Taewoo Yi

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.

Novel biodegradation pathways of cyclohexane by Rhodococcus sp. EC1

The metabolism of cyclohexanes by Rodococcus sp. EC1 was investigated using a sequential tracking method of degradation intermediate. Evidence for the formation of cyclohexanol, cyclohexaone, 2-cyclohexen-1-one, and phenol was presented. EC1 metabolized cyclohexane to phenol by aromatization of 2-cyclohexen-1-one, and furthermore gamma-butyrolactone as an intermediate of 2-cyclohexen-1-one was formed. Aromatization by EC1 was confirmed using tetrahydrofuran. Tetrahydrofuran was metabolized through aromatization reaction, involving furan and 2,3-dihydrofuran as key intermediates. EC1 can degrade cyclohexane and tetrahydrofuran in aromatization via desaturation.

Biodegradation of petroleum hydrocarbons by Neosartorya sp. BL4

A new petroleum hydrocarbon-degrading fungus, isolated from an oil contaminant soil, was identified as Neosartorya (teleomorph of Aspergillus) sp. This isolate was able to degrade total petroleum hydrocarbons (TPHs) without a lag phase, but degradation rates decreased with increasing initial TPH concentrations (5,000–20,000 mg L−1). The TPH degradation by the isolate showed a substrate inhibition behavior with an inhibition constant (Ki) of 1,860 mg L−1. Dual lag phase of TPH degradation indicated the ability to adapt its metabolic activity to utilize different types of hydrocarbons as an electron donor. Initially n-alkanes were rapidly removed without lag phase in the whole range of substrate and heavy molecular weight alkanes (HMWAs; C23-C24) and low molecular weight alkanes (LMWAs C9-C15) out of n-alkane hydrocarbons were degraded rapidly, whereas the removal of mid molecular weight alkanes (MMWAs; C16-C22) was relatively slower. Relatively slow degradation of MMWAs is probably caused by biotransformation of HMWAs or non-alkane hydrocarbons to MMWAs.

Fate and behavior of extended-spectrum β-lactamase-producing genes in municipal sewage treatment plants

Extended-spectrum β-lactamases (ESBLs) have the capability of hydrolyzing a variety of the newer β-lactam antibiotics, including the third-generation cephalosporins and monobactams known as a rapidly evolving group of ESBLs. The purpose of this study was to investigate the occurrence and fate of β-lactamase producing genes (CTX-M type 1, type2, CTX-M probe for all groups except CTX-M-1, and TEM, SHV, OXA) through wastewater treatment utilities. β-lactamase producing genes in influent, digested sludge, activated sludge, and disinfected effluent were monitored. The results showed that influent contained high level of all target genes, and all CTX-M types, SHV, and OXA gene decreased significantly in biological treatment process such as activated sludge process and anaerobic digestion, however, TEM type was not effectively eliminated. Possibly, host microbes of TEM could be most resistant in target genes or to some extent gene transfer occurred in wastewater treatment processes. All target genes were significantly reduced during disinfection. Consequently, wastewater treatment process apparently reduced host microbes carrying β-lactamase producing genes effectively, although they are selectively removed in biological processes. In addition, the significant reduction during disinfection was shown, although slightly differences of removal efficiency were observed in resistance.

Effects of granular activated carbon on methane removal performance and methanotrophic community of a lab-scale bioreactor.

Two identical lab-scale bioreactor systems were operated to examine the effects of granular activated carbon (GAC) on methane removal performance and methanotrophic community. Both bioreactor systems removed methane completely at a CH4 loading rate of 71.2 g-CH4·d−1 for 17 days. However, the methane removal efficiency declined to 88% in the bioreactor without GAC, while the bioreactor amended with GAC showed greater methane removal efficiency of 97% at a CH4 loading rate of 107.5 g-CH4·d−1. Although quantitative real-time PCR showed that methanotrophic populations were similar levels of 5–10 × 108 pmoA gene copy number·VSS−1 in both systems, GAC addition changed the methanotrophic community composition of the bioreactor systems. Microarray assay revealed that GAC enhanced the type I methanotrophic genera including Methylobacter, Methylomicrobium, and Methylomonas of the system, which suggests that GAC probably provided a favorable environment for type I methanotrophs. These results indicated that GAC is a promising support material in bioreactor systems for CH4 mitigation.