Effect of nutrient limitation on biofilm formation and phosphatase activity of a Citrobacter sp

Effect of nutrients deficiency on biofilm formation and single cell protein production with a purple non-sulphur bacteria enriched culture

Purple non-sulphur bacteria (PNSB) are of interest for biorefinery applications to create biomolecules, but their production cost is expensive due to substrate and biomass separation costs. This research has utilized fuel synthesis wastewater (FSW) as a low-cost carbon-rich substrate to produce single-cell protein (SCP) and examines PNSB biofilm formation using this substrate to achieve a more efficient biomass-liquid separation. In this study, PNSB were grown in Ca, Mg, S, P, and N-deficient media using green shade as biofilm support material. Among these nutrient conditions, only N-deficient and control (nutrient-sufficient) conditions showed biofilm formation. Although total biomass growth of the control was 1.5 times that of the N-deficient condition and highest overall, the total biofilm-biomass in the N-deficient condition was 2.5 times greater than the control, comprising 49% of total biomass produced. Total protein content was similar between these four biomass samples, ranging from 35.0 ± 0.2% to 37.2 ± 0.0%. The highest protein content of 44.7 ± 1.3% occurred in the Mg-deficient condition (suspended biomass only) but suffered from a low growth rate. Overall, nutrient sufficient conditions are optimal for overall protein productivity and dominated by suspended growth, but where fixed growth systems are desired for cost-effective harvesting, N-deficient conditions provide an effective means to maximize biofilm production without sacrificing protein content.

Antibiotic-Induced Biofilm Formations in Pseudomonas aeruginosa Strains KPW.1-S1 and HRW.1-S3 are Associated with Increased Production of eDNA and Exoproteins, Increased ROS Generation, and Increased Cell Surface Hydrophobicity

Pseudomonas aeruginosa is a medically important opportunistic pathogen due to its intrinsic ability to form biofilms on different surfaces as one of the defense mechanisms for survival. The fact that it can form biofilms on various medical implants makes it more harmful clinically. Although various antibiotics are used to treat Pseudomonas aeruginosa infections, studies have shown that sub-MIC levels of antibiotics could induce Pseudomonas biofilm formation. The present study thus explored the effect of the aminoglycoside antibiotic gentamicin on the biofilm dynamics of two Pseudomonas aeruginosa strains KPW.1-S1 and HRW.1-S3. Biofilm formation was found to be increased in the presence of increased concentrations of gentamicin. Confocal, scanning electron microscopy, and other biochemical tests deduced that biofilm-forming components exoproteins, eDNA, and exolipids as exopolymeric substances in Pseudomonas aeruginosa biofilms were increased in the presence of gentamicin. An increase in reactive oxygen species generation along with increased cell surface hydrophobicity was also seen for both strains when treated with gentamicin. The observed increase in the adherence of the cells accompanied by the increase in the components of exopolymeric substances may have largely contributed to the increased biofilm production by the Pseudomonas aeruginosa strains under the stress of the antibiotic treatment.

Impact of phosphate concentration on the metabolome of biofilms of the marine bacterium Pseudoalteromonas lipolytica

INTRODUCTION

Marine biofilms are the most widely distributed mode of life on Earth and drive biogeochemical cycling processes of most elements. Phosphorus (P) is essential for many biological processes such as energy transfer mechanisms, biological information storage and membrane integrity.

OBJECTIVES

Our aim was to analyze the effect of a gradient of ecologically relevant phosphate concentrations on the biofilm-forming capacity and the metabolome of the marine bacterium Pseudoalteromonas lipolytica TC8.

METHODS

In addition to the evaluation of the effect of different phosphate concentration on the biomass, structure and gross biochemical composition of biofilms of P. lipolytica TC8, untargeted metabolomics based on liquid chromatography-mass spectrometry (LC-MS) analysis was used to determine the main metabolites impacted by P-limiting conditions. Annotation of the most discriminating and statistically robust metabolites was performed through the concomitant use of molecular networking and MS/MS fragmentation pattern interpretation.

RESULTS

At the lowest phosphate concentration, biomass, carbohydrate content and three-dimensional structures of biofilms tended to decrease. Furthermore, untargeted metabolomics allowed for the discrimination of the biofilm samples obtained at the five phosphate concentrations and the highlighting of a panel of metabolites mainly implied in such a discrimination. A large part of the metabolites of the resulting dataset were then putatively annotated. Ornithine lipids were found in increasing quantity when the phosphate concentration decreased, while the opposite trend was observed for oxidized phosphatidylethanolamines (PEs).

CONCLUSION

This study demonstrated the suitability of LC-MS-based untargeted metabolomics for evaluating the effect of culture conditions on marine bacterial biofilms. More precisely, these results supported the high plasticity of the membrane of P. lipolytica TC8, while the role of the oxidized PEs remains to be clarified.

