Microbial Diversity Of Biofilms Research Articles

Effect of Particle Concentration and Pipe Materials on the Formation of Biofilms in Drinking Water Distribution Systems

Microorganism rebreeding and biofilm shedding enter the water body in the process of a drinking water distribution system (DWDS), which poses a threat to public health. Particles in water can gather pollutants as well as providing favorable growth conditions for bacteria. To date, there are a few studies which focus on the relationship between particles and biofilm formation. Therefore, the microbial diversity of biofilms in the different pipe materials and the effect on particle concentration on biofilm formation were investigated in this study. Experiments were carried out under a simulative DWDS (including iron (DI) and polyvinyl chloride (PVC) pipe). The results showed that the microbial diversity in biofilms followed this order: DI pipe > PVC pipe > DI pipe (upper). Moreover, the microbial biomass of biofilm and the fluorescence intensity of extracellular polymeric substances (EPS, produced by microorganisms) were the largest in the absence of particles. The amount of biofilm bacterial and the fluorescence intensity of EPS both showed first an increasing and then decreasing trend with particle concentration increasing. When particle concentration was relatively low, the absorption of particles and bacteria played a major role, however, with the increasing particle concentration, more stable particle–particle were formed and thus, EPS was easily extracted, resulting in the increase of fluorescence intensity of EPS.

Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW)

In this study, integrated fixed-film activated sludge (IFAS) microbial development and degradation efficiency were investigated for oil sands process-affected water (OSPW) remediation. IFAS microbial community was characterized using 454 high-throughput 16S rRNA gene pyrosequencing that revealed that the IFAS seed sludge (activated sludge [AS] from the Gold Bar Wastewater Treatment Plant [GBWTP]) showed the greatest richness and evenness of bacterial community, as compare to other biomass samples. The Chao 1 value and the Shannon diversity index showed that the bacterial richness and microbial diversity in biofilms were significantly higher than those in flocs in both IFAS systems. Proteobacteria, Nitrospirae, Acidobacteria, and Bacteroidetes were dominant phyla in both flocs and biofilms in IFAS reactors. It is also noted that the phyla and class distributions of flocs and biofilms were significantly different. Principal coordinate analysis (PCoA) indicated that there were substantial differences between OSPW indigenous microbes and flocs and biofilm microbes in IFAS. Overall, a relatively low ozone dose (30mg/L utilized) combined with IFAS reactor treatment significantly increased the organic contaminants removal. The combined ozonation and IFAS system showed the promise for OSPW treatment.

Structure and microbial diversity of biofilms on different pipe materials of a model drinking water distribution systems.

The experiment was conducted in three model drinking water distribution systems (DWDSs) made of unplasticized polyvinyl chloride (PVC), silane cross-linked polyethylene (PEX) and high density polyethylene (HDPE) pipes to which tap water was introduced. After 2 years of system operation, microbial communities in the DWDSs were characterized with scanning electron microscopy, heterotrophic plate count, and denaturing gradient gel electrophoresis. The most extensive biofilms were found in HDPE pipes where bacteria were either attached to mineral deposits or immersed in exopolymers. On PEX surfaces, bacteria did not form large aggregates; however, they were present in the highest number (1.24 × 107 cells cm−2). PVC biofilm did not contain mineral deposits but was made of single cells with a high abundance of Pseudomonas aeruginosa, which can be harmful to human health. The members of Proteobacteria and Bacteroidetes were found in all biofilms and the water phase. Sphingomonadales and Methylophilaceae bacteria were found only in PEX samples, whereas Geothrix fermentans, which can reduce Fe(III), were identified only in PEX biofilm. The DNA sequences closely related to the members of Alphaproteobacteria were the most characteristic and intense amplicons detected in the HDPE biofilm.

Biogeochemical activity of microbial biofilms in the water column overlying uranium mine tailings

To describe microbial diversity, biofilm composition and biogeochemical potential within biofilms in the water overlying uranium tailings characterized by high pH, high metal concentration and low permeability. To estimate microbial diversity in biofilms formed in water columns overlying uranium mine tailings, culture-dependent and culture-independent methods were employed. High-throughput sequencing revealed the presence of 11 phyla; however, the majority of the sequences were affiliated with four major lineages (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) as confirmed by culture-based methods. Dominant phylotypes were closely related to methylotrophs (Methylobacterium) and bacterial groups able to utilize complex hydrocarbons (Aquabacterium and Dechloromonas). Microbial diversity in biofilms from the 13 m depth was significantly different that in biofilms from 1 to 41 m (P < 0·05). Phylotypes closely related to iron-reducing bacteria were identified at each depth; whereas sulphate-, thio-sulphate-, sulphite- and sulphur-reducing bacteria, at low abundance, were only detected at lower depths. Confocal scanning laser microscopy (CSLM) was used to investigate polymer quantity and composition of the biofilm components, and principal component analysis of the CLSM data revealed that the relative abundance of α-L-fucose and N-acetyl-glucosamine/lipopolysaccharide residues separated tailings-water interface biofilms from those from other depths. Reduced (ferrous) iron was detected within all the biofilm samples examined by scanning X-ray transmission microscopy. Microbial communities within the water column covering a highly alkaline uranium tailings body form biofilms with microenvironments where iron reduction takes place. This study demonstrates the biogeochemical potential of microbial biofilm communities in the water column covering an alkaline uranium tailings body; specifically, the nature of the bacterial groups detected (Aquabacterium, Dechloromonas) and the presence of reduced iron suggest that complex hydrocarbons are available for bacterial growth and geochemical change, such as iron reduction, can occur even though the system bulk phase is predominantly oxic.

