Tae Gwan Kim

Effects of water temperature and backwashing on bacterial population and community in a biological activated carbon process at a water treatment plant

Bacterial community dynamics was examined in an actual biological activated carbon (BAC) process for four consecutive seasons, using quantitative polymerase chain reaction and pyrosequencing. The BAC stably removed organic carbons for the period, although the water temperature substantially varied over the study period. Neither the population density nor community organization was correlated with time and temperature. However, the similarity degree between communities significantly reduced with time and temperature differences. Community analyses indicated that the community evolved over time, resulting in four distinct groups, and that the abundances of particular bacteria were significantly correlated with time and temperature, as well as their interaction. Additionally, backwashing did not affect the BAC bacterial population, community organization (diversity, evenness, and richness), or composition, although backwashing dislodged a large number of bacteria from the BAC (≈1015 · m−3). These results suggest that water temperature is an important factor driving community dynamics and that backwashing is a harmless management option for biomass control.

Isolation and characterization of a facultative methanotroph degrading malodor-causing volatile sulfur compounds

Simultaneous removal of methane and malodor-causing volatile sulfur compounds (MVSCs), both emitted from landfills, is a desirable characteristic for methane-mitigation approaches. A methanotrophic bacterium was isolated from a microbial consortium, enriched with methane and dimethyl sulfide (DMS). It grew in the complex nutrient medium R2A without methane, and stably exhibited methanotrophic activity after facultative growth. It was identified as Sphingopyxis sp. MD2 by comparison of the 16S rRNA gene. It belongs to Sphingomonadales, whose members have not shown methanotrophic activity, phylogenetically distinct from orders of known methanotrophs. The MD2 biomass increased at a growth rate of 1.18d(-1) when methane was used as the sole growth substrate. An inhibition test with allylthiourea and PCR/sequencing confirmed the presence of particulate methane monooxygenase in MD2. DMS decreased the methane oxidation rate (2634±146 μmole g DCW(-1) h(-1)) by 12%, while H(2)S had no effect on the methane oxidation rate. Interestingly, methanethiol (MT) enhanced the methane oxidation rate by more than 50%. MD2 degraded H(2)S and MT, regardless of the presence of methane. MD2 also degraded DMS in the presence of methane, indicating co-metabolism. These combined results indicate that MD2 may be a promising biological resource for simultaneous removal of methane and MVSCs.

Comparison of droplet digital PCR and quantitative real-time PCR in mcrA-based methanogen community analysis

Two different quantitative PCR platforms, droplet digital PCR (dd-PCR) and quantitative real-time PCR (qPCR), were compared in a mcrA-based methanogen community assay that quantifies ten methanogen sub-groups. Both technologies exhibited similar PCR efficiencies over at least four orders of magnitude and the same lower limits of detection (8 copies μL-DNA extract−1). The mcrA-based methanogen communities in three full-scale anaerobic digesters were examined using the two technologies. dd-PCR detected seven groups from the digesters, while qPCR did five groups, indicating that dd-PCR is more sensitive for DNA quantification. Linear regression showed quantitative agreements between both of the technologies (R2 = 0.59–0.98) in the five groups that were concurrently detected. Principal component analysis from the two datasets consistently indicated a substantial difference in the community composition among the digesters and revealed similar levels of differentiation among the communities. The combined results suggest that dd-PCR is more promising for examining methanogenic archaeal communities in biotechnological processes.

Depth profiles of methane oxidation potentials and methanotrophic community in a lab-scale biocover

The depth profiles of the CH4 oxidation potentials and the methanotrophic community were characterized in a lab-scale soil mixture biocover. The soil mixture samples were collected from the top (0-10cm), middle (10-40cm), and bottom (40-50cm) layers of the biocover where most of methane was oxidized at the top layer due to consumption of O2. Batch tests using serum bottles showed that the middle and bottom samples displayed CH4 oxidation activity under aerobic conditions, and their CH4 oxidation rates were 85 and 71% of the rate of top sample (8.40μmolgdry sample(-1)h(-1)), respectively. The numbers of methanotrophs in the middle and bottom were not significantly different from those in the top sample. There was no statistical difference in the community stability indices (diversity and evenness) among the methanotrophic communities of the three layer samples, even though the community structures were distinguished from each other. Based on microarray analysis, type I and type II methanotrophs were equally present in the top sample, while type I was more dominant than type II in the middle and bottom samples. We suggested that the qualitative difference in the community structures was probably caused by the difference in the depth profiles of the CH4 and O2 concentrations. The results for the CH4 oxidation potential, methanotrophic biomass, and community stability indices in the middle and bottom layer samples indicated that the deeper layer in the methanotrophic biocover serves as a bioresource reservoir for sustainable CH4 mitigation.

Use of artificial DNA with multiple probe sites as reference DNA templates for quantitative real-time PCR to examine methanogen communities

Isolation of reference DNA templates for quantitative real-time PCR assays is an expensive, labor-intensive and time-consuming process if they are not readily available. Two artificial DNA templates with multiple probe sites were designed for quantifying methanogens and their 10 subgroups, based on the methyl coenzyme M reductase gene (mcrA). Their standards were comparable to each other. PCR amplification efficiencies (cycle vs. cumulative fluorescence) of the artificial DNAs were also comparable to those of the observed methanogen groups from anaerobic digesters. The artificial templates can be alternatives to the actual references.