Wetting properties of dehydrated biofilms under different growth conditions

Biofilms are resilient to environmental conditions and often resistant even to strong disinfectants. It is crucial to investigate their interfacial properties, which can be effectively characterized by wetting analysis. Wetting phenomena on biofilm surfaces have been poorly investigated in literature, in particular a systematic study of wetting on real biofilm-coated substrates including the application of external body forces (forced wetting, i.e.: centrifugal and gravitational forces) is missing. The aim of this work is to study the role of nutrient and shear flow conditions on wetting properties of Pseudomonas fluorescens dehydrated biofilms, grown on glass substrates. An innovative device (Kerberos®), capable to study spreading/sliding behavior under the application of external body forces, is used here for a systematic analysis of wetting/de-wetting liquid droplets on horizontal substrates under the action of tangential forces. Results prove that, under different growth conditions, (i.e., nutrients and imposed flow), biofilms exhibit different wetting properties. At lower nutrient/shear flow conditions, biofilms show spreading/sliding behavior close to that of pure glass. At higher nutrient and shear flow conditions, droplets on biofilms show spreading followed by imbibition soon after deposition, which leads to peculiar droplet depinning during the rotation test. Wetting properties are derived as a function of the rotation speed from both top and side views videoframes through a dedicated image analysis technique. A detailed analysis of biofilm formation and morphology/topography is also provided here.

A fixed-film bioscrubber of Microbacterium esteraromaticum SBS1-7 for toluene/styrene biodegradation

In the present study, a fixed-film bioscrubber (FFBS) of BTEX-degrading bacterium Microbacterium esteraromaticum SBS1-7 with 'AQUAPOROUSGEL® or APG' supporting material was continuously fed with toluene- or styrene-contaminated gas stream for 172 days. Response Surface Methodology (RSM) was used to optimize the biofilm formation on APG as well as the toluene biodegradation in mineral salt medium (MM). The results suggested that 1000 ppm of yeast extract (YE) was necessary for biofilm formation of SBS1-7. The optimized combination of YE and toluene concentration exhibiting the highest biofilm formation and toluene removal was further employed in an up-scale FFBS operation. The maximum Elimination Capacity (EC_max) of 203 g·m^-3·h^-1 was obtained at the toluene Inlet Loading Rate (ILR) of 295 g·m^-3·h^-1. FFBS of SBS1-7 was able to withstand a 5-day shutdown and required only 24 h to recover. Moreover, when the inlet Volatile Organic Compound was shifted to styrene, FFBS required only 24 h for adaptation and the system was able to efficiently remove ~95% of styrene after that. Finally, the performance of the bioscrubber when operated in 2 different modes of operation (FFBS vs Biotricking Filter or BTF) were compared. This study evidently demonstrated the robustness and stability of FFBS with M. esteraromaticum SBS1-7.

Influence of the Intrinsic Characteristics of Cementitious Materials on Biofouling in the Marine Environment

Coastal marine ecosystems provide essential benefits and services to humanity, but many are rapidly degrading. Human activities are leading to significant land take along coastlines and to major changes in ecosystems. Ecological engineering tools capable of promoting large-scale restoration of coastal ecosystems are needed today in the face of intensifying climatic stress and human activities. Concrete is one of the materials most commonly used in the construction of coastal and marine infrastructure. Immersed in seawater, concretes are rapidly colonized by microorganisms and macroorganisms. Surface colonization and subsequent biofilm and biofouling formation provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. The new challenge of the 21st century is to develop innovative concretes that, in addition to their usual properties, provide improved bioreceptivity in order to enhance marine biodiversity. The aim of this study is to master and clarify the intrinsic parameters that influence the bioreceptivity (biocolonization) of cementitious materials in the marine environment. By coupling biofilm (culture-based methods) and biofouling (image-analysis-based method and wet-/dry-weight biomass measurement) quantification techniques, this study showed that the application of a curing compound to the concrete surface reduced the biocolonization of cementitious materials in seawater, whereas green formwork oil had the opposite effect. This study also found that certain surface conditions (faceted and patterned surface, rough surface) promote the bacterial and macroorganism colonization of cementitious materials. Among the parameters examined, surface roughness proved to be the factor that promotes biocolonization most effectively. These results could be taken up in future recommendations to enable engineers to eco-design more eco-friendly marine infrastructure and develop green-engineering projects.

Biofouling control by phosphorus limitation strongly depends on the assimilable organic carbon concentration

Nutrient limitation is a biofouling control strategy in reverse osmosis (RO) membrane systems. In seawater, the assimilable organic carbon content available for bacterial growth ranges from about 50 to 400 μg C·L^-1, while the phosphorus concentration ranges from 3 to 11 μg P·L^-1. Several studies monitored biofouling development, limiting either carbon or phosphorus. The effect of carbon to phosphorus ratio and the restriction of both nutrients on membrane system performance have not yet been investigated. This study examines the impact of reduced phosphorus concentration (from 25 μg P·L^-1 and 3 μg P·L^-1, to a low concentration of ≤0.3 μg P·L^-1), combined with two different carbon concentrations (250 C L^-1 and 30 μg C·L^-1), on biofilm development in an RO system. Feed channel pressure drop was measured to determine the effect of the developed biofilm on system performance. The morphology of the accumulated biomass for both carbon concentrations was characterized by optical coherence tomography (OCT) and the biomass amount and composition was quantified by measuring total organic carbon (TOC), adenosine triphosphate (ATP), total cell counts (TCC), and extracellular polymeric substances (EPS) concentration for the developed biofilms under phosphorus restricted (P-restricted) and dosed (P-dosed) conditions. For both carbon concentrations, P-restricted conditions (≤0.3 μg P·L^-1) limited bacterial growth (lower values of ATP, TCC). A faster pressure drop increase was observed for P-restricted conditions compared to P-dosed conditions when 250 μg C·L^-1 was dosed. This faster pressure drop increase can be explained by a higher area covered by biofilm in the flow channel and a higher amount of produced EPS. Conversely, a slower pressure drop increase was observed for P-restricted conditions compared to P-dosed conditions when 30 μg C·L^-1 was dosed. Results of this study demonstrate that P-limitation delayed biofilm formation effectively when combined with low assimilable organic carbon concentration and thereby, lengthening the overall membrane system performance.

