobiose was found to consist of d-glucose and l-fucose, with a molecular weight of 326 Da and a structure of d-Glcp-β-(1→4)-l-Fucp. The prebiotic activity of glucofucobiose was compared with that of 2'-fucosyllactose (2'-FL), the most abundant oligosaccharide in human milk. According to the results, glucofucobiose could significantly promote the proliferation of six probiotic strains, and short-chain fatty acid production of five probiotic strains on glucofucobiose was substantially higher than that on 2'-FL at 48 h of fermentation. Overall, this study proposed a new technology for obtaining fucosylated oligosaccharides. The prepared glucofucobiose was found to exhibit potential prebiotic activity and should be further assessed.

Combinatorial Metabolic Engineering and Enzymatic Catalysis Enable Efficient Production of Colanic Acid

Colanic acid can promote the lifespan of humans by regulating mitochondrial homeostasis, and it has widespread applications in the field of health. However, colanic acid is produced at a low temperature (20 °C) with low titer. Using Escherichia coli K-12 MG1655, we constructed the SRP-4 strain with high colanic acid production at 30 °C by enhancing the precursor supply and relieving the regulation of transcription for colanic acid synthesis genes by the RCS system. After media optimization, the colanic acid titer increased by 579.9-fold and reached 12.2 g/L. Subsequently, we successfully purified the colanic acid hydrolase and reduced the molecular weight of colanic acid (106.854 kDa), thereby eliminating the inhibition of high-molecular-weight colanic acid on strain growth. Finally, after adding the colanic acid hydrolase (4000 U/L), the colanic acid with low molecular weight reached 24.99 g/L in 3-L bioreactor, the highest titer reported so far. This high-producing strain of colanic acid will promote the application of low-molecular-weight colanic acid in the field of health.

Fucose-containing bacterial exopolysaccharides: Sources, biological activities, and food applications

Bacterial exopolysaccharides are high molecular weight polysaccharides that are secreted by a wide range of bacteria, with diverse structures and easy preparation. Fucose, fucose-containing oligosaccharides (FCOs), and fucose-containing polysaccharides (FCPs) have important applications in the food and medicine fields, including applications in products for removing Helicobacter pylori and infant formula powder. Fucose-containing bacterial exopolysaccharide (FcEPS) is a prospective source of fucose, FCOs, and FCPs. This review systematically summarizes the common sources and applications of FCPs and FCOs and the bacterial strains capable of producing FcEPS reported in recent years. The repeated-unit structures, synthesis pathways, and factors affecting the production of FcEPS are reviewed, as well as the degradation methods of FcEPS for preparing FCOs. Finally, the bioactivities of FcEPS, including anti-oxidant, prebiotic, anti-cancer, anti-inflammatory, anti-viral, and anti-microbial activities, are discussed and may serve as a reference strategy for further applications of FcEPS in the functional food and medicine industries.

Increased Production of Colanic Acid by an Engineered Escherichia coli Strain, Mediated by Genetic and Environmental Perturbations

Colanic acid (CA) is a major exopolysaccharide synthesized by Escherichia coli that serves as a constituent of biofilm matrices. CA demonstrates potential applications in the food, cosmetics, and pharmaceutical industry. Moreover, L-fucose, a monomeric constituent of CA, exhibits various physiological activities, such as antitumor, anti-inflammatory, and skin-whitening. Here, the effects of genetic and environmental perturbations were investigated for improving CA production by E. coli. When rcsF, a positive regulator gene of CA synthesis, was expressed in E. coli ΔwaaF, a CA-producing strain constructed previously, the CA titer increased to 3051.2 mg/L as compared to 2052.8 mg/L observed with E. coli ΔwaaF. Among the environmental factors tested, namely, osmotic and oxidative stresses and pH, pH was a primary factor that significantly improved CA production. When the pH of the culture medium of E. coli ΔwaaF + rcsF was maintained at 7, the CA titer significantly increased to 4351.6 mg/L. The CA yield obtained with E. coli ΔwaaF + rcsF grown at pH 7 was 5180.4 mg CA/g dry cell weight, which is the highest yield of CA reported so far. This engineered E. coli system with optimization of environmental conditions can be employed for fast and economically-feasible production of CA.

