Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater

Insights into the life-cycle of aerobic granular sludge in a continuous flow membrane bioreactor by tracing its heterogeneous properties at different stages

This work gave insights into the life-cycle of aerobic granular sludge (AGS) by tracing its heterogeneity in the basic properties at different stages in a closed system (a continuous flow membrane bioreactor, MBR), including physical and chemical characteristics and microbial communities. The results indicate that the entire life-cycle consists of the following four stages, namely, the initial, growing, mature and cleaved stages, where multiple AGS properties synergistically affect the rheological properties of the AGS over its life-cycle. The storage modulus (G') of AGS reached its maximum value at the mature stage, whose value was significantly and positively correlated with the protein (PN) in extracellular polymeric substances (EPS) and granule size, specifically the peak area of granule size distribution, but this value was strongly and negatively correlated with the roughness. The AGS at the mature stage would be more vulnerable to be destroyed than that at other stages under the condition of higher shear strain, such as γ = 50%, which was associated with larger granule size and fewer polysaccharide (PS)-related functional groups (especially in the soluble microbial products (SMPs) in the outermost layer of AGS), and the decrease in PS was correlated with a higher relative abundance of Chloroflexi. Additionally, the value of shear strain that AGS was subjected to had a good linear correlation (R2=0.993) with the Young's modulus, which indicated the ability of AGS to resist deformation improved with increasing values of shear strain.

Highly Enriched Anammox Bacteria with a Novel Granulation Model Regulated by Epistylis spp. in Domestic Wastewater Treatment

Anammox granulation is an efficient solution proffered to enrich slow-growing anammox bacteria (AnAOB), but the lack of effective granulation strategies for low-strength domestic wastewater impedes its application. In this study, a novel granulation model regulated by Epistylis spp. for highly enriched AnAOB was revealed for the first time. Notably, anammox granulation was achieved within 65 d of domestic wastewater treatment. The stalks of Epistylis spp. were found to act as the skeleton of granules and provide attachment points for bacterial colonization, and the expanded biomass layer in turn provided more area for the unstalked free-swimming zooids. Additionally, Epistylis spp. exerted much less predation stress on AnAOB than on nitrifying bacteria, and AnAOB tended to grow in aggregates in the interior of granules, thus favoring the growth and retention of AnAOB. Ultimately, the relative abundance of AnAOB reached up to a maximum of 8.2% in granules (doubling time of 9.9 d) compared to 1.1% in flocs (doubling time of 23.1 d), representing the most substantial disparity between granules and flocs. Overall, our findings advance the current understanding of interactions involved in granulation between protozoa and microbial communities and offer new insight into the specific enrichment of AnAOB under the novel granulation model.

Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness

Nutrient-transporting channels have been recently discovered in mature Escherichia coli biofilms, however the relationship between intra-colony channel structure and the surrounding environmental conditions is poorly understood. Using a combination of fluorescence mesoscopy and a purpose-designed open-source quantitative image analysis pipeline, we show that growth substrate composition and nutrient availability have a profound effect on the morphology of intra-colony channels in mature E. coli biofilms. Under all nutrient conditions, intra-colony channel width was observed to increase non-linearly with radial distance from the centre of the biofilm. Notably, the channels were around 25% wider at the centre of carbon-limited biofilms compared to nitrogen-limited biofilms. Channel density also differed in colonies grown on rich and minimal media, with the former creating a network of tightly packed channels and the latter leading to well-separated, wider channels with defined edges. Our approach paves the way for measurement of internal patterns in a wide range of biofilms, offering the potential for new insights into infection and pathogenicity.

Characterization of ammonia remover Bacillus albus (ASSF01) in terms of biofilm-forming ability with application in aquaculture effluent treatment

Presence of higher concentration of ammonia (> 0.5 mg/L) as well as nitrite (> 0.2 mg/L) in aquaculture environment create difficulties for fish survival. The existing methods for removal of these pollutants are time-consuming. A stable biofilm-based system for ammonia removal from aquaculture wastewater was developed in the current study to overcome the limitations of conventional treatment processes. In order to do so, initially the bacterial candidate was well characterized and tested for rapid biofilm development. The ammonia bioremediating Bacillus albus (ASSF01), from the activated sludge of shrimp farm, with a generation time of 67 min 12 s in suspension culture, was a structured biofilm former. The staining based measurement showed biofilm initiation from the very first hour of incubation. This finding was further validated using scanning electron microscopy (SEM), profilometry, and ellipsometry with Brewster angular microscopy (BAM). Hurst exponent (H) calculation using the profilometer and ellipsometer data yielded a value of H of above 0.9 and 0.62, indicating positive correlation or persistence behavior, hence a stable biofilm former. Each method of biofilm measurement, in spite of variation in complexity and sensitivity, was equally effective for biofilm progression analysis. The generation time of ASSF01 upon immobilization was 15 min and 36 s, ensuring rapid development of stable system. Response surface methodology (RSM)-based optimization of aquaculture wastewater treatment by the isolate in a biofilm reactor at ambient temperature revealed the optimum influent concentration of ammonia (3.2 mg/L), nitrate (6.89 mg/L), and phosphate (1.17 mg/L) to be reduced to discharge level (as per aquaculture requirement) with 14 h of hydraulic retention time. This study demonstrates the potential of the isolate as an efficient bioremediant for treating ammonia-containing aquaculture wastewater in a single unit biofilm reactor, ensuring rapid stabilization, environmental protection, and aquaculture sustenance.

Rapid granulation of aerobic granular sludge and maintaining its stability by combining the effects of multi-ionic matrix and bio-carrier in a continuous-flow membrane bioreactor

The present investigation aimed at providing a novel approach to promote the rapid granulation and stability of aerobic granular sludge (AGS) in a continuous-flow membrane bioreactor (MBR). By operating two identical MBRs with or with no bio-carrier for 125 days, it was found that the combination of multi-ionic matrix and bio-carrier could promote the rapid formation and maintain the long-term stability of AGS. The primary AGS was first observed inside the reactor on day 14, and the mature AGS appeared soon and kept stable for more than 4 months (its average size still was about 800 μm on day 125). Suitable filling ratio of bio-carrier was beneficial to form a stable and regular circulating water flow inside, and adding divalent metal ions quickly reduced the negative charges of tiny sludge particles, which were two essential factors leading to the rapid granulation of AGS and maintaining its stability. The multi-ionic matrix not only enhanced the biological aggregation process, but also facilitated the expansion of the cultivated AGS into a new multi-habitat system of Mn-AGS, in which, complex microbial communities with rich bio-diversity robustly promoted the efficient removal of organic pollutants and nutrients.