Effects of proton exchange membrane on the performance and microbial community composition of air-cathode microbial fuel cells

This study investigated the effects of proton exchange membranes (PEMs) on performance and microbial community of air-cathode microbial fuel cells (MFCs). Air-cathode MFCs with reactor volume of 1L were constructed in duplicate with or without PEM (designated as ACM-MFC and AC-MFC, respectively) and fed with a mixture of glucose and acetate (1:1, w:w). The maximum power density and coulombic efficiency did not differ between MFCs in the absence or presence of a PEM. However, PEM use adversely affected maximum voltage production and the rate of organic compound removal (p<0.05). Quantitative droplet digital PCR indicated that AC-MFCs had a greater bacterial population than ACM-MFCs (p<0.05). Likewise, ribosomal tag pyrosequencing revealed that the diversity index of bacterial communities was greater for AC-MFCs (p<0.05). Network analysis revealed that the most abundant genus was Enterococcus, which comprised ≥62% of the community and was positively associated with PEM and negatively associated with the rate of chemical oxygen demand (COD) removal (Pearson correlation>0.9 and p<0.05). Geobacter, which is known as an exoelectrogen, was positively associated with maximum power density and negatively associated with PEM. Thus, these results suggest that the absence of PEM favored the growth of Geobacter, a key player for electricity generation in MFC systems. Taken together, these findings demonstrate that MFC systems without PEM are more efficient with respect to power production and COD removal as well as exoelectrogen growth.

Characterization of tobermolite as a bed material for selective growth of methanotrophs in biofiltration

Tobermolite was characterized as a bed material for methanotrophic biofiltration. A lab-scale biofilter packed with tobermolite was operated for different operation times under identical conditions. The three different runs showed similar acclimation patterns of methane oxidation, with methane removal efficiency increasing rapidly for the first few days and peaking within three weeks, after which the efficiency remained stable. The mean methane removal capacities ranged from 766gm(-3)d(-1) to 974gm(-3)d(-1) after acclimation. Pyrosequencing indicated that the methanotrophic proportion (methanotroph/bacteria) increased to 71-94% within three weeks. Type I methanotrophs Methylocaldum and Methylosarcina were dominant during the initial growth period, then Methylocaldum alone dominated the methanotrophic community. A community comparison showed that total bacterial and methanotrophic communities were temporally stable after the initial growth period. Quantitative PCR showed that methanotrophic density increased during the first 3-4 weeks, then remained stable over 120 days. Tobermolite can provide a special habitat for the selective growth of methanotrophs, resulting in rapid acclimation. Tobermolite also allows the microbial community and methanotrophic density to remain stable, resulting in stable methane biofiltration.

Suppression of methanogenesis in hydrogen fermentation by intermittent feeding

This study investigated whether intermittent feeding by using a concentrated carbon source is an appropriate method for selective enrichment of hydrogenesis by means of methanogen suppression. In a conventional reactor fed continuously for 10 d, methanogens increased from 2.8 × 107 to 1.1 × 109 gene copy number (GCN)/mg-cell dry weight, and methane concentration in the resulting biogas was 5.8%. However, when a carbon source was intermittently supplied for 10 d to the reactor, the number of methanogens was reduced 98.9% from 2.77 × 107 to 1.2 × 103 GCN/mg-cell dry weight, and methane was not detected during this period of intermittent feeding. Intermittent feeding shifted the dominants in the reactor from Clostridiaceae (70.5%) and Lactobacillaceae (11.0%) to Acetobacteraceae (62.0%) and Clostridiaceae (38.0%). In the reactor operated in continuous feeding mode after intermittent feeding, methane concentration was below 0.3% and the portion of methanogens in the bacterial community was maintained below 0.2%. These results suggest that the intermittent feeding of a carbon source during hydrogen production processes is a suitable method to suppress the activity of methanogens.

Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters

Droplet digital PCR (ddPCR) is a new DNA quantification platform without an external DNA calibrator. This study examined methanogen communities in four full-scale anaerobic digesters treating municipal sewage sludge, using ddPCR with taxon-specific primer/TaqMan probe sets (5 orders, 11 families, and 13 genera), many of which were developed in this study. Total methanogen abundance was positively correlated with hydraulic retention time (HRT) and temperature (p < 0.05), though the effect of HRT was stronger (r = 0.864 vs. 0.682, respectively). Moreover, total abundance was strongly correlated with biogas production rate (r = 0.896). HRT was positively correlated with seven methanogenic taxa, while temperature was positively or negatively correlated with 13 taxa (p < 0.05). For instance, the predominant genera Methanosaeta and Methanosarcina were negatively and positively associated, respectively, with temperature only (p < 0.05). Redundancy analysis and principal component analysis using the absolute-abundance dataset indicated that only temperature explained the variability in the methanogen communities at all classification levels. Therefore, HRT was the most important operational factor to influence net methanogen abundance and activity, while temperature governed the composition of the methanogen community. ddPCR enabled absolute quantification of methanogens without the external DNA standards and linked methanogen communities and operational factors, suggesting that it is a promising tool for analyzing the microbial ecology of anaerobic digestion.

Isolation and characterization of a novel electricity-producing yeast, Candida sp. IR11.

A novel iron-reducing yeast, Candida sp. IR11, was isolated from an anodic biofilm in a MFC reactor fed glucose as a feedstock. 200-250 mV of voltage was produced in the air-cathode MFC inoculated with a pure culture of the strain IR11 where glucose was supplied as a feedstock. When the strain IR11 was inoculated into a conventional MFC treating rejected wastewater from an upflow anaerobic sludge blanket, maximum power density and coulombic efficiency were enhanced from 15.2 ± 0.36 to 20.6 ± 1.52 mW m(-2) and from 14.4 ± 0.45% to 21.9 ± 0.71%, respectively. In addition, the inoculation with IR11 improved COD removal from 79.1 ± 1.53% to 91.3 ± 5.29%. The quantitative PCR results showed that the strain IR11 successfully attached the anodic biofilm of the MFC reactors. These results indicate that Candida sp. IR11 is a promising biocatalyst for the enhancement of MFC performance.