Effects of Beef Juice on Biofilm Formation by Shiga Toxin-Producing Escherichia coli on Stainless Steel

Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne illnesses worldwide, with beef and beef products as a common food reservoir. STEC strains may be present in beef-processing environments in the form of biofilms. The exudate of raw beef, also referred to as beef juice, has been identified as an important source of bacterial contamination on food-processing surfaces. This study applied beef juice as a food-based model to study its effects on biofilm formation of six STEC isolates on stainless steel. Crystal violet staining and cell enumeration demonstrated that beef juice inhibited the biofilm formation of strains O113, O145, and O91 up to 24 h at 22°C, but that biofilm increased (p < 0.05) thereafter over 72 h. Biofilms formed by O157, O111, and O45 were not affected by the addition of beef juice over the whole incubation period. Electron microscopy showed that the morphology of biofilm cells was altered and more extracellular matrix was produced with beef juice than with M9 medium. The present study demonstrated that beef juice residues on stainless steel can enhance biofilm formation of some STEC strains. Thorough and frequent cleaning of meat residues and exudate during meat production and handling is critical to reduce STEC biofilm formation even at 13°C.

Balancing carbon, nitrogen and phosphorus concentration in seawater as a strategy to prevent accelerated membrane biofouling

Membrane biofouling remains a significant challenge in seawater reverse osmosis desalination for drinking water production. This study investigated nutrient imbalance as the cause of biofouling in lab-scale experiments and carried out a year-long field-testing at a seawater desalination pilot plant. Lab experiments showed that growth medium with excess of organic carbon (C) but with low nitrogen (N) and phosphorus (P) accelerated the formation of bacterial biofilm. Balancing C to N and P ratios by adding N and P to growth medium increased the proliferation of free-living cells but reduced attached form of bacteria as biofilm. The cell excretion of excess C in the form of extracellular polysaccharides (EPS) was considered as a strategy for nutrient storage for future use. Cell enzyme activity assays indicated some of the bacteria had enhanced enzyme activities to degrade polysaccharides in the absence of organic C in growth medium, possibly using EPS in the biofilm. A year-long field study indicated that accelerated biofouling of seawater reverse osmosis (SWRO) membranes was associated with the elevated content of total organic carbon (TOC) in the intake seawater. Adding N and P to the intake seawater to balance the increase of TOC resulted in reduction of membrane biofouling. Microbial community analysis of the biofouling layer using 16S rRNA gene sequencing indicated biofouling communities varied with seasonal changes. Dosing of N and P did not induce dramatic changes in the fouling microbial community growing on the membrane surface. The outcome of this work implies that membrane biofouling associated with the elevated concentration of TOC in intake seawater is caused by imbalance of C:N:P in the source seawater which occurs often during algal blooms. Addition of N and P to rebalance the nutrients can prevent accelerated SWRO membrane biofouling.

Cadmium-resistant rhizobacterium Bacillus cereus M4 promotes the growth and reduces cadmium accumulation in rice (Oryza sativa L.)

Rice farmland cadmium pollution is an increasing problem for food safety. Cd-resistant bacterial strain was isolated from rice rhizosphere soil and identified as Bacillus cereus M4. Treatment with M4 fermentation broth increased rice seedlings growth in vermiculite, while reduced Cd accumulation in grains of rice grown in Cd-contaminated potted soil from 0.309 to 0.186 mg/kg. Indoleacetic acid (IAA) was detected in M4 metabolites and in potted soil solutions supplemented with M4 broth. M4 broth increased the abundance of Bacillus from 0.54% to 0.95% and changed the soil bacterial community composition. These findings indicate that M4 promotes rice growth by secreting IAA and altering the rhizospheric soil microenvironment, via soil solution composition and microbial community, which may affect Cd translocation from soil to rice roots, thereby decreasing grain Cd accumulation. Therefore, B. cereus M4 is potentially suitable for the bioremediation of Cd-contaminated paddy soils.