Microbiological and Clinical Aspects of Raoultella spp

The genus Raoultella was established in 2001. Species of Raoultella and Klebsiella share many ecological, biochemical, clinical, and microbiological features. Given the shortcomings of available technology for species identification in the clinical microbiology laboratory, are practically indistinguishable. Since the late 2000s there has been an increase in case reports of human Raoultella infections. Therefore, several authors are postulating that Raoultella spp. are rare and/or emerging pathogens.

Conclusions:Raoultella spp. are very similar to Klebsiella spp. The epidemiology and the clinical relevance of the human Raoultella spp. infections is uncertain and further studies are required. The previous difficulties in the identification of Raoultella spp. and the introduction of more precise identification techniques may explain the recent increase in the number of case reports. Raoultella spp. might be rather underdiagnosed than rare or emerging pathogens.

Exopolysaccharide anchoring creates an extreme resistance to sedimentation

By evolving strains of E. coli that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Mutations in rcsC, lpp, igaA, or the yjbEFGH operon were sufficient to stimulate sedimentation resistance, while mutations altering the cps promoter, cdgI, or yjbF provided phenotypic enhancements. The sedimentation resistances changed in response to temperature, growth phase, and carbon source and each mutant exhibited significantly reduced biofilm formation. We discovered that the degree of colony mucoidy exhibited by these mutants was not related to the degree of Rcs pathways activation or to the amount of CAP that was produced; rather, it was related to the fraction of CAP that was shed as a true exopolysaccharide. Therefore, these and other mutations that activate this phenotype are likely to be absent from genetic screens that relied on centrifugation to harvest bacteria. We also found that this anchored CAP form is not linked to LPS cores and may not be attached to the outer membrane.IMPORTANCEBacteria can partition in aqueous environments between surface-dwelling, planktonic, sedimentary, and biofilm forms. Residence in each location provides an advantage depending on nutritional and environmental stresses and a community of a single species is often observed to be distributed throughout two or more of these niches. Another adaptive strategy is to produce an extracellular capsule, which provides an environmental shield for the microbe and can allow escape from predators and immune systems. We discovered that bacteria can either shed or stably anchor capsules to dramatically alter their propensity to sediment. The degree to which the bacteria anchor their capsule is controlled by a stress sensing system, suggesting that anchoring may be used as an adaptive response to severe environmental challenges.

Overproduction of Exopolysaccharide Colanic Acid by Escherichia coli by Strain Engineering and Media Optimization

Colanic acid (CA) is one of the major bacterial exopolysaccharides. Due to its biological activities, CA has a significant commercial value. However, the cultivation conditions have not been optimized for the large-scale production of CA. Here, we constructed a CA-overproducing Escherichia coli strain (ΔwaaF) and statistically optimized its culture media for maximum CA production. Glucose and tryptone were found the optimal carbon and nitrogen sources, respectively. Fractional factorial design indicated tryptone and Na₂HPO₄ as the critical nutrients for CA production. Through further optimization, we achieved a maximum CA production of 1910.0 mg/L, which is approximately 12-fold higher than the amount obtained using the non-optimized medium initially used. The predicted value of CA production was comparable with experimental value (2052.8 mg/L) under the optimized conditions. This study constitutes a successful demonstration of media optimization for increased CA production, and paves the way for future research for achieving large-scale CA production.

Extraction of Extracellular Matrix in Static and Dynamic Candida Biofilms Using Cation Exchange Resin and Untargeted Analysis of Matrix Metabolites by Ultra-High-Performance Liquid Chromatography-Tandem Quadrupole Time-of-Flight Mass Spectrometry (UPLC-Q-TOF-MS)

Fungal infections caused by Candida albicans poses a great threat to human health. The ability of biofilm formation is believed to be associated with resistance-related Candida infections. Currently, knowledge on extracellular matrix (EM) of C. albicans biofilm is limited. In this study, we introduced ion exchange resin, i.e., cation exchange resin (CER) and anion exchange resin (AER), in EM extraction of C. albicans biofilm as well as several non-albicans Candida (NAC) biofilms under static and dynamic states in combination with vortexing and ultrasonication (VU). The metabolites extracted from the dynamic C. albicans biofilm matrix using the CER-VU and VU were identified with ultra-high-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) via untargeted filtration. Compared with other physical and chemical extraction methods, CER-VU was demonstrated to be an ideal approach with high-yield acquisitions of EM constituents including proteins, triglycerides and carbohydrates and low-level damages on fungal cell viability and integrity. The untargeted MS analysis further showed the high efficacy of CER-VU, as a large quantity of metabolites (217 versus 198) was matched comprising a great number of lipids, carbohydrates, amino acids, nucleic acids and their derivatives together with a high involvement of signaling pathways compared with the VU alone. However, combining the results from both the CER-VU and VU methods could generate more metabolites. In summary, the EM analysis of the dynamic C. albicans biofilm expands our understanding upon a comprehensive depiction of matrix components and provides another effective approach for EM extraction.