Non-Invasive Measurement, Mathematical Simulation and In Situ Detection of Biofilm Evolution in Porous Media: A Review

The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

Do Mixed-Species Biofilms Dominate in Chronic Infections?-Need for in situ Visualization of Bacterial Organization

Chronic infections present a serious economic burden to health-care systems. The severity and prevalence of chronic infections are continuously increasing due to an aging population and an elevated number of lifestyle related diseases such as diabetes. Treatment of chronic infections has proven difficult, mainly due to the presence of biofilms that render bacteria more tolerant toward antimicrobials and the host immune response. Chronic infections have been described to harbor several different bacterial species and it has been hypothesized that microscale interactions and mixed-species consortia are present as described for most natural occurring biofilms i.e., aquatic systems and industrial settings, but also for some commensal human biofilms i.e., the mouth microbiota. However, the presence of mixed-species biofilms in chronic infections is most often an assumption based on culture-based methods and/or by means of molecular approaches, such as PCR and sequencing performed from homogenized bulk tissue samples. These methods disregard the spatial organization of the bacterial community and thus valuable information on biofilm aggregate composition, spatial organization, and possible interactions between different species is lost. Hitherto, only few studies have made visual in situ presentations of mixed-species biofilms in chronic infections, which is pivotal for the description of bacterial composition, spatial distribution, and interspecies interaction on the microscale. In order for bacteria to interact (synergism, commensalism, mutualism, competition, etc.) they need to be in close proximity to each other on the scale where they can affect e.g., solute concentrations. We argue that visual proof of mixed species biofilms in chronic infections is scarce compared to what is seen in e.g., environmental biofilms and call for a debate on the importance of mixed-species biofilm in chronic infections.

Application of molecular techniques in biohydrogen production as a clean fuel

Considering the future energy demand and pollution to the environment, biohydrogen, a biofuel, produced from biological sources have garnered increased attention. The present review emphasis the various techniques and methods employed to enumerate the microbial community and enhancement of hydrogen production by dark fermentation. Notably, molecular techniques such as terminal restriction fragment length polymorphism (T-RFLP), quantitative real-time PCR (q-PCR), fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), and next generation sequencing (NGS) have been extensively discussed on identifying the microbial population in hydrogen production. Further, challenges and merits of the molecular techniques have been elaborated.

Multi-Parameter Laser Imaging Reveals Complex Microscale Biofilm Matrix in a Thick (4,000 μm) Aerobic Methanol Oxidizing Community

Although methanol has frequently been used as an inexpensive supplementary carbon source to support treatment processes, knowledge of the resultant microbial biofilms, their 3D architecture, microenvironments, exopolymer chemistry and populations remains limited. We supplied methanol as a supplementary carbon source to biofilms developing in rotating annular reactors. Analysis of circulation waters (1.0 l d^-1) indicated that dissolved organic carbon was reduced by 25%, NO₃-nitrogen by 95%, and total phosphorus by 70%. Analyses of populations using culture based techniques and fluorescence in situ hybridization indicated enrichment of nitrifiers, denitrifiers, and methylotrophic bacteria relative to reference biofilms not receiving methanol. The biofilms that developed were up to 4,000 μm thick. Staining with fluor conjugated lectins in combination with nucleic acid stains, revealed the presence of discrete bacterial cells inside complex globular polymeric structures. These structures were in turn surrounded by an interstitial polymer containing a variety of bacterial cell types. The globular structures bound FITC-conjugated lectins, from Canavalia ensiformis and Ulex europeaus. The FITC-lectin of Phaseolus vulgaris bound the surface of the globular structures and more generally within the matrix. Chemical analyses of the polymer paralleled the results of lectin analyses indicating that the dominant neutral sugars were glucose, galactose, mannose, rhamnose, with fucose and ribose as minor constituents. Amino sugars were not detected. Dual channel imaging with pH sensitive probes indicated that pH gradients from pH 4 to 7 occurred across the globular microcolonies. Critically for the maintenance of aerobic conditions throughout the thick biofilm it was extensively penetrated by a fine fissure network revealed by the location of fluorescent latex microbeads as detected by confocal laser scanning microscopy. Microelectrode studies confirmed the absence of any detectable Eh gradients within the biofilm. However, mobility of various size-fractionated fluorescent probes indicated that the basal region was only penetrated by the lowest molecular weight probes with a hydrated radius of 2.2 nm or less. These observations indicate the selection of a unique, thick (>4,000 μm) microbial community in which a self-organized architecture promotes the maintenance of optimal conditions and metabolism throughout the biofilm community.

Effect of Organic Loading Rates on biodegradation of linear alkyl benzene sulfonate, oil and grease in greywater by Integrated Fixed-film Activated Sludge (IFAS)

In this study, performance of Integrated Fixed-film Activated Sludge (IFAS) system in treatment of Linear Alkylbenzene Sulfonate (LAS), and oil & grease in synthetic greywater and effect of Organic Loading Rates (OLRs) on removal efficiency within a period of 105 days were investigated. Present study was carried out in a pilot scale under such conditions as temperature of 30 ± 1 °C, dissolved oxygen of 2.32 ± 0.91 mg/l, pH of 8.01 ± 0.95 and OLRs of 0.11-1.3gCOD/L.d. Also, Scanning Electron Microscopy (SEM) images were employed to specify rate of the biofilm formed on the media inside the reactor IFAS. The best removal efficiency for COD, LAS and oil and grease were respectively obtained as 92.52%, 94.24% and 90.07% in OLR 0.44gCOD/L.d. The assessment of loading rate indicated that with increased OLR to 0.44gCOD/L.d, removal efficiency of COD, oil and grease was increased while with increased OLR, removal efficiency was decreased. In doing so, based on the statistical test ANOVA, such a difference between removal efficiencies in diverse OLRs was significant for COD (p = 0.003), oil and grease (p = 0.01). However, in terms of LAS, with increased value of OLR to 0.44gCOD/L.d, the removal efficiency was increased and then with higher OLRs, removal efficiency was slightly decreased that is insignificant (p = 0.35) based on the statistical test ANOVA. The SEM images also showed that the biofilm formed on the media inside IFAS reactor plays a considerable role in adsorption and biodegradation of LAS, and oil & grease in greywater. The linear relation between inlet COD values and rate of removed LAS indicated that the ratio of inlet COD (mg/L) to removed LAS (mg/L) was 0.4. Therefore, use of IFAS system for biodegradation of LAS, oil and grease in greywater can be an applicable option.

Influence analysis for the behavior of dewaterability of excess sludge in a two-stage vermifilter

To improve excess sludge dewaterability, a two-stage vermifilter was developed to qualitatively and quantitatively analyze sludge physico-chemical properties (fractal dimension, zeta potential, extracellular polymeric substances (EPS), particle size distribution, etc.) and to correlate them with sludge dewatering characteristics (specific resistance to filtration (SRF) and capillary suction time (CST)). Results demonstrated that sludge dewatering performance was significantly improved after the primary vermifilter VF₁ and the second-stage vermifilter VF₂. In addition, the further VF₂ treatment exhibited higher effects on sludge dewatering performance. The particle boundary of sludge after VF₂ treatment was clearer and smoother than VF₁ sludge (VF₁S), apart from the fact that sludge morphological structure got denser and more compact. Comparing with VF₁S, the fractal dimension D₁ calculated within 1D topological space was closer to 1 after VF₂ treatment, and the fractal dimension D₂ within 2D topological space closer to 2, indicating a better dewatering performance after VF₂ treatment. Additionally, the changes of sludge floc surface properties (such as zeta potential and EPS) resulted in small particles agglomerating into larger ones and then the increase of particle diameter. In summary, the two-stage vermifilter got a better sludge dewatering performance, and thus beneficial for subsequent processing of sludge.

Biofilm, pathogenesis and prevention--a journey to break the wall: a review

Biofilms contain group(s) of microorganisms that are found to be associated with the biotic and abiotic surfaces. Biofilms contain either homogenous or heterogeneous populations of bacteria which remain in the matrix made up of extracellular polymeric substances secreted by constituent population of the biofilm. Biofilms can be either single or multilayered. Biofilms are an increasing issue of concern that is gaining importance with each passing day. Due to the ubiquitous nature of biofilms, it is difficult to eradicate them. It has been seen that many infectious diseases harbour biofilms of bacterial pathogens as the reservoir of persisting infections which can prove fatal at times. The presence of biofilms can be seen in diseases like endocarditis, cystic fibrosis, periodontitis, rhinosinusitis and osteomyelitis. The presence of biofilms has been mostly seen in medical implants and urinary catheters. Various signalling events including two-component signalling, extra cytoplasmic function and quorum sensing are involved in the formation of biofilms. The presence of an extracellular polymeric matrix in biofilms makes it difficult for the antimicrobials to act on them and make the bacteria tolerant to antibiotics and other drugs. The aim of this review was to discuss about the basic formation of a biofilm, various signalling cascades involved in biofilm formation, possible mechanisms of drug resistance in biofilms and recent therapeutic approaches involved in successful eradication of biofilms.

Removal of pathogenic bacterial biofilms by combinations of oxidizing compounds

Bacterial biofilms are commonly formed on medical devices and food processing surfaces. The antimicrobials used have limited efficacy against the biofilms; therefore, new strategies to prevent and remove these structures are needed. Here, the effectiveness of brief oxidative treatments, based on the combination of sodium hypochlorite (NaClO) and hydrogen peroxide (H2O2) in the presence of copper sulfate (CuSO4),were evaluated against bacterial laboratory strains and clinical isolates, both in planktonic and biofilm states. Simultaneous application of oxidants synergistically inactivated planktonic cells and prevented biofilm formation of laboratory Escherichia coli, Salmonella enterica serovar Typhimurium, Klebsiella pneumoniae, and Staphylococcus aureus strains, as well as clinical isolates of Salmonella enterica subsp. enterica, Klebsiella oxytoca, and uropathogenic E. coli. In addition, preformed biofilms of E. coli C, Salmonella Typhimurium, K. pneumoniae, and Salmonella enterica exposed to treatments were removed by applying 12 mg/L NaClO, 0.1 mmol/L CuSO4, and 350 mmol/L H2O2for 5 min. Klebsiella oxytoca and Staphylococcus aureus required a 5-fold increase in NaClO concentration, and the E. coli clinical isolate remained unremovable unless treatments were applied on biofilms formed within 24 h instead of 48 h. The application of treatments that last a few minutes using oxidizing compounds at low concentrations represents an interesting disinfection strategy against pathogens associated with medical and industrial settings.

Extracellular polymeric substance architecture influences natural genetic transformation of Acinetobacter baylyi in biofilms

Genetic exchange by natural transformation is an important mechanism of horizontal gene transfer in biofilms. Thirty-two biofilm metrics were quantified in a heavily encapsulated Acinetobacter baylyi strain and a miniencapsulated mutant strain, accounting for cellular architecture, extracellular polymeric substances (EPS) architecture, and their combined biofilm architecture. In general, transformation location, abundance, and frequency were more closely correlated to EPS architecture than to cellular or combined architecture. Transformation frequency and transformant location had the greatest correlation with the EPS metric surface area-to-biovolume ratio. Transformation frequency peaked when EPS surface area-to-biovolume ratio was greater than 3 μm(2)/μm(3) and less than 5 μm(2)/μm(3). Transformant location shifted toward the biofilm-bulk fluid interface as the EPS surface area-to-biovolume ratio increased. Transformant biovolume was most closely correlated with EPS biovolume and peaked when transformation occurred in close proximity to the substratum. This study demonstrates that biofilm architecture influences A. baylyi transformation frequency and transformant location and abundance. The major role of EPS may be to facilitate the binding and stabilization of plasmid DNA for cellular uptake.

Characterization of SDS-degrading Delftia acidovorans and in situ monitoring of its temporal succession in SDS-contaminated surface waters

Incomplete removal of sodium dodecyl sulfate (SDS) in wastewater treatment plants may result in SDS residues escaping and finding their way into receiving water bodies like rivers, lakes, and sea. Introduction of effective microorganisms into the aerobic treatment facilities can reduce unpleasant by-products and SDS residues. Selecting effective microorganisms for SDS treatment is a big challenge. Current study reports the isolation, identification, and in situ monitoring of an effective SDS-degrading isolate from detergent-polluted river waters. Screening was carried out by the conventional enrichment culture technique and the isolate was tentatively identified by using fatty acid methyl ester and 16S ribosomal RNA (rRNA) sequence analyses. Fatty acids produced by the isolate investigated were assumed as typical for the genus Comamonas. 16S rRNA sequence analysis also confirmed that the isolate had 95% homology with Delftia acidovorans known as Comamonas or Pseudomonas acidovorans previously. D. acidovorans exhibited optimum growth at SDS concentration of 1 g l(-1) but tolerated up to 10 g l(-1) SDS. 87% of 1.0 g l(-1) pure SDS was degraded after 11 days of incubation. The temporal succession of D. acidovorans in detergent-polluted river water was also monitored in situ by using Comamonas-specific fluorescein-labeled Cte probe. Being able to degrade SDS and populate in SDS-polluted surface waters, D. acidovorans isolates seem to be very helpful in elimination of SDS.

Investigation of microbial biofilm structure by laser scanning microscopy

Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.

Bacterial succession and degradative changes by biofilm on plastic medium for wastewater treatment

Biofilms contain a diverse range of microorganisms and their varying extracellular polysaccharides. The present study has revealed biofilm succession associated with degradative effects on plastic (polypropylene) and contaminants in sludge. The wet weight of biofilm significantly (p < 0.05) increased; from 0.23 ± 0.01 to 0.44 ± 0.01 g. Similarly, the dry weight of the biofilm increased from 0.02 to 0.05 g. Significant reduction in pathogens (E. coli and feacal coliforms) by MPN technique (>80%) and in chemical parameters (decrease in COD, BOD5 of 73.32 and 69.94%) representing diminution of organic pollutants. Energy dispersive X-ray spectroscopy (EDS) of plastic revealed carbon and oxygen contents, further surface analysis of plastic by scanning electron microscopy (SEM) revealed emergence of profound bacterial growth on the surface. Fourier transform infrared (FTIR) spectroscopy conforms its biotransformation under aerobic conditions after 8 weeks. New peaks developed at the region 1050 and 969 cm(-1) indicating CO and CC bond formation. Thus plastic with 6 weeks old aerobic biofilm (free of pathogens, max. weight, and OD, efficient COD & BOD removal ability) is suggested to be maintained in fixed biofilm reactors for wastewater treatment.

Long-term impact of anaerobic reaction time on the performance and granular characteristics of granular denitrifying biological phosphorus removal systems

Removal of nitrogen and phosphorus (P) from wastewater is successfully and widely practiced in systems employing both granular sludge technology and enhanced biological P removal (EBPR) processes; however, the key parameter, anaerobic reaction time (AnRT), has not been thoroughly investigated. Successful EBPR is highly dependent on an appropriate AnRT, which induces carbon and polyphosphate metabolism by phosphorus accumulating organisms (PAOs). Therefore, the long-term impact of AnRT on denitrifying P removal performance and granular characteristics was investigated in three identical granular sludge sequencing batch reactors with AnRTs of 90 (R1), 120 (R2) and 150 min (R3). The microbial community structures and anaerobic stoichiometric parameters related to various AnRTs were monitored over time. Free nitrite acid (FNA) accumulation (e.g., 0.0008-0.0016 mg HNO2-N/L) occurred frequently owing to incomplete denitrification in the adaptation period, especially in R3, which influenced the anaerobic/anoxic intracellular intermediate metabolites and activities of intracellular enzymes negatively, resulting in lower levels of poly-P and reduced activity of polyphosphate kinase. As a result, the Accumulibacter-PAOs population decreased from 51 ± 2.5% to 43 ± 2.1% when AnRT was extended from 90 to 150 min, leading to decreased denitrifying P removal performance. Additionally, frequent exposure of microorganisms to the FNA accumulation and anaerobic endogenous conditions in excess AnRT cases (e.g., 150 min) stimulated increased extracellular polymeric substances (EPS) production by microorganisms, resulting in enhanced granular formation and larger granules (size of 0.6-1.2 mm), but decreasing anaerobic PHA synthesis and glycogen hydrolysis. Phosphorus removal capacity was mediated to some extent by EPS adsorption in granular sludge systems that possessed more EPS, longer AnRT and relatively higher GAOs.

Stress relaxation analysis facilitates a quantitative approach towards antimicrobial penetration into biofilms

Biofilm-related infections can develop everywhere in the human body and are rarely cleared by the host immune system. Moreover, biofilms are often tolerant to antimicrobials, due to a combination of inherent properties of bacteria in their adhering, biofilm mode of growth and poor physical penetration of antimicrobials through biofilms. Current understanding of biofilm recalcitrance toward antimicrobial penetration is based on qualitative descriptions of biofilms. Here we hypothesize that stress relaxation of biofilms will relate with antimicrobial penetration. Stress relaxation analysis of single-species oral biofilms grown in vitro identified a fast, intermediate and slow response to an induced deformation, corresponding with outflow of water and extracellular polymeric substances, and bacterial re-arrangement, respectively. Penetration of chlorhexidine into these biofilms increased with increasing relative importance of the slow and decreasing importance of the fast relaxation element. Involvement of slow relaxation elements suggests that biofilm structures allowing extensive bacterial re-arrangement after deformation are more open, allowing better antimicrobial penetration. Involvement of fast relaxation elements suggests that water dilutes the antimicrobial upon penetration to an ineffective concentration in deeper layers of the biofilm. Next, we collected biofilms formed in intra-oral collection devices bonded to the buccal surfaces of the maxillary first molars of human volunteers. Ex situ chlorhexidine penetration into two weeks old in vivo formed biofilms followed a similar dependence on the importance of the fast and slow relaxation elements as observed for in vitro formed biofilms. This study demonstrates that biofilm properties can be derived that quantitatively explain antimicrobial penetration into a biofilm.