Spatial Environmental Heterogeneity Determines Young Biofilm Assemblages on Microplastics in Baltic Sea Mesocosms

Microplastics in aquatic environments provide novel habitats for surface-colonizing microorganisms. Given the continuing debate on whether substrate-specific properties or environmental factors prevail in shaping biofilm assemblages on microplastics, we examined the influence of substrate vs. spatial factors in the development of bacterial assemblages on polyethylene (PE), polystyrene (PS), wood, and seston and in the free-living fraction. Further, the selective colonization of microplastics by potential pathogens was investigated because among the bacterial species found in microplastic-associated biofilms are potentially pathogenic Vibrio spp. Due to their persistence and great dispersal potential, microplastics could act as vectors for these potential pathogens and for biofilm assemblages in general. Incubation experiments with these substrates were conducted for 7 days during a summer cruise along the eastern Baltic Sea coastline in waters covering a salinity gradient of 4.5-9 PSU. Bacterial assemblages were analyzed using 16S rRNA-gene amplicon sequencing, distance-based redundancy analyses, and the linear discriminant analysis effect size method to identify taxa that were significantly more abundant on the plastics. The results showed that the sample type was the most important factor structuring bacterial assemblages overall. Surface properties were less significant in differentiating attached biofilms on PE, PS, and wood; instead, environmental factors, mainly salinity, prevailed. A potential role for inorganic-nutrient limitations in surface-specific attachment was identified as well. Alphaproteobacteria (Sphingomonadaceae, Devosiaceae, and Rhodobacteraceae) and Gammaproteobacteria (Alteromonadaceae and Pseudomonas) were distinctive for the PE- and PS-associated biofilms. Vibrio was more abundant on the PE and PS biofilms than on seston, but its abundances were highest on wood and positively correlated with salinity. These results corroborate earlier findings that microplastics constitute a habitat for biofilm-forming microorganisms distinct from seston, but less from wood. In contrast to earlier reports of low Vibrio numbers on microplastics, these results also suggest that vibrios are early colonizers of surfaces in general. Spatial as well as temporal dynamics should therefore be considered when assessing the potential of microplastics to serve as vectors for bacterial assemblages and putative pathogens, as these parameters are major drivers of biofilm diversity.

Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Background

Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers.

Results

The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories “Carbohydrate transport and metabolism” (G), “Amino acid transport and metabolism” (E), “Coenzyme transport and metabolism” (H), “Inorganic ion transport and metabolism” (P), and “membrane biogenesis-related proteins” (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis – revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe²⁺ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts.

Conclusion

The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1330-5) contains supplementary material, which is available to authorized users.

Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms

The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study. MM-OCE, together with atomic force microscopy (AFM), revealed that the biofilms developed from a drinking water source with high divalent ions were stiffer compared to biofilms developed either from the drinking water source with low divalent ions or the water containing a scale inhibitor (a polyphosphate). The higher stiffness of biofilms developed from the water containing high divalent ions was attributed to the high content of calcium carbonate, suggested by biofilm composition examination. In addition, by examining the biofilm structure using optical coherence tomography (OCT), the highest biofilm thickness was found for biofilms developed from the water containing the polyphosphate. Compared to the stiff biofilms developed from the water containing high divalent ions, the soft and thick biofilms developed from the water containing polyphosphate will be expected to have higher detachment under drinking water flow. This study suggested that water chemistry could be used to predict the biofilm properties and subsequently design the microbial safety control strategies.

A variety of analytical techniques are revealing the complex influences of ions in drinking water supplies on the structure of biofilms. Such biofilms often contaminate water supply pipes and machinery. Yun Shen and colleagues at the University of Illinois at Urbana-Champaign in the USA investigated the effects of ions with a double positive charge – ‘divalent cations’ – and polyphosphate ions. Divalent cations, especially calcium and magnesium ions, are abundant in drinking water in many regions, promoting the formation of limescale deposits. Polyphosphates are commonly added to water supplies to reduce limescale formation, inhibit corrosion and discourage biofilm formation. The research revealed that divalent cations increase biofilm stiffness, while polyphosphates promote softer but thicker biofilms that are more easily removed. The results will help optimize water treatment procedures to control both microbial contamination and limescale problems.

The effects of extrinsic factors on the structural and mechanical properties of Pseudomonas fluorescens biofilms: A combined study of nutrient concentrations and shear conditions

The growth of biofilms on surfaces is a complicated process influenced by several environmental factors such as nutrient availability and fluid shear. In this study, combinations of growth conditions were selected for the study of Pseudomonas fluorescens biofilms including as cultivation time (24- or 48 h), nutrient levels (1:1 or 1:10 King B medium), and shear conditions (75 RPM shaking, 0.4 mL min ^-1 or 0.7 mL min ^-1). The use of Confocal Laser Scanning Microscopy (CLSM) determined biofilm structure, while liquid-phase Atomic Force Microscopy (AFM) techniques resolved the mechanical properties of biofilms. Under semi-static conditions, high nutrient environments led to more abundant biofilms with three times higher EPS content compared to biofilms grown under low nutrient conditions. AFM results revealed that biofilms formed under these conditions were less stiff, as shown by their Young's modulus values of 2.35 ± 0.08 kPa, compared to 4.98 ± 0.02 kPa for that of biofilms formed under low nutrient conditions. Under dynamic conditions, however, biofilms exposed to low nutrient conditions and high shear rates led to more developed biofilms compared to other tested dynamic conditions. These biofilms were also found to be significantly more adhesive compared to their counterparts grown at higher nutrient conditions.