Classification of Clinical Isolates of Klebsiella pneumoniae Based on Their in vitro Biofilm Forming Capabilities and Elucidation of the Biofilm Matrix Chemistry With Special Reference to the Protein Content

Klebsiella pneumoniae is a human pathogen, capable of forming biofilms on abiotic and biotic surfaces. The limitations of the therapeutic options against Klebsiella pneumoniae is actually due to its innate capabilities to form biofilm and harboring determinants of multidrug resistance. We utilized a newer approach for classification of biofilm producing Klebsiella pneumoniae isolates and subsequently we evaluated the chemistry of its slime, more accurately its biofilm. We extracted and determined the amount of polysaccharides and proteins from representative bacterial biofilms. The spatial distribution of sugars and proteins were then investigated in the biofilm matrix using confocal laser scanning microscopy (CLSM). Thereafter, the extracted matrix components were subjected to sophisticated analysis incorporating Fourier transform infrared (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, one-dimensional gel-based electrophoresis (SDS-PAGE), high performance liquid chromatography (HPLC), and MALDI MS/MS analysis. Besides, the quantification of its total proteins, total sugars, uronates, total acetyl content was also done. Results suggest sugars are not the only/major constituent of its biofilms. The proteins were harvested and subjected to SDS-PAGE which revealed various common and unique protein bands. The common band was excised and analyzed by HPLC. MALDI MS/MS results of this common protein band indicated the presence of different proteins within the biofilm. The 55 different proteins were identified including both cytosolic and membrane proteins. About 22 proteins were related to protein synthesis and processing while 15 proteins were identified related to virulence. Similarly, proteins related to energy and metabolism were 8 and those related to capsule and cell wall synthesis were 4. These results will improve our understanding of Klebsiella biofilm composition and will further help us design better strategies for controlling its biofilm such as techniques focused on weakening/targeting certain portions of the slime which is the most common building block of the biofilm matrix.

Review - Bacteria and their extracellular polymeric substances causing biofouling on seawater reverse osmosis desalination membranes

Biofouling in seawater reverse osmosis (SWRO) membranes is a critical issue faced by the desalination industry worldwide. The major cause of biofouling is the irreversible attachment of recalcitrant biofilms formed by bacteria and their extracellular polymeric substances (EPS) on membrane surfaces. Transparent exopolymer particles (TEP) and protobiofilms are recently identified as important precursors of membrane fouling. Despite considerable amount of research on SWRO biofouling, the control of biofouling still remains a challenge. While adoption of better pretreatment methods may help in preventing membrane biofouling in new desalination setups, it is also crucial to effectively disperse old, recalcitrant biofilms and prolong membrane life in operational plants. Most current practices employ the use of broad spectrum biocides and chemicals that target bacterial cells to disperse mature biofilms, which are evidently inefficient. EPS, being known as the strongest structural framework of biofilms, it is essential to breakdown and disintegrate the EPS components for effective biofilm removal. To achieve this, it is necessary to understand the chemical composition and key elements that constitute the EPS of major biofouling bacterial groups in multi-species, mature biofilms. However, significant gaps in understanding the complexity of EPS are evident by the failure to achieve effective prevention and mitigation of fouling in most cases. Some of the reasons may be difficulty in sampling membranes from fully operational full-scale plants, poor understanding of microbial communities and their ecological shifts under dynamic operational conditions within the desalination process, selection of inappropriate model species for laboratory-scale biofouling studies, and the laborious process of extraction and purification of EPS. This article reviews the novel findings on key aspects of SWRO membrane fouling and control measures with particular emphasis on the key sugars in EPS. As a novel strategy to alleviate biofouling, future control methods may be aimed towards specifically disintegrating and breaking down these key sugars rather than using broad spectrum chemicals such as biocides that are currently used in the industry.

Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium

Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional analysis of the SA187 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization and plant colonization. A high number of genes were also found to be involved in survival, defense against oxidative stress and production of antimicrobial compounds and toxins. Moreover, different metabolic pathways were identified that potentially contribute to plant growth promotion. The information encoded in the genome of SA187 reveals the characteristics of a dualistic lifestyle of a bacterium that can adapt to different environments and promote the growth of plants. This information provides a better understanding of the mechanisms involved in plant-microbe interaction and could be further exploited to develop SA187 as a biological agent to improve agricultural practices in marginal and arid lands.

Hydrophobic features of EPS extracted from anaerobic granular sludge: an investigation based on DAX-8 resin fractionation and size exclusion chromatography

The hydrophobic fractionation of extracellular polymeric substances (EPS) extracted from anaerobic granular sludge was performed on the DAX-8 resin (two elution pH conditions, i.e., pH 2 and pH 5 were tested). The impact of seven different EPS extraction methods on EPS hydrophobicity features was assessed. The results showed that the extraction methods and bulk solution pH influenced dramatically the biochemical composition of the EPS, and in turn, the hydrophobicity determined. Besides, EPS extracting reagents i.e., formaldehyde, ethanol, sodium dodecyl sulfate (SDS), and Tween 20 not only introduced extra carbon content in the total organic carbon (TOC) measurement but also interacted with the DAX-8 resin. By comparing the apparent molecular weight (aMW) distribution of untreated and pH-adjusted EPS samples, more complete EPS aMW information was preserved at pH 5. Thus, elution at pH 5 was preferred in this study for the qualitative analysis of EPS hydrophobic features. The hydrophobic fraction of EPS retained by the resin at pH 5 was ascribed to a wide aMW range, ranging from >440 to 0.3 kDa. Within this range, EPS molecules ranging from 175 to 31 kDa were mostly retained by the DAX-8 resin, which indicates that these EPS molecules are highly hydrophobic.

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System

The biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. The Populus root microbiome is a diverse community that has high abundance of β- and γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand the contribution of individual microbiome members in a community, we studied the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Both strains increased lateral root formation and root hair production in Arabidopsis plate assays and are predicted to encode for different functions related to growth and plant growth promotion in Populus hosts. Inoculation individually, with either bacterial isolate, increased root growth relative to uninoculated controls, and while root area was increased in mixed inoculation, the interaction term was insignificant indicating additive effects of root phenotype. Complementary data including photosynthetic efficiency, whole-transcriptome gene expression and GC-MS metabolite expression data in individual and mixed inoculated treatments indicate that the effects of these bacterial strains are unique and additive. These results suggest that the function of a microbiome community may be predicted from the additive functions of the individual members.

Impacts of hydrophilic colanic acid on bacterial attachment to microfiltration membranes and subsequent membrane biofouling

In order to examine the interactions between physicochemical properties of specific extracellular polymeric substances (EPS) and membrane biofouling, we investigated the impacts of hydrophilic colanic acid, as a model extracellular polysaccharide component, on initial bacterial attachment to different microfiltration (MF) membranes and membrane biofouling by using Escherichia coli strains producing different amounts of colanic acid. In a newly designed microtiter plate assay, the bacterial attachment by an E. coli strain RcsF(+), which produces massive amounts of colanic acid, decreased only to a hydrophobic membrane because the colanic acid made cell surfaces more hydrophilic, resulting in low cell attachment to hydrophobic membranes. The bench-scale cross-flow filtration tests followed by filtration resistance measurement revealed that RcsF(+) caused severe irreversible membrane fouling (i.e., pore-clogging), whereas less extracellular polysaccharide-producing strains caused moderate but reversible fouling to all membranes used in this study. Further cross-flow filtration tests indicated that colanic acid liberated in the bulk phase could rapidly penetrate pre-accumulated biomass layers (i.e., biofilms) and then directly clogged membrane pores. These results indicate that colanic acid, a hydrophilic extracellular polysaccharide, and possible polysaccharides with similar characteristics with colanic acid are considered as a major cause of severe irreversible membrane fouling (i.e., pore-clogging) regardless of biofilm formation (dynamic membrane).