Hydrodynamic dispersion within porous biofilms

Many microorganisms live within surface-associated consortia, termed biofilms, that can form intricate porous structures interspersed with a network of fluid channels. In such systems, transport phenomena, including flow and advection, regulate various aspects of cell behavior by controlling nutrient supply, evacuation of waste products, and permeation of antimicrobial agents. This study presents multiscale analysis of solute transport in these porous biofilms. We start our analysis with a channel-scale description of mass transport and use the method of volume averaging to derive a set of homogenized equations at the biofilm-scale in the case where the width of the channels is significantly smaller than the thickness of the biofilm. We show that solute transport may be described via two coupled partial differential equations or telegrapher's equations for the averaged concentrations. These models are particularly relevant for chemicals, such as some antimicrobial agents, that penetrate cell clusters very slowly. In most cases, especially for nutrients, solute penetration is faster, and transport can be described via an advection-dispersion equation. In this simpler case, the effective diffusion is characterized by a second-order tensor whose components depend on (1) the topology of the channels' network; (2) the solute's diffusion coefficients in the fluid and the cell clusters; (3) hydrodynamic dispersion effects; and (4) an additional dispersion term intrinsic to the two-phase configuration. Although solute transport in biofilms is commonly thought to be diffusion dominated, this analysis shows that hydrodynamic dispersion effects may significantly contribute to transport.

Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis

An investigation of bacterial diversity in compost was performed using molecular chronometer in order to reveal its phylogeny. Thirty-three bacterial isolates isolated from compost were analyzed by 16S rRNA gene sequencing which revealed phylogenetic lineage of class Bacilli, γ, β-Proteobacteria, and Actinobacteria. Among these lineages, isolates belonging to class Bacilli consisted of species from genera Staphylococcus, Bacillus, Terribacillus, and Lysinibacillus. From phylum Actinobacteria: Microbacterium barkeri and Kocuria sp. were identified. Other bacterial groups had phylogenetic linkage with genera Comamonas and Acidovorax (class β-Proteobacteria); Serratia, Klebsiella, and Enterobacter (class γ-Proteobacteria). Similar isolates were analyzed through ARDRA. Amplified product of 16S rRNA gene from each isolates was subjected to cleavage by enzymes HpaII, HinfI, and MspI in separate reaction tubes. HpaII generated 2-6 bands ranging from 90-688 bp, HinfI generated 2-5 bands of 71-1,038 bp, and MspI 2-7 bands of 69-793 bp. The restriction patterns from HpaII, HinfI, and MspI were normalized separately and combined by means of pattern recognition software "Diversity Database." HpaII had highest discrimination index (0.72) than HinfI (0.68) and MspI (0.65), and the combination of all three showed discrimination index (0.69). Numerical analysis of ARDRA patterns demonstrated sufficient phylogenetic information for characterizing bacterial diversity. Phylogenetic relationship obtained among isolates through ARDRA was compared with 16S rRNA gene sequence and ARDRA results showed sufficiently similar 16S rRNA gene sequence analysis, but not an overlapping. It has been observed that ARDRA technique facilitates the identification of bacteria in less than 36 h as compared to traditional 16S rRNA gene sequencing.

Application of lyophilization to prepare the nitrifying bacterial biofilm for imaging with scanning electron microscopy

Structure of bacterial biofilms may be investigated using several variants of scanning electron microscopy (SEM). We apply lyophilization to prepare nitrifying bacterial biofilm for conventional SEM imaging in high-vacuum mode (CSEM). We therefore replace standard biofilm fixation in glutaraldehyde cross-linking, ethanol dehydration, and critical-point drying (CPD) with less-invasive low-temperature drying by sublimation in vacuum. We compare this approach with: (1) standard preparation with glutaraldehyde fixation, ethanol dehydration, and CPD before CSEM, (2) cryo-sputter preparation of rapidly frozen biofilm in hydrated state (cryo-SEM), and (3) in situ observation without any sample pretreatment in environmental SEM. Combined imaging with these modalities revealed two distinct immobilization patterns on the polyurethane foam: (1) large irregular aggregates (flocs) of bacterial biofilm that exist as irregular biofilm fragments, rope-like structures, or biofilm layers on the foam surface; (2) biofilm threads adherent to the surface of polyurethane foam. Our results indicate that lyophilization was suitable for preservation of bacterial cells and many forms of structure of extracellular matrix. The lyophilized material could be imaged with high resolution (using CSEM) to generate structural information complementary to that obtained with other SEM techniques.

Spatial Architecture of Nitrifying Bacteria Biofilm Immobilized on Polyurethane Foam in an Automatic Biodetector for Water Toxicity

We describe the architecture of nitrifying bacteria biofilms immobilized on a three-dimensional (3D) polyurethane foam that permits efficient water flow through a bioreactor. The 3D spatial organization of immobilized bacterial colonies is characterized on three resolution levels with X-ray tomography, light confocal microscopy, and scanning electron microscopy (SEM). Using these techniques we demonstrate biofilm distribution in the foam and the existence of several modes of binding of bacteria to the foam. Computed X-ray tomography permits observation of the distribution of the biofilm in the whole open cellular polyurethane material volume and estimation of biofilm volume. SEM and confocal laser scanning microscopy techniques permit 3D visualization of biofilm structure. Three distinct immobilization patterns could be observed in the open cellular polyurethane material: (1) large irregular aggregates of bacterial biofilm that exist as irregular biofilm fragments, rope-like structures, or biofilm layers on the foam surface; (2) spherical (pom-pom) aggregates of bacteria localized on the external surface of biofilm; and (3) biofilm threads adherent to the surface of polyurethane foam. Finally, we demonstrate that immobilized bacteria exhibit metabolic activity and growth.

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.