Backscattered electron imaging and electron backscattered diffraction in the study of bacterial attachment to titanium alloy structure

The application of secondary electron (SE) imaging, backscattered electron imaging (BSE) and electron backscattered diffraction (EBSD) was investigated in this work to study the bacterial adhesion and proliferation on a commercially pure titanium (cp Ti) and a Ti6Al4V alloy (Ti 64) with respect to substrate microstructure and chemical composition. Adherence of Gram-positive Staphylococcus epidermidis 11047 and Streptococcus sanguinis GW2, and Gram-negative Serratia sp. NCIMB 40259 and Escherichia coli 10418 was compared on cp Ti, Ti 64, pure aluminium (Al) and vanadium (V). The substrate microstructure and the bacterial distribution on these metals were characterised using SE, BSE and EBSD imaging. It was observed that titanium alloy-phase structure, grain boundaries and grain orientation did not influence bacterial adherence or proliferation at microscale. Adherence of all four strains was similar on cp Ti and Ti 64 surfaces whilst inhibited on pure Al. This work establishes a nondestructive and straight-forward statistical method to analyse the relationship between microbial distribution and metal alloy structure.

Construction and evaluation of a modular biofilm-forming chamber for microbial recovery of neodymium and semi-continuous biofilm preparation. Tolerance of Serratia sp.N14 on acidic conditions and neutralized aqua regia

Recovery of neodymium from liquid metallic wastes and scrap leachates is a crucial step for its recycling, which can take place through the immobilized biofilms of Serratia sp. N14. These biofilms are produced in a fermentor vessel with a turnaround time of 10-14 days, which is unacceptable from an economic point of view for an industrial process. This study proposes the construction and evaluation of a modular system, whereby a biofilm-forming chamber is inserted into the continuous biomass outflow of the main chemostat vessel, for an alternative semi-continuous and economic production of biofilm. The activity of the biofilm from the outflow chamber was found to be the same as the one from the main chamber, which was stored in a cold room (4°C), for 9-12 months, depending on a 24 h nucleation step.Moreover, the ability of the biofilm to function in the presence of a leaching agent (aqua regia) or in acidic conditions was also evaluated. The biofilm of the main chamber can remain active even at 50% neutralized aqua regia (pH 3.0), while at acidic conditions, phosphate release of the cells is reduced to 50%. This strain proves to be very tolerant in low pH or high salt concentration solutions. The biofilm produced from the outflow of the main fermentor vessel is of acceptable activity, rather than being disposed.

Data on preparation of psychrotolerant bacterium Shewanella olleyana sp. nov. cells for transmission electron microscopy

This data article contains transmission electron microscopy (TEM) images of psychrotolerant bacterium Shewanella olleyana sp. nov. Cells of S. olleyana were grown following an optimized culture conditions in liquid medium. Procedure for the preparation of cells suitable for TEM is described in detail.

Biofilm formation and extracellular polymeric substances (EPS) production by Bacillus subtilis depending on nutritional conditions in the presence of polyester film

The influence of biofilm formation as the mode of microorganism growth on degradation of synthetic polymers represents an important research topic. This study focuses on the effect of biofilm developed by Bacillus subtilis (BS) cultivated submerged under various nutrition conditions on biodeterioration of poly(ε-caprolactone) film. Polymer in the film form (thickness 0.7 mm) was incubated for 21 days either continuously or by regularly renewed system. The scission of polyester chain bonds took place in all biotic media and was enhanced by biofilm formation in nutrient-rich media.

Antibiofilm peptides increase the susceptibility of carbapenemase-producing Klebsiella pneumoniae clinical isolates to β-lactam antibiotics

Multidrug-resistant carbapenemase-producing Klebsiella pneumoniae (KpC) strains are becoming a common cause of infections in health care centers. Furthermore, Klebsiella can develop multicellular biofilms, which lead to elevated adaptive antibiotic resistance. Here, we describe the antimicrobial and antibiofilm activities of synthetic peptides DJK-5, DJK-6, and 1018 against five KpC isolates. Using static microplate assays, it was observed that the concentration required to prevent biofilm formation by these clinical isolates was below the MIC for planktonic cells. More-sophisticated flow cell experiments confirmed the antibiofilm activity of the peptides against 2-day-old biofilms of different KpC isolates, and in some cases, the peptides induced significant biofilm cell death. Clinically relevant combinations of DJK-6 and β-lactam antibiotics, including the carbapenem meropenem, also prevented planktonic growth and biofilm formation of KpC strain1825971. Interestingly, peptide DJK-6 was able to enhance, at least 16-fold, the ability of meropenem to eradicate preformed biofilms formed by this strain. Using peptide DJK-6 to potentiate the activity of β-lactams, including meropenem, represents a promising strategy to treat infections caused by KpC isolates.

Continuous biocatalytic recovery of neodymium and europium

Bacterial biofilms recover key rare earth elements as nanocrystalline metal phosphates via robust phosphatase activity, more efficiently than polyacrylamide gel-immobilized cells and show promise for bioremediation and biocatalyst manufacturing.