Dual Roles of Capsular Extracellular Polymeric Substances in Photocatalytic Inactivation of Escherichia coli: Comparison of E. coli BW25113 and Isogenic Mutants

The dual roles of capsular extracellular polymeric substances (EPS) in the photocatalytic inactivation of bacteria were demonstrated in a TiO2-UVA system, by comparing wild-type Escherichia coli strain BW25113 and isogenic mutants with upregulated and downregulated production of capsular EPS. In a partition system in which direct contact between bacterial cells and TiO2 particles was inhibited, an increase in the amount of EPS was associated with increased bacterial resistance to photocatalytic inactivation. In contrast, when bacterial cells were in direct contact with TiO2 particles, an increase in the amount of capsular EPS decreased cell viability during photocatalytic treatment. Taken together, these results suggest that although capsular EPS can protect bacterial cells by consuming photogenerated reactive species, it also facilitates photocatalytic inactivation of bacteria by promoting the adhesion of TiO2 particles to the cell surface. Fluorescence microscopy and scanning electron microscopy analyses further confirmed that high capsular EPS density led to more TiO2 particles attaching to cells and forming bacterium-TiO2 aggregates. Calculations of interaction energy, represented by extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) potential, suggested that the presence of capsular EPS enhances the attachment of TiO2 particles to bacterial cells via acid-base interactions. Consideration of these mechanisms is critical for understanding bacterium-nanoparticle interactions and the photocatalytic inactivation of bacteria.

Exopolysaccharides enriched in rare sugars: bacterial sources, production, and applications

Microbial extracellular polysaccharides (EPS), produced by a wide range of bacteria, are high molecular weight biopolymers, presenting an extreme diversity in terms of chemical structure and composition. They may be used in many applications, depending on their chemical and physical properties. A rather unexplored aspect is the presence of rare sugars in the composition of some EPS. Rare sugars, such as rhamnose or fucose, may provide EPS with additional biological properties compared to those composed of more common sugar monomers. This review gives a brief overview of these specific EPS and their producing bacteria. Cultivation conditions are summarized, demonstrating their impact on the EPS composition, together with downstream processing. Finally, their use in different areas, including cosmetics, food products, pharmaceuticals, and biomedical applications, are discussed.

Plant-derived compounds as natural antimicrobials to control paper mill biofilms

Biofilms can cause severe problems in industrial paper mills, particularly of economic and technological types (clogging of filters, sheet breaks or holes in the paper, machine breakdowns, etc.). We present here some promising results on the use of essential oil compounds to control these biofilms. Biofilms were grown on stainless-steel coupons with a microbial white water consortium sampled from an industrial paper mill. Five essential oil compounds were screened initially in the laboratory in terms of their antimicrobial activity against planktonic cells and biofilms. The three most active compounds were selected and then tested in different combinations. The combination finally selected was tested at the pilot scale to confirm its efficiency under realistic conditions. All the compounds tested were as active against biofilms as they were against planktonic cells. The most active compounds were thymol, carvacrol, and eugenol, and the most efficient combination was thymol–carvacrol. At a pilot scale, with six injections a day, 10 mM carvacrol alone prevented biocontamination for at least 10 days, and a 1 mM thymol–carvacrol combination enabled a 67 % reduction in biofilm dry matter after 11 days. The use of green antimicrobials could constitute a very promising alternative or supplement to the treatments currently applied to limit biofilm formation in the environment of paper mill machines.

How firebrats (Thysanura: Lepismatidae) detect and nutritionally benefit from their microbial symbionts Enterobacter cloacae and Mycotypha microspora

The phylogenetically ancient firebrats, Thermobia domestica (Packard) (Thysanura: Lepismatidae), lack any form of long-distance communication, yet are able to locate mates in sustained hot and humid microhabitats, typically within human habitations where they feed on dried goods, including cellulosic substrates. We have recently shown that firebrats aggregate in response to two symbiotic microorganisms in their feces, the bacterium Enterobacter cloacae and the fungus Mycotypha microspora. Our objectives were to determine how firebrats detect M. microspora and E. cloacae, and whether these microbial symbionts nutritionally benefit firebrats. Applied to a glass surface in bioassays, E. cloacae as well as the isolated exopolysaccharide of E. cloacae induced arrestment of firebrats, whereas M. microspora induced arrestment only in the presence of cellulosic substrate. When M. microspora and E. cloacae were grown aerobically on cellulose agar, only M. microspora yielded zones of clearing indicative of enzymatic cellulose degradation. Firebrats also arrested in response to d-glucose, which is a constituent of the exopolysaccharide and which is produced by the cellulase of M. microspora during cellulose degradation. First- to third-instar nymphs of firebrats that were fed E. cloacae, M. microspora, or a nutrient-rich diet developed equally well. By consuming E. cloacae and M. microspora, and by spreading them through feces, firebrats appear able to occupy nutrient-poor habitats that otherwise would not support development of their offspring.

Mini-review: microbial problems in paper production

Paper mills are open systems, which provide favorable conditions for microbial growth. Microbial contamination can cause substantial economic losses, including the deterioration of raw materials, interference with production processes by breakdowns and lowering product quality, and eventually, problems in wastewater treatment. Damage is caused by acidification, attack on raw materials, the formation of odorous products, discoloration of pigments, and the formation of methane and hydrogen, thereby producing potentially explosive conditions. Population analyses have revealed that a wide variety of microorganisms are involved, but there appear to be no typical strains associated with paper mills. Current trends in process engineering, such as chlorine-free bleaching, processing at neutral pH, closed cycles, and the use of recycled paper also favor microbial growth and biofilm (slime) formation. A fundamental problem associated with slimes is the extensive matrix of extracellular polymeric substances, which is composed of a large variety of highly hydrated polysaccharides, proteins, nucleic acids, and lipids. No 'silver bullet' against biofouling can be expected, and effective countermeasures have to be based on holistic approaches.

Development and validation of a colorimetric assay for simultaneous quantification of neutral and uronic sugars

A colorimetric assay based on the conventional anthrone reaction was investigated for specific quantification of uronic acids (UA) in the presence of neutral sugars and/or proteins. Scanning of glucose (Glu) and glucuronic acid (GlA) was performed after the reaction with anthrone and a double absorbance reading was made, at 560 nm and at 620 nm, in order to quantify the UA and neutral sugars separately. The assay was implemented on binary or ternary solutions containing Glu, GlA and bovine serum albumin (BSA) in order to validate its specificity towards sugars and check possible interference with other biochemical components such as proteins. Statistical analysis indicated that this assay provided correct quantification of uronic sugars from 50 to 400 mg/l and of neutral sugars from 20 to 80 mg/l, in the presence of proteins with concentrations reaching 600 mg/l. The proposed protocol can be of great interest for simultaneous determination of uronic and neutral sugars in complex biological samples. In particular, it can be used to correctly quantify the Extracellular Polymeric Substances (EPS) isolated from the biological matrix of many bacterial aggregates, even in the presence of EPS extractant such as EDTA.

Probing roles of lipopolysaccharide, type 1 fimbria, and colanic acid in the attachment of Escherichia coli strains on inert surfaces

The roles of bacterial surface polymers in reversible (phase I) and irreversible (phase II) attachment (i.e., lipopolysaccharides (LPS), type 1 fimbria, and capsular colanic acid (CA)) were investigated in situ by combining fluorescence microscopy and atomic force microscopy. Fluorescence microscopy was used to evaluate the phase I attachment by counting the total number of cells on the substrata, and AFM was applied to image the phase II cells and measure the lateral detachment force to characterize phase II attachment. Also, by comparing the number of cells in phases I and II, the transformation ratio was calculated and used as an index to evaluate the roles of different polymers in the attachment process. Escherichia coli K-12 and its six mutants, which had different surface polymers in terms of LPS structures, CA contents, and type 1 fimbriae, were used as the test strains. Six different materials were applied as substrata, including glass, two metals (aluminum and stainless steel), and three plastics (polyvinyl chloride, polycarbonate, and polyethylene). The results indicated that LPS significantly enhanced phases I and II attachment as well as the transformation ratio from phase I to II. Like LPS, type 1 fimbriae largely increased the phase I attachment and the transformation ratio; however, they did not significantly influence the adhesion strength in phase II. CA had a negative effect on attachment in phases I and II by decreasing the adhered number of cells and the lateral detachment force, respectively, but had no influence on the transformation ratio.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006

This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.

Characterization of the mineral fraction associated to extracellular polymeric substances (EPS) in anaerobic granular sludges

The extracellular polymeric substances (EPS) extracted from four anaerobic granular sludges contain an important mineral fraction (20-77% of the EPS dry weight). The composition of the mineral fraction of EPS depends strongly of the extraction method applied and to a lesser extend of the origin of the anaerobic sludge. Centrifugation, sonication, and heating extraction procedures yield a similar mineral composition. However, extraction using a cationic exchange resin (CER) leads to an increase of the Na(+) content in the EPS extract because the CER promotes an exchange of divalent and trivalent inorganic elements in the EPS extracts toward Na(+). Chemical extraction protocols were also shown to contaminate the EPS extracts by impurities or carry over of the extractant itself (e.g., ethanol). A part of the mineral fraction is bound to the EPS organic matter and structures the EPS matrix in the granules. Scanning electron microscopic analysis (SEM-EDX) showed that, in addition, solid particles such as CaCO(3) and Ca(5)OH(PO(4))(3) containing various metallic elements (i.e., Al, Fe, Cu, Mn...) are present in the EPS as well. This inorganic fraction, too often neglected in EPS studies, can influence the physicochemical properties of EPS.

