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Daniel B Oerther

Publications and source records attributed to Daniel B Oerther.

9 recordsLinked to original sources
PubMed2006

Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene.

We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards.

Animals↗
PubMed2006

Culture-based MEMS device to track Gordonia in activated sludge.

Previously, we reported on the use of microelectromechanical systems (MEMS) fabrication technologies to develop paraffin surfaces for miniaturization of culture-based detection and rapid quantification of Mycolata in environmental samples. In the current study, the novel culture-based biochip was calibrated with a broad range of pure cultures of Mycolata including Gordonia spp. isolated from activated sludge foam. The biochip successfully recovered Gordonia amarae spiked into a sample of mixed liquor collected from a municipal activated sludge system. Comparisons of these results with molecular biology-based assays including 16S rRNA-targeted fluorescence in situ hybridization (FISH) and antibody staining demonstrated that the biochip provides a more rapid and user-friendly platform for reliable identification and quantification of Mycolata in full-scale municipal activated sludge sewage treatment plants. The results of this work successfully demonstrate an alternative platform technology for inexpensive monitoring of environmental microorganisms using existing expertise by potential users in the area of bacterial cultivation.

Calibration↗
PubMed2006

Identifying pioneer bacterial species responsible for biofouling membrane bioreactors.

More effective control of membrane biofouling in membrane bioreactors (MBRs) lies in the fundamental understanding of the pioneer microorganisms responsible for surface colonization that leads to biofilm formation. In this study, the composition of the planktonic and sessile microbial communities inhabiting four laboratory-scale MBR systems were compared using amplified ribosomal DNA restriction analysis (ARDRA) and 16S ribosomal DNA gene sequencing. The ARDRA results suggest that the microbial communities on membrane surfaces could be very different from the ones in the suspended biomass. Phylogenetic analysis based on the 16S rRNA gene sequences provided a list of bacteria that might be the pioneers of surface colonization on microfiltration membranes. The results further suggested that research on the mechanisms of cell attachment in such an engineering environment could be critical for future development of appropriate biofouling control strategies.

Bacteria↗
PubMed2006

16S ribosomal RNA tools identify an unexpected predominance of Paenibacillus-like bacteria in an industrial activated sludge system suffering from poor biosolids separation.

Molecular biology tools targeting 16S ribosomal RNA (16S rRNA) were used to identify a predominant bacterial population in a full-scale dairy wastewater activated sludge system suffering from poor biosolids separation. Gram and acridine orange staining indicated that viable, Gram-positive microorganisms were present in samples removed from the influent waste stream and represented approximately 50% of total cell counts in samples removed from the mixed liquor. Subsequently, the "full-cycle 16S rRNA approach" showed that phylogenetic relatives of Paenibacillus spp., a low guanine-plus-cytosine percent DNA-content, Gram-positive microorganism, represented up to 30% of total 4,6-diamidino-2-phenylindole (DAPI)-stained cell counts in samples of mixed liquor. Although fluorescent in situ hybridizations with 16S rRNA-targeted oligonucleotide hybridization probes identified Paenibacillus-like spp. in samples removed from the influent waste stream, their abundance was less than 10% of total stained cell counts. Results of this study suggest that Paenibacillus-like spp. were present in low abundance in the influent waste stream, increased in relative abundance within the treatment system, and should be examined further as a candidate bacterial population responsible for poor biosolids separation. This study demonstrates that the full-cycle 16S rRNA approach can be used to identify candidate bacterial populations that may be responsible for operational upsets in full-scale activated sludge systems without prior information from cultivation or microscopic analyses.

Bacillaceae↗
PubMed2005

Effect of activated sludge properties and membrane operation conditions on fouling characteristics in membrane bioreactors.

