Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storage

Low Turnover of Soil Bacterial rRNA at Low Temperatures

Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with ¹⁴C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.

Quantifying in situ growth rate of a filamentous bacterial species in activated sludge using rRNA:rDNA ratio

If the in situ growth rate of filamentous bacteria in activated sludge can be quantified, researchers can more accurately assess the effect of operating conditions on the growth of filaments and improve the mathematical modeling of filamentous bulking. We developed a method to quantify the in situ specific growth rate of Sphaerotilus natans (a model filament) in activated sludge using the species-specific 16S rRNA:rDNA ratio. Primers targeting the 16S rRNA of S. natans were designed, and real-time PCR and RT-PCR were used to quantify DNA and RNA levels of S. natans, respectively. A positive linear relationship was found between the rRNA:rDNA ratio (from 440 to 4500) and the specific growth rate of S. natans (from 0.036 to 0.172 h^-1) using chemostat experiments. The in situ growth rates of S. natans in activated sludge samples from three water reclamation facilities were quantified, illustrating how the approach can be applied in a complex environment such as activated sludge.

Challenges in determining causation in structure-function studies using molecular biological techniques

The use of molecular biological techniques for determining the levels and types of different microbial populations in bioreactors has led to the emergence of the microbial community 'structure-function' paradigm that is often used in research. Typically, lab- or full-scale systems are monitored for the relevant parameters, and these parameters are related to the changes in microbial populations. Research in activated sludge phenomena, such as filamentous bulking, filamentous foaming, nitrogen removal, and phosphorus removal, are replete with many examples of this 'structure-function' paradigm, most commonly those that involve 16S rRNA gene-based analysis of the microbial populations. In many cases, such studies assume a causal microbial population (e.g., a species that causes bulking or foaming), or conclude in identifying a causal population. However, assigning cause to specific organisms and populations is problematic in a complex environment such as wastewater bioreactors. The Koch-Henle postulates, the gold standard in evaluating causation of disease, have limitations when applied to systems with mixed microbial communities with complex interactions, particularly if pure cultures are not available. Molecular techniques that allow specific identification and quantification of organisms have been used by researchers to overcome the limitations of culture-based techniques, and at the same time, raised new questions on the applicability of causation postulates in environmental systems. In this paper, various causation criteria improving on the Koch-Henle postulates are presented. Complicating issues in assigning cause in wastewater bioreactors are identified. Approaches for determining cause-effect relationships are illustrated using 16S rDNA-based investigations of filaments that cause bulking and foaming in activated sludge. The hope is that a causation framework that accounts for the assumptions in molecular studies, as applied to wastewater treatment research, will lead to improved experimental design and analysis of data.

Comparative evaluation of the microbial community in biological processes treating industrial and domestic wastewaters

AIMS

Comparison of the microbial composition and process performance between laboratory scale processes treating domestic and vegetable oil wastewaters.

METHODS AND RESULTS

Two laboratory scale modified Ludzack-Ettinger processes were operated under similar operating conditions. One process was fed domestic wastewater and the other an industrial wastewater, vegetable oil effluent. Nitrogen removal capacities of the processes were similar. The industrial process exhibited a lower COD removal capacity and oxygen utilization rate, although a greater mixed liquor volatile suspended solids concentration was observed in the industrial process. Fluorescent in situ hybridization (FISH) with probes EUBmix, ALF1b, BET42a, GAM42a and HGC69a revealed that 81% and 72% of total cells stained with 4', 6-diamidino-2-phenylindole (DAPI) within the domestic and industrial processes respectively bound to EUBmix. This indicated a slightly lower Eubacterial population within the industrial process. The alpha-proteobacteria was the dominant community in the industrial process (31% of EUBmix), while the beta-proteobacteria dominated the domestic process (33% of EUBmix).

CONCLUSIONS

The findings served to establish a difference in the microbial population between the processes. Therefore, the class alpha-proteobacteria could play a primary role in the degradation of vegetable oil effluent.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research will aid in process design and retrofitting of biological processes treating vegetable oil effluent.