Biogeochemical behaviour and bioremediation of uranium in waters of abandoned mines

The discharges of uranium and associated radionuclides as well as heavy metals and metalloids from waste and tailing dumps in abandoned uranium mining and processing sites pose contamination risks to surface and groundwater. Although many more are being planned for nuclear energy purposes, most of the abandoned uranium mines are a legacy of uranium production that fuelled arms race during the cold war of the last century. Since the end of cold war, there have been efforts to rehabilitate the mining sites, initially, using classical remediation techniques based on high chemical and civil engineering. Recently, bioremediation technology has been sought as alternatives to the classical approach due to reasons, which include: (a) high demand of sites requiring remediation; (b) the economic implication of running and maintaining the facilities due to high energy and work force demand; and (c) the pattern and characteristics of contaminant discharges in most of the former uranium mining and processing sites prevents the use of classical methods. This review discusses risks of uranium contamination from abandoned uranium mines from the biogeochemical point of view and the potential and limitation of uranium bioremediation technique as alternative to classical approach in abandoned uranium mining and processing sites.

Biofilm-mediated enhanced crude oil degradation by newly isolated pseudomonas species

The bioavailability of organic contaminants to the degrading bacteria is a major limitation to efficient bioremediation of sites contaminated with hydrophobic pollutants. Such limitation of bioavailability can be overcome by steady-state biofilm-based reactor. The aim of this study was to examine the effect of such multicellular aggregation by naturally existing oil-degrading bacteria on crude oil degradation. Microorganisms, capable of utilizing crude oil as sole carbon source, were isolated from river, estuary and sea-water samples. Biochemical and 16S rDNA analysis of the best degraders of the three sources was found to belong to the Pseudomonas species. Interestingly, one of the isolates was found to be close to Pseudomonas otitidis family which is not reported yet as a degrader of crude oil. Biodegradation of crude oil was estimated by gas chromatography, and biofilm formation near oil-water interface was quantified by confocal laser scanning microscopy. Biofilm supported batches of the isolated Pseudomonas species were able to degrade crude oil much readily and extensively than the planktonic counterparts. Volumetric and topographic analysis revealed that biofilms formed in presence of crude oil accumulate higher biomass with greater thickness compared to the biofilms produced in presence of glucose as sole carbon source.

Advances in biofilm reactors for production of value-added products

Biofilms are defined as microbial cell layers, which are irreversibly or reversibly attached on solid surfaces. These attached cells are embedded in a self-produced exopolysaccharide matrix, and exhibit different growth and bioactivity compared with suspended cells. With their high biomass density, stability, and potential for long-term fermentation, biofilm reactors are employed for the fermentation and bioconversion, which need large amount of biomass. During the past decade, biofilm reactors have been successfully applied for production of many value-added products. This review article summarizes the applications of biofilm reactors with different novel designs. Advantages and concerns using biofilm reactors, potential uses for industrial-scale production, and further investigation needs are discussed.

Scanning electron microscope imaging of bacteria based on DNA sequence

AIMS

To develop a scanning electron microscopic approach using in situ hybridization (SEM-ISH) for gaining both genetic and morphological information about target bacteria.

METHODS AND RESULTS

Target cells were hybridized with DNA-targeted polynucleotide probes, and a tyramide signal amplification system was used to increase the sensitivity. The protocol of SEM-ISH enabled to detect low copy number target DNA sequences in individual cells.

CONCLUSIONS

SEM-ISH allowed the in situ detection of bacteria carrying a specific gene.

SIGNIFICANCE AND IMPACT OF THE STUDY

Combining morphological study with SEM and ISH techniques appears to be a valuable tool to understand the spatial distribution of target cells in complex microbial communities on various materials.

Microstructure and composition of biosynthetically synthesised hydroxyapatite

Biosynthetic hydroxyapatite (HA) manufactured utilising the bacterium Serratia sp. NCIMB40259 was characterised using X-ray diffraction (XRD), Fourier transform infra-red spectroscopy (FTIR), energy dispersive X-ray analysis (EDX) scanning electron microscopy (SEM), transmission electron microscopy (TEM) and electron diffraction (ED). SEM/EDX showed that the non-sintered material consisted mainly of calcium-deficient HA (CDHA) with a Ca/P ratio of 1.61 +/- 0.06 and crystal size (from TEM) of 50 +/- 10 nm. ED analysis of non-sintered powder showed resolvable ring patterns ascribed to (0002), (1122) and (0006) planes of crystalline HA. The crystallinity of the samples improved with heat treatment from approximately 9.4% (non-sintered) to 53% (1,200 degrees C). Samples heated at 600 degrees C and sintered at 1,200 degrees C were identified by XRD and FTIR as mainly CDHA with some sodium calcium phosphate in the sintered samples. Ca/P ratios (SEM/EDX) were 1.62 and 1.52, respectively. Single crystal spot patterns characteristic of HA were seen with commercial HA and Serratia HA heated at 600 degrees C. After sintering at 1,200 degrees C the material consisted of needle-like crystals with a length between 86 and 323 nm (from TEM) or 54-111 nm (from XRD) and lattice parameters of a = 9.441 A and c = 6.875 A. This study indicated that the material produced by Serratia bacteria was initially mainly nanophase calcium deficient hydroxyapatite, which sintered to a more highly crystalline form. With further refinements the method could be used as an inexpensive route for hydroxyapatite production for biomaterials applications.