Extraction of extracellular polymeric substances (EPS) from anaerobic granular sludges: comparison of chemical and physical extraction protocols

The characteristics of the extracellular polymeric substances (EPS) extracted with nine different extraction protocols from four different types of anaerobic granular sludge were studied. The efficiency of four physical (sonication, heating, cationic exchange resin (CER), and CER associated with sonication) and four chemical (ethylenediaminetetraacetic acid, ethanol, formaldehyde combined with heating, or NaOH) EPS extraction methods was compared to a control extraction protocols (i.e., centrifugation). The nucleic acid content and the protein/polysaccharide ratio of the EPS extracted show that the extraction does not induce abnormal cellular lysis. Chemical extraction protocols give the highest EPS extraction yields (calculated by the mass ratio between sludges and EPS dry weight (DW)). Infrared analyses as well as an extraction yield over 100% or organic carbon content over 1 g g(-1) of DW revealed, nevertheless, a carry-over of the chemical extractants into the EPS extracts. The EPS of the anaerobic granular sludges investigated are predominantly composed of humic-like substances, proteins, and polysaccharides. The EPS content in each biochemical compound varies depending on the sludge type and extraction technique used. Some extraction techniques lead to a slightly preferential extraction of some EPS compounds, e.g., CER gives a higher protein yield.

Coexistence of antibiotic-producing and antibiotic-sensitive bacteria in biofilms is mediated by resistant bacteria

Antibiotic-sensitive bacteria have been found to coexist with antibiotic-producing bacteria in biofilms, but little is known about how the former develop in such an environment. Here we isolated pyocyanin-sensitive bacteria belonging to the genus Brevibacillus from a biofilm derived from soil extract and based on the preestablished biofilm of a pyocyanin producer, Pseudomonas aeruginosa strain P1. In addition, pyocyanin-resistant strains belonging to the genus Raoultella were isolated from the same biofilm. Microbial relationships within biofilms were examined by using three strains, strain P1, Brevibacillus strain S1, and Raoultella strain R1, each of which individually formed a biofilm within 2 days in a flow cell. Strain S1 did not fully develop on the preestablished biofilm of strain P1 during 4 days of cultivation, whereas a mutant of strain P1 which was deficient in pyocyanin production allowed strain S1 to cocolonize within a biofilm. On the other hand, strain R1 developed on the biofilm of strain P1 regardless of pyocyanin production. When mixed 1:1 inocula of strains S1 and R1 were introduced into the strain P1 biofilm, all three species were found in the 4-day biofilm. In the mixed biofilm, strain S1 was surrounded by the layer of strain R1 and seemed to be separated from strain P1 and the outflow solution. However, strain S1 did not survive in a three-species mixed culture under planktonic conditions. These results indicate that the survival of sensitive bacteria in biofilm with a pyocyanin producer is achieved by covering them with a layer of resistant bacteria. We also evaluated the influence of antibiotic production on the producer.

Fluorescent in situ hybridization and flow cytometry as tools to evaluate the treatments for the control of slime-forming enterobacteria in paper mills

Slime formation is a serious problem nowadays in the paper industry. Some enterobacteria are associated with the formation of slime deposits in paper and board mills. Detection and characterization of slime forming bacteria, belonging to the genus Enterobacter, Raoultella, and Klebsiella have been achieved by fluorescence in situ hybridization (FISH), using one probe based on the enterobacterial repetitive intergenic consensus sequence and other two rRNA targeted oligonucleotide probes. The effects of three kinds of antimicrobiological products (biocides, dispersants, and enzymes) on these enterobacterial cells were analyzed by flow cytometry (FC). Biocides B: utrol 1009 and 1072 were the most effective microbiocides against all enterobacterial cells analyzed, reaching 90% of dead bacteria after 24 h. However, the enzymatic treatment (Buzyme) was not equally efficient on enterobacteria and its microbiocide capacity varied depending on the type of microorganism. FISH and FC were effective tools to detect important slime forming enterobacteria and to select specific treatments to control microbial problems in the paper industry.