Classification and identification of fungal sequences using characteristic restriction endonuclease cut order

Restriction Fragment Length Polymorphism (RFLP) is a powerful molecular tool that is extensively used in the molecular fingerprinting and epidemiological studies of microorganisms. In a wet-lab setting, the DNA is cut with one or more restriction enzymes and subjected to gel electrophoresis to obtain signature fragment patterns, which is utilized in the classification and identification of organisms. This wet-lab approach may not be practical when the experimental data set includes a large number of genetic sequences and a wide pool of restriction enzymes to choose from. In this study, we introduce a novel concept of Enzyme Cut Order - a biological property-based characteristic of DNA sequences which can be defined and analyzed computationally without any alignment algorithm. In this alignment-free approach, a similarity matrix is developed based on the pairwise Longest Common Subsequences (LCS) of the Enzyme Cut Orders. The choice of an ideal set of restriction enzymes used for analysis is augmented by using genetic algorithms. The results obtained from this approach using internal transcribed spacer regions of rDNA from fungi as the target sequence show that the phylogenetically-related organisms form a single cluster and successful grouping of phylogenetically close or distant organisms is dependent on the choice of restriction enzymes used in the analysis. Additionally, comparison of trees obtained with this alignment-free and the legacy method revealed highly similar tree topologies. This novel alignment-free method, which utilizes the Enzyme Cut Order and restriction enzyme profile, is a reliable alternative to local or global alignment-based classification and identification of organisms.

Is gas-discharge plasma a new solution to the old problem of biofilm inactivation?

Conventional disinfection and sterilization methods are often ineffective with biofilms, which are ubiquitous, hard-to-destroy microbial communities embedded in a matrix mostly composed of exopolysaccharides. The use of gas-discharge plasmas represents an alternative method, since plasmas contain a mixture of charged particles, chemically reactive species and UV radiation, whose decontamination potential for free-living, planktonic micro-organisms is well established. In this study, biofilms were produced using Chromobacterium violaceum, a Gram-negative bacterium present in soil and water and used in this study as a model organism. Biofilms were subjected to an atmospheric pressure plasma jet for different exposure times. Our results show that 99.6 % of culturable cells are inactivated after a 5 min treatment. The survivor curve shows double-slope kinetics with a rapid initial decline in c.f.u. ml(-1) followed by a much slower decline with D values that are longer than those for the inactivation of planktonic organisms, suggesting a more complex inactivation mechanism for biofilms. DNA and ATP determinations together with atomic force microscopy and fluorescence microscopy show that non-culturable cells are still alive after short plasma exposure times. These results indicate the potential of plasma for biofilm inactivation and suggest that cells go through a sequential set of physiological and morphological changes before inactivation.

Model system studies of the influence of bacterial biofilm formation on mineral surface reactivity

Biofilm development on mineral surfaces and related changes in surface reactivity were studied using batch and flow through experiments. An artificial groundwater was used as the primary nutrient medium, Pseudomonas aeruginosa (PAO1) was the model microbial organism and 'mineral' surfaces were kept as simple as possible by using glass or a polished quartz tile. Experiments were also completed with very low concentrations (100 mg l(-1)) of iron, Fe(2+ ), in the solution. In situ confocal laser scanning microscopy of developing colonies during the live growth phase, and of thick, mature biofilms, revealed only sporadic coverage of biofilm cells and associated polymers at the 'mineral-microbe interface'. Imaging and analysis of biofilm-conditioned surfaces doped with Fe(2+ )-rich solutions allowed the locus and form of Fe-rich mineral precipitation to be determined and show that biological surface components can cause mineral precipitation from dilute dissolved species which might otherwise remain in solution.

Monoaromatics removal from polluted water through bioreactors-a review

Water contaminated by oil products is becoming a major problem in water supplies as these organic compounds cause hazards for human health. Different types of aerobic and anaerobic bioreactors have been widely used for water cleanup from organic pollutants such as petroleum hydrocarbons. Many studies report that aerobic biofilm processes are a very efficient method for monoaromatic hydrocarbons removal from contaminated water as they are able to reduce up to 99% of the pollutants from water, but generally these works do not discuss possible pollutant loss through gas stripping. On the other hand, some research is related to the ability of anaerobic bioreactors for monoaromatics treatment and results have shown that anaerobic immobilized reactors are able to remove monoaromatic compounds from water with maximal efficiencies between 95-99%. But here again, no data are found about the amount of volatile organic compounds that can be found in the biogas. Also, the data generated when a solid biomass support (activated carbon, polyurethane, etc.) is present in the medium do not take care about possible solute sorption phenomena. This paper reviews various properties of monoaromatic compounds including benzene, toluene, ethylbenzene and mixture of xylenes. The sources of pollutants, various analytical methods suitable for identification and quantitative measurement of monoaromatics, and knowledge gained on the true removal rates by aerobic and anaerobic bioreactors are reviewed and discussed in this study.

A multiscale theoretical model for diffusive mass transfer in cellular biological media

An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers. The final expression for the local effective diffusion coefficient is: D(Abeta)=lambda(beta)D(Aupsilon), where D(Aupsilon) is the diffusion coefficient in water, and lambda(beta) is a function of the composition and fundamental geometric and physicochemical system properties, including the size of solute molecules, the size of extra-cellular polymer fibers, and the mass permeability of the cell membrane. Furthermore, the analysis sheds some light on the function of the extra-cellular hydrogel as a diffusive barrier to solute molecules approaching the cell membrane, and its implications on the transport of chemotherapeutic agents within a cellular biological medium. Finally, the model predicts the qualitative trend as well as the quantitative variability of a large number of published experimental data on the diffusion coefficient of oxygen in cell-entrapping gels, microbial flocs, biofilms, and mammalian tissues.

Biological phenol removal using immobilized cells in a pulsed plate bioreactor: effect of dilution rate and influent phenol concentration

The continuous aerobic biodegradation of phenol in synthetic wastewater was carried out using Nocardia hydrocarbonoxydans immobilized over glass beads packed between the plates in a pulsed plate bioreactor at a frequency of pulsation of 0.5s(-1) and amplitude of 4.7 cm. The influence of dilution rate and influent phenol concentration on start up and steady state performance of the bioreactor was studied. The time taken to reach steady state has increased with increase in dilution rate and influent phenol concentration. It was found that, as the dilution rate is increased, the percentage degradation has decreased. Steady state percentage degradation was also reduced with increased influent phenol concentration. Almost 100% degradation of 300 and 500 ppm influent phenol could be achieved at a dilution rate of 0.4094 h(-1) and more than 99% degradation could be achieved with higher dilution rates. At a higher dilution rate of 1.0235 h(-1) and at concentrations of 800 and 900 ppm the percentage degradation has reduced to around 94% and 93%, respectively. The attached biomass dry weight, biofilm thickness and biofilm density at steady state were influenced by influent phenol concentration and dilution rate.

Microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (Vega Baja, Puerto Rico)

Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source). Approximately 20% of the isolates were also capable of complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the ∝, β and γ subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA) containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal φ29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50°C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA]) were repeatedly detected. Genes for degradation of MTBE, nitroaromatics and chlorinated compounds were also present, indicating a broad catabolic potential of the treatment unit. FGA’s demonstrated the early establishment of a diverse community with concurrent aerobic and anaerobic processes contributing to the bioremediation process.

Influence of nutrients, hexadecane, and temporal variations on nitrification and exopolysaccharide composition of river biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001. The reactors were supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane. The impact of these treatments on nitrification and on the exopolysaccharide composition of river biofilms was determined. The results showed that the biofilms had higher NH4+oxidation, NO3–production, and N2O production activities in fall 1999 than fall 2001 when grown with CNP but had higher activities in fall 2001 than fall 1999 when grown with individual nutrients. The exopolysaccharide amounts and proportions were generally higher in fall 1999 than fall 2001, as a consequence of the higher nutrient levels in the river water in the first year of this study. The addition of P and especially CNP stimulated NH4+oxidation by the biofilms, showing a P limitation in this river ecosystem. The presence of hexadecane negatively affected these activities and lowered the amounts of exopolysaccharides in CNP and P biofilms in fall 1999 but increased the biofilm activities and exopolysaccharide amounts in CNP biofilm in fall 2001. Antagonistic, synergistic, and independent effects between nutrients and hexadecane were also observed. This study demonstrated that the biofilm autotrophic nitrification activity in the South Saskatchewan River was limited by P, that this activity and the exopolysaccharide amounts and proportions were dependent on the nutrient concentrations in the river water, and suggested that exopolysaccharides may play a protective role for biofilm microorganisms against toxic pollutants.Key words: river biofilms, nitrification, nutrients, hexadecane, exopolysaccharides.

Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be cyclic and predictable from year to year and that there are interactive effects between nutrients and the contaminant hexadecane.

Architecture of a nascent Sphingomonas sp. biofilm under varied hydrodynamic conditions

The architecture of a Sphingomonas biofilm was studied during early phases of its formation, using strain L138, a gfp-tagged derivative of Sphingomonas sp. strain LB126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. Spatial and temporal distribution of cells and exopolymer secretions (EPS) within the biofilm, development of microcolonies under flow conditions representing varied Reynolds numbers, and changes in diffusion length with reference to EPS production were studied by sequential sacrificing of biofilms grown in multichannel flow cells and by time-lapse confocal imaging. The area of biofilm in terms of microscopic images required to ensure representative sampling varied by an order of magnitude when area of cell coverage (2 x 10(5) microm(2)) or microcolony size (1 x 10(6) microm(2)) was the biofilm parameter under investigation. Hence, it is necessary to establish the inherent variability of any biofilm metric one is attempting to quantify. Sphingomonas sp. strain L138 biofilm architecture consisted of microcolonies and extensive water channels. Biomass and EPS distribution were maximal at 8 to 9 mum above the substratum, with a high void fraction near the substratum. Time-lapse confocal imaging and digital image analysis showed that growth of the microcolonies was not uniform: adjacently located colonies registered significant growth or no growth at all. Microcolonies in the biofilm had the ability to move across the attachment surface as a unit, irrespective of fluid flow direction, indicating that movement of microcolonies is an inherent property of the biofilm. Width of water channels decreased as EPS production increased, resulting in increased diffusion distances in the biofilm. Changing hydrodynamic conditions (Reynolds numbers of 0.07, 52, and 87) had no discernible influence on the characteristics of microcolonies (size, shape, or orientation with respect to flow) during the first 24 h of biofilm development. Inherent factors appear to have overriding influence, vis-a-vis environmental factors, on early stages of microcolony development under these laminar flow conditions.

Molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-reducing bioreactor

Bioremediation of perchlorate-contaminated groundwater can occur via bacterial reduction of perchlorate to chloride. Although perchlorate reduction has been demonstrated in bacterial pure cultures, little is known about the efficacy of using perchlorate-reducing bacteria as inoculants for bioremediation in the field. A pilot-scale, fixed-bed bioreactor containing plastic support medium was used to treat perchlorate-contaminated groundwater at a site in Southern California. The bioreactor was inoculated with a field-grown suspension of the perchlorate-respiring bacterium Dechlorosoma sp. strain KJ and fed groundwater containing indigenous bacteria and a carbon source amendment. Because the reactor was flushed weekly to remove accumulated biomass, only bacteria capable of growing in biofilms in the reactor were expected to survive. After 26 days of operation, perchlorate was not detected in bioreactor effluent. Perchlorate remained undetected by ion chromatography (detection limit 4 mug L(-1)) during 6 months of operation, after which the reactor was drained. Plastic medium was subsampled from top, middle, and bottom locations of the reactor for shipment on blue ice and storage at -80 degrees C prior to analysis. Microbial community DNA was extracted from successive washes of thawed biofilm material for PCR-based community profiling by 16S-23S ribosomal intergenic spacer analysis (RISA). No DNA sequences characteristic of strain KJ were recovered from any RISA bands. The most intense bands yielded DNA sequences with high similarities to Dechloromonas spp., a closely related but different genus of perchlorate-respiring bacteria. Additional sequences from RISA profiles indicated presence of representatives of the low G+C gram-positive bacteria and the Cytophaga-Flavobacterium-Bacteroides group. Confocal scanning laser microscopy and fluorescence in situ hybridization (FISH) were also used to examine biofilms using genus-specific 16S ribosomal RNA probes. FISH was more sensitive than RISA profiling in detecting possible survivors from the initial inoculum. FISH revealed that bacteria hybridizing to Dechlorosoma probes constituted <1% of all cells in the biofilms examined, except in the deepest portions where they represented 3-5%. Numbers of bacteria hybridizing to Dechloromonas probes decreased as biofilm depth increased, and they were most abundant at the biofilm surface (23% of all cells). These spatial distribution differences suggested persistence of low numbers of the inoculated strain Dechlorosoma sp. KJ in parts of the biofilm nearest to the plastic medium, concomitant with active colonization or growth by indigenous Dechloromonas spp. in the biofilm exterior. This study demonstrated the feasibility of post hoc analysis of frozen biofilms following completion of field remediation studies.

Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system

In this study, we examined the long-term development of the overall structural morphology and community composition of a biofilm formed in a model drinking water distribution system with biofilms from 1 day to 3 years old. Visualization and subsequent quantification showed how the biofilm developed from an initial attachment of single cells through the formation of independent microcolonies reaching 30 micro m in thickness to a final looser structure with an average thickness of 14.1 micro m and covering 76% of the surface. An analysis of the community composition by use of terminal restriction fragment length polymorphisms showed a correlation between the population profile and the age of the sample, separating the samples into young (1 to 94 days) and old (571 to 1,093 days) biofilms, whereas a limited spatial variation in the biofilm was observed. A more detailed analysis with cloning and sequencing of 16S rRNA fragments illustrated how a wide variety of cells recruited from the bulk water initially attached and resulted in a species richness comparable to that in the water phase. This step was followed by the growth of a bacterium which was related to Nitrospira, which constituted 78% of the community by day 256, and which resulted in a reduction in the overall richness. After 500 days, the biofilm entered a stable population state, which was characterized by a greater richness of bacteria, including Nitrospira, Planctomyces, Acidobacterium, and Pseudomonas. The combination of different techniques illustrated the successional formation of a biofilm during a 3-year period in this model drinking water distribution system.

A three-dimensional, stochastic simulation of biofilm growth and transport-related factors that affect structure

Biofilm structural heterogeneity affects a broad range of microbially catalysed processes. Solute transport limitation and autoinhibitor production, two factors that contribute to heterogeneous biofilm development, were investigated using BacMIST, a computer simulation model. BacMIST combines a cellular automaton algorithm for biofilm growth with Brownian diffusion for solute transport. The simulation represented the growth of microbial unit cells in a three-dimensional domain modelled after a repeating section of a constant depth film fermenter. The simulation was implemented to analyse the effects of various levels of transport limitation on a growing single-species biofilm. In a system with rapid solute diffusion, cells throughout the biofilm grew at their maximum rate, and no solute gradient was formed over the biofilm thickness. In increasingly transport-limited systems, the rapidly growing fraction of the biofilm population decreased, and was found exclusively at the biofilm–liquid interface. Trans-biofilm growth substrate gradients also deepened with increasing transport limitation. Autoinhibitory biofilm growth was simulated for various rates of microbially produced inhibitor transport. Inhibitor transport rates affected both the biofilm population dynamics and the resulting biofilm structures. The formation of networks of void spaces in slow-growing regions of the biofilm and the development of columns in the fast-growing regions suggested a possible mechanism for the microscopically observed evolution of channels in biofilms.

Patchy biofilm coverage can explain the potential advantage of BGAC reactors

An adsorbing biofilm carrier, like granular activated carbon (GAC), can be the source of an extra flux of pollutant to the biofilm in addition to the bulk liquid. This double flux can improve the performance of a biological GAC (BGAC) reactor as compared to a nonabsorbing carrier reactor but only under conditions of pollutant partial penetration in the biofilm. Pollutant partial penetration in a biofilm often occurs in treatment processes where very low effluent concentrations are required. However, under these conditions, adsorption in BGAC reactors is questionable and requires the existence of biofilm free areas on the GAC carrier. The purpose of this investigation is to prove that under normal BGAC fluidized bed reactor operational conditions patchy biofilm coverage with exposed areas of GAC develops. Adsorption and desorption through these exposed areas can explain the widely debated advantage of BGAC reactors regarding higher biofilm activity. The patchy-like nature of the biofilm coverage on the GAC particles was verified using experimental and modeling tools. Comparison between a nonadsorbing granular carbon carrier and a GAC carrier with an atrazine degrading biofilm (Pseudomonas ADP) under conditions of atrazine partial penetration in the biofilm showed higher biodegradation and lower effluent atrazine concentrations in the BGAC reactor.

Impact of seasonal variations and nutrient inputs on nitrogen cycling and degradation of hexadecane by replicated river biofilms

Biofilm communities cultivated in rotating annular bioreactors using water from the South Saskatchewan River were assessed for the effects of seasonal variations and nutrient (C, N, and P) additions. Confocal laser microscopy revealed that while control biofilms were consistently dominated by bacterial biomass, the addition of nutrients shifted biofilms of summer and fall water samples to phototrophic-dominated communities. In nutrient-amended biofilms, similar patterns of nitrification, denitrification, and hexadecane mineralization rates were observed for winter and spring biofilms; fall biofilms had the highest rates of nitrification and hexadecane mineralization, and summer biofilms had the highest rates of denitrification. Very low rates of all measured activities were detected in control biofilms (without nutrient addition) regardless of season. Nutrient addition caused large increases in hexadecane mineralization and denitrification rates but only modest increases, if any, in nitrification rates, depending upon the season. Generally, both alkB and nirK were more readily PCR amplified from nutrient-amended biofilms. Both genes were amplified from all samples except for nirK from the fall control biofilm. It appears that bacterial production in the South Saskatchewan River water is limited by the availability of nutrients and that biofilm activities and composition vary with nutrient availability and time of year.

Biomass and porosity profiles in microbial granules used for aerobic wastewater treatment

AIMS

To obtain biomass and porosity profiles for aerobically grown granules of different diameters and to determine a suitable range of granule diameters for application in wastewater treatment.

METHODS AND RESULTS

Microbial granules were cultivated in an aerobic granulated sludge reactor with model wastewaters containing acetate, or ethanol plus acetate, or glucose as the main carbon source. Granules were formed by retaining microbial aggregates using a settling time of 2 min. Sampled granules had diameters ranging from 0.45 to 3 mm. Microbial biomass in the granules was detected with the nucleic acid stain SYTO 9 and confocal laser scanning microscopy. The thickness of the microbial biomass layer was proportional to the granule diameter, and had a maximum value of 0.8 mm. The thickness of the microbial biomass layer correlated with the penetration depth of 0.1 microm fluorescent beads into the granule.

CONCLUSIONS

The microbial biomass and porosity studies suggest that aerobically grown microbial granules should have diameters less than a critical diameter of 0.5 mm, if deployed for wastewater treatment applications. This critical diameter is based on the assumption that whole granules should have a porous biomass-filled matrix.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work could contribute to the development of aerobic granulation technology for effective biological wastewater treatment.