Bioremediation of cadmium by growing Rhodobacter sphaeroides: kinetic characteristic and mechanism studies

The removal kinetic characteristic and mechanism of cadmium by growing Rhodobacter sphaeroides were investigated. The removal data were fitted to the second-order equation, with a correlation coefficient, R2=0.9790-0.9916. Furthermore, it was found that the removal mechanism of cadmium was predominantly governed by bioprecipitation as cadmium sulfide with biosorption contributing to a minor extent. Also, the results revealed that the activities of cysteine desulfhydrase in strains grown in the presence of 10 and 20 mg/l of cadmium were higher than in the control, while the activities in the presence of 30 and 40 mg/l of cadmium were lower than in the control. Content analysis of subcellular fractionation showed that cadmium was mostly removed and transformed by precipitation on the cell wall.

Biodegradation of sodium benzoate by a Gram-negative consortium in a laboratory-scale fluidized bed bioreactor

Gram-negative bacteria with the potential to metabolize n-alkanes and cyclic hydrocarbons were isolated from local soils and identified using 16S rDNA sequence analysis. Three isolates (CS1CO, GL1CO, GCI1CO) were identified as strains of Pseudomonas (P.) aeruginosa and a further strain (DSS2) as P. putida. Isolates were co-cultured in a laboratory-scale fluidized bed biofilm bioreactor (FBBR) utilizing sodium benzoate as the sole carbon source, under two batch and/or one continuous growth conditions. Biofilm and planktonic bacterial growth dynamics were monitored by plate counts, and optical density measurements (230 nm) determined benzoate biodegradation. Overall higher attached and planktonic bacterial counts, and benzoate depletion, were determined under batch compared to continuous conditions, and the bioreactor performed better during the second batch phase when compared to the first batch phase. It thus appeared that both the planktonic and biofilm components of the system were necessary for the most successful sodium benzoate degradation in this system.

Effect of biofilm formation by Pseudoalteromonas spongiae on induction of larval settlement of the polychaete Hydroides elegans

The effects of culture conditions and chloramphenicol treatment on the induction of the marine bacterium Pseudoalteromonas spongiae to larval settlement of Hydroides elegans were investigated. The results showed that P. spongiae cells grown in the medium containing both yeast extract and peptone (YP-grown P. spongiae) was highly inductive to larval settlement, whereas P. spongiae cells grown in the medium containing only peptone (P-grown P. spongiae) or YP-grown P. spongiae cells treated with chloramphenicol at the onset of biofilm development (YPC-grown P. spongiae) did not induce larval settlement. Analysis of biofilm formation, biofilm structure, and the surface protein profile indicated that only the induction-capable YP-grown P. spongiae formed a well-developed biofilm, while the P-grown P. spongiae and the YPC-grown P. spongiae did not. We report here for the first time that bacterial biofilm formation was associated with its induction of larval settlement.

Novel membrane bioreactor: Able to cope with fluctuating loads, poorly water soluble VOCs, and biomass accumulation

Biological waste gas treatment is an attractive method for controlling air emissions of volatile organic compounds (VOCs). Microorganisms degrade the VOCs to harmless products such as carbon dioxide (CO(2)), biomass and water. In spite of the advantages, significant unresolved challenges remain for biological waste gas treatment. Fluctuating loads in waste gas streams, especially of VOCs with low water solubility, can often not be satisfactorily removed. Concentration peaks leave the reactor virtually untreated, while periods without VOCs in the waste gas lead to starvation of the bacteria. Furthermore, bioreactors are often subject to clogging due to biomass accumulation. In the current work, a flat sheet membrane bioreactor was developed which was able to buffer fluctuating loads of toluene, our model compound, by absorption in silicone oil prior to degradation and which continuously removed and discharged excess biomass from the reactor. The absorption and the biodegradation were both membrane based. An inverse bacterial biofilm developed on the membrane, which separated the culture medium from the absorbent. The culture medium was constantly passed along the biofilm, introducing shear stresses on the surface and thereby removing excess, inactive biomass. The toluene surface elimination capacity was virtually independent of the gas flow rate for the tested steady-state conditions and reached a maximum of 0.6 g m(-2) h(-1). Experiments with fluctuating inlet mass flow rates of toluene confirmed the excellent buffering capability of the set-up. The reactor was successfully operated for 162 days without clogging.

Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea

Strain UST040317-058T, comprising non-pigmented, rod-shaped, facultatively anaerobic, Gram-negative cells that are motile by means of single polar flagella, was isolated from the surface of a marine sponge (Ircinia dendroides) collected from the Mediterranean Sea. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a separate cluster with the recognized bacterium Shewanella algae IAM 14159T, with which it showed a sequence similarity of 95.0 %. The sequence similarity between strain UST040317-058T and its other (six) closest relatives ranged from 91.6 to 93.8 %. Strain UST040317-058T showed oxidase, catalase and gelatinase activities. The typical respiratory quinones for shewanellas, menaquinone MK-7 and ubiquinones Q-7 and Q-8, were also detected. The predominant fatty acids in strain UST040317-058T were i15 : 0, 16 : 0, 17 : 1ω8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1ω7c), altogether representing 56.9 % of the total. The DNA G+C content was 39.9 mol%. The strain could be differentiated from other Shewanella species by its inability to reduce nitrate or produce H2S and by 10–22 additional phenotypic characteristics. On the basis of the phylogenetic and phenotypic data presented in this study, strain UST040317-058T represents a novel species in the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed. The type strain is UST040317-058T (=JCM 13528T=NRRL B-41466T).

Carbon : nitrogen : phosphorus ratios influence biofilm formation byEnterobacter cloacaeandCitrobacter freundii

AIMS

To test the effects of C : N : P ratio modification of a well-known nutrient medium formulation, the Endo formulation on biofilm formation by Enterobacter cloacae Ecl and Citrobacter freundii Cf1 in both single-species and binary species biofilms.

METHODS AND RESULTS

The C : N : P atom : atom ratio of a well-known nutrient medium formulation, the Endo formulation, that has been applied in fermentative biohydrogen studies, was modified to include two different C concentrations, one containing 17.65 g l(-1) and the other 8.84 g l(-1) sucrose, each containing four different C : N : P ratios, two at higher C : N : P ratios (334 : 84 : 16.8 and 334 : 84 : 3) and two at lower C : N : P ratios (334 : 28 : 5.6 and 334 : 28 : 1). Attached cells were enumerated after dislodging the biofilms that had formed on granular activated carbon (GAC). The modified medium containing 17.65 g l(-1) sucrose and having a C : N : P ratio of 334 : 28 : 5.6 resulted in significantly (P < 0.05) higher counts of attached cells for both single-species biofilms at 7.73 log(10) CFU g(-1) GAC and 9.3 log(10)CFU g(-1) GAC for Ent. cloacae Ecl and Cit. freundii Cf1, respectively, and binary species biofilms at 8.2 log(10) CFU g(-1) GAC and 6.34 log(10) CFU g(-1) GAC for Ent. cloacae Ecl and Cit. freundii Cf1, respectively. Scanning electron micrographs showed qualitative evidence that the 334 : 28 : 5.6 ratio encouraged more complex and extensive biofilm growth for both single-species and binary species biofilms.

CONCLUSIONS

The differences in the attachment numbers between the different ratios were found not to be a result of the individual actions of the bacterial isolates involved but rather because of the effects of the various C : N : P ratios. The 334 : 28 : 5.6 ratio showed significantly (P < 0.05) higher counts of attached cells for both single-species and binary species biofilms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicates that C : N : P ratios should be a key consideration with regard to maximizing biofilm formation in shake flask and fluidized bed bioreactor studies as well as understanding fundamental factors affecting biofilm growth in natural environments.

rRNA sequence-based scanning electron microscopic detection of bacteria

A new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rRNA-targeted oligonucleotide probes (SEM-ISH). Target cells were hybridized with oligonucleotide probes after gold labeling. Gold enhancement was used for amplification of probe signals from hybridized cells. The hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. SEM-ISH was applied to analyze bacterial community composition in freshwater samples, and bacterial cell counts determined by SEM-ISH with rRNA-targeted probes for major phyla within the domain Bacteria were highly correlated to those by fluorescent in situ hybridization (FISH). The bacterial composition on surface of river sediment particles before and after cell dispersion treatment by sonication was successfully revealed by SEM-ISH. Direct enumeration of bacterial cells on the surface of sonicated sediment particles by SEM-ISH demonstrated that members of Cytophaga-Flavobacterium existed tightly on the surface of particles. SEM-ISH allows defining the number and distribution of phylogenetically defined cells adherent to material surfaces, which is difficult in FISH, and it gives new insight into electron microscopic studies of microorganisms in their natural environment.

A novel non line-of-sight method for coating hydroxyapatite onto the surfaces of support materials by biomineralization

A novel method is described for the non line-of-sight coating of hydroxyapatite onto polyurethane reticulated foam and titanium discs. This utilises a biofilm of Serratia sp. NCIMB 40259 which, when challenged with a solution containing calcium chloride and phosphatase substrate, manufactures biofilm-bound material identified as hydroxyapatite by X-ray powder diffraction analysis. Non-invasive magnetic resonance imaging was used to visualize the biofilm coating throughout the foam labyrinth and to measure the thickness of the film within reticulated foam cubes in situ. The film developed within the cube matrices was similar to that measured on the surface of a glass slide. Using LaPO(4) deposition as a model system the metallised biofilm was visualised in two-dimensional slices throughout three-dimensional images acquired by magnetic resonance imaging. A similar encrustation of hydroxyapatite on the surface of biofilm grown on titanium discs was confirmed by scanning electron microscopy. Potential applications for bio-hydroxyapatite as possible bone implant precursors are discussed.