Biofouling control is considered to be a major challenge in operating membrane bioreactors (MBRs) for the treatment of wastewater. This study examined the impact of biological, chemical, and physical properties of activated sludge on membrane filtration performance in laboratory-scale MBRs. Sludges with different microbial communities were produced using pseudo-continuous stirred-tank reactors and pseudo-plug flow reactors treating a synthetic paper mill wastewater. Various filtration resistances were used to investigate membrane fouling characteristics, and molecular biology tools targeting 16S ribosomal DNA gene sequences were used to identify predominant bacterial populations in the sludges or attached to the fouled membranes. Filtration experiments using axenic cultures of Escherichia coli, Acinetobacter calcoaceticus, and Gordonia amarae were also performed to better understand the initiation and development of biofouling. The results showed that the tendency of membranes to biofoul depended upon membrane operating conditions as well as the properties of the activated sludge in the MBR systems. Specific bacterial populations, which were not dominant in the activated sludges, were selectively accumulated on the membrane surface leading to the development of irreversible biofouling.

Bacteria↗
PubMed2005

Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge.

Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to investigate the reproducibility and stability in the bacterial community structure of laboratory-scale sequencing batch bioreactors (SBR) and to assess the impact of solids retention time (SRT) on bacterial diversity. Two experiments were performed. In each experiment two sets of replicate SBRs were operated for a periods of three times the SRT. One set was operated at an SRT of 2 days and another set was operated at an SRT of 8 days. Samples for T-RFLP analysis were collected from the two sets of replicate reactors. HhaI, MspI, and RsaI T-RFLP profiles were analyzed using cluster analysis and diversity statistics. Cluster analysis with Ward's method using Jaccard distance and Hellinger distance showed that the bacterial community structure in both sets of reactors from both experimental runs was dynamic and that replicate reactors were clustered together and evolved similarly from startup. Richness (S), evenness (E), the Shannon-Weaver index (H), and the reciprocal of Simpson's index (1/D) were calculated, and the values were compared between the two sets of reactors. Evenness values were higher for reactors operated at an SRT of 2 days. Statistically significant differences in diversity (H and D) between the two sets of reactors were tested using a randomization procedure, and the results showed that reactors from both experimental runs that were operated at an SRT of 2 days had higher diversity (H and D) at the 5% level. T-RFLP analysis with diversity indices proved to be a powerful tool to analyze changes in the bacterial community diversity in response to changes in the operational parameters of activated-sludge systems.

Bacteria↗
PubMed2004

Developing rapid detection of mycobacteria using microwaves.

In this paper, we describe the development of a culture-based biochip device for rapid detection of mycobacteria in environmental samples. Individual biochips rely upon the unique paraffinophilic nature of mycobacteria to rapidly and selectively adhere to the surface of the device. We used prototype biochips to experimentally demonstrate the concept of rapid and selective detection of mycobacteria by testing pure cultures and using epifluorescence microscopy to visualize microorganisms on the surface. As an alternative, rapid approach for identifying the biomass on the biochip surface, we used microwaves in the 10 to 26 GHz frequency range. The results of this study indicate that different microorganisms are responsible for specific shifts in resonance frequencies of a microwave cavity. By combing the semi-selective paraffin surface of the biochip with the microorganism-specific response to the microwaves, we have developed an improved analytical system with the potential to rapidly identify and enumerate mycobacteria in environmental samples in as little as 2 h.

Biosensing Techniques↗
PubMed2004

Bacterial competition in activated sludge: theoretical analysis of varying solids retention times on diversity.

A mechanistic model for activated sludge sewage treatment was developed to predict exploitative competition of six aerobic heterotrophic bacterial species competing for three essential resources. The central hypothesis of the model is that in a multispecies/limiting resource system the number of coexisting bacterial species, N, exceeds the number of limiting resources, K, available for them. The explanation for this is that for certain species combinations, the dynamics of the competition process generate oscillations in the abundances of species, and these oscillations allow the coexistence of greater number of species than the number of limiting resources ( N > K). This result is a direct contradiction of an existing activated sludge steady state competition theory, "the principle of competitive exclusion," which states that the competition process proceeds to equilibrium, allowing only N </= K species to coexist. The model was used to investigate the effect of varying solids retention times on the diversity of species using the conventional, completely mixed activated sludge configuration. The results of model simulations showed that for a certain range of solids retention times (2.28-5.66 days) the competition of six species for three essential resources produces oscillations within the structure of the bacterial community allowing for the sustained growth of more than three species on three resources.

Bacterial Physiological Phenomena↗