Dairy Biofilm: Impact of Microbial Community on Raw Milk Quality

AbstractThe aims of this study were (1) to characterize the dairy biofilm, and (2) to evaluate the impact on the raw milk quality. The ecological profile of biofilm revealed that gram‐positive bacteria and fungi exhibited a significantly higher biofilm organization than gram‐negative (43–64%). From 16S rDNA sequencing, microbial diversity of biofilm was constituted by Lactococcus lactis, Staphylococcus xylosus, Bacilus cereus, Candida albicans. The milk analysis in input and in output of pipelines has revealed that the rate of milk microbial community has increased to attempt 97 to 100%. The investigation of the impact of biofilm on the physicochemical properties of material has showed a decrease of hydrophobicity of stainless steel which become hydrophilic after 7 h of contact (ΔGiwi = 6.62 mJ/m2) and the increase of the electron donor character (γ− = 44.8 mJ/m2). While, after 24 h of contact, results showed a decrease of the hydrophilicity degree and surface energy components of stainless steel that become hydrophobic (ΔGiwi = −56.51 mJ/m2) and lowly electron donor (γ− = 2.3 mJ/m2).Practical ApplicationsDairy biofilm formation on stainless steel was investigated employing thermodynamic approach. The results revealed that the microbial adhesion on substrata was dependent on two factors: materials species and microorganisms community. These findings have important potential in the food process applicability as they suggest that the variation of surface chemistry could contribute to understand the biofilm formation to surface and also favor the protective biofilms approach on industry workshop surfaces that favors the antimicrobial coating of devices makes it simultaneously anti‐adhesive and give it antimicrobial activity.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In particular, culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address these limitations and demonstrate it by specifically targeting bacterial cells within a complex biofilm from a hospital bathroom sink drain. A newly developed, automated platform was used to generate genomic DNA by the multiple displacement amplification (MDA) technique from hundreds of single cells in parallel. MDA reactions were screened and classified by 16S rRNA gene PCR sequence, which revealed a broad range of bacteria covering 25 different genera representing environmental species, human commensals, and opportunistic human pathogens. Here we focus on the recovery of a nearly complete genome representing a novel strain of the periodontal pathogen Porphyromonas gingivalis (P. gingivalis JCVI SC001) using the single-cell assembly tool SPAdes. Single-cell genomics is becoming an accepted method to capture novel genomes, primarily in the marine and soil environments. Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility.

Denitrification performance and microbial diversity in a packed-bed bioreactor using biodegradable polymer as carbon source and biofilm support

A novel kind of biodegradable polymer, i.e., starch/polycaprolactone (SPCL) was prepared and used as carbon source and biofilm support for biological denitrification in a packed-bed bioreactor. The denitrification performances and microbial diversity of biofilm under different operating conditions were investigated. The results showed that the average denitrification rate was 0.64±0.06kgN/(m3d), and NH3–N formation (below 1mg/L) was observed during denitrification. The nitrate removal efficiency at 15°C was only 55.06% of that at 25°C. An initial excess release of DOC could be caused by rapid biodegradation of starch in the surfaces of SPCL granules, then it decreased to 10.08mg/L. The vast majority of species on SPCL biofilm sample (99.71%) belonged to six major phyla: Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Spirochaetes and Actinobacteria. Proteobacteria were the most abundant phylum (85.50%) and mainly consisted of β-proteobacteria (82.39%). Diaphorobacter and Acidovorax constituted 52.75% of the identified genera which were denitrifying bacteria.

Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches.

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm.

Microbial diversity in biofilms on water distribution pipes of different materials

The effects of pipe materials on biofilm formation potential (BFP) and microbial communities in biofilms were analyzed. Pipe coupons made of six different materials (CU, copper; CP, chlorinated poly vinyl chloride; PB, polybutylene; PE, polyethylene; SS, stainless steel; ST, steel coated with zinc) were incubated in drinking water, mixed water (inoculated with 10% (v/v) of river water) and drinking water inoculated with Escherichia coli JM109 (E. coli), respectively. The highest BFPs were observed from steel pipes, SS and ST, while CU showed the lowest BFP values. Of the plastic materials, the BFP of CP in drinking water (96 pg ATP/cm(2)) and mixed water (183 pg ATP/cm(2)) were comparable to those of CU, but the other plastic materials, PB and PE, displayed relatively high BFP. The Number of E. coli in the drinking water inoculated with cultures of E. coli strain showed similar trends with BFP values of the pipe coupons incubated in drinking water and mixed water. Molecular analysis of microbial communities indicated the presence of alpha- and beta-proteobacteria, actinobacteria and bacteroidetes in biofilm on the pipe materials. However, the DGGE profile of bacterial 16S rDNA fragments showed significant differences among different materials, suggesting that the pipe materials affect not only BFP but also microbial diversity. Some plastic materials, such as CP, would be suitable for plumbing, particularly for drinking water distribution pipes, due to its low BFP and little microbial diversity in biofilm.

Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms

Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. Cells throughout anode biofilms of Geobacter sulfurreducens reduced the metabolic stains: 5-cyano-2,3-ditolyl tetrazolium chloride and Redox Green, suggesting metabolic activity throughout the biofilm. To compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, anode biofilms were encased in resin and sectioned into inner (0-20 microm from anode surface) and outer (30-60 microm) fractions. Transcriptional analysis revealed that, at a twofold threshold, 146 genes had significant (P<0.05) differences in transcript abundance between the inner and outer biofilm sections. Only 1 gene, GSU0093, a hypothetical ATP-binding cassette transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting lower metabolic rates. However, differences in transcript abundance were relatively low (<threefold) and the expression of genes for the tricarboxylic acid cycle enzymes was not significantly lower. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of this study suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms.