16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥ 1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Fouling in membrane bioreactors used in wastewater treatment

Physico-chemical treatment techniques for wastewater laden with heavy metals

Recent advances in membrane bioreactors (MBRs): membrane fouling and membrane material.

We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.

Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA

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.

Culture-Based MEMS Device to Track Gordonia in Activated Sludge

Respirometric evaluation of side-stream treatment of reject water as a source of nitrifying bacteria for main-stream activated sludge bioreactors

Teaching biology to engineers is a challenge. For environmental engineers, biological principles are necessary to understand microorganisms that are removed from drinking water as well as microorganisms that treat waste in sewage treatment plants and bioremediation field sites. At the University of Cincinnati, we integrated state-of-the-art research in environmental microbiology within our graduate and undergraduate environmental engineering curricula. For the past three years, we taught a novel course entitled, Molecular Biology in Environmental Engineering. Course evaluations over the past three years suggested that the course was successful for primarily two reasons, namely: (1) the course employed a problem-based learning approach to underlie all learning activities; and (2) experiments were conducted by student teams facilitating interpersonal communication as a primary means of learning from peers. This paper outlines the specific experimental procedures employed in the laboratory, as well as evaluates the results of student input from assessment tools including: one-on-one interviews with the instructor; anonymous student surveys; group interviews with an independent third party; and follow-up surveys conducted with graduates of the course. The results from our three-year pilot study suggest that the approaches followed in this course could be adapted to introduce engineering students to advanced research topics from many fields of fundamental science. Teaching Biology to Engineers at the University of Cincinnati. Biology has become a pervasive science; underlying many of the societal questions of the early 21 century including the threat of bioterrorism and the ethical dilemmas associated with cloning of human beings. As technologically proficient scholars, all engineers need to be trained to understand the basic tenants of biology. In a more advanced manner, environmental engineering students need to understand the microbiology of public health as well as the capabilities of microorganisms to degrade environmental pollutants. At the University of Cincinnati, we have developed a new course entitled, Molecular Biology in Environmental Engineering. This course serves as a capstone in a series of four courses that introduce engineers to biology. During the third year of a five-year undergraduate B.S. program, all civil engineering students at the University of Cincinnati are required to enroll in Introduction to Environmental Engineering. In this course, all of our students are first introduced to biological waste treatment and public health microbiology. The first exposure of students to biology occurs in a lecturediscussion format with assigned readings from the required textbook. The primary emphasis of P ge 821.1 Proceedings of the 2003 American Society for Engineering Education Annual Conference & Exposition Copyright  2003, American Society for Engineering Education this course is providing an overview of biology as it relates to engineering and helping to link high school biology with college-level biology. We have found that many engineering students in our program have not participated in a biology course since their sophomore or junior year in high school. Thus, although our ABET accredited program provides adequate emphasis on chemistry, physics, and mathematics, we find that our students lack an appreciation for and an understanding of the basic tenants of biology. For example, most students cannot define biology beyond the study of life, and we spend a significant portion of class time developing a definition of life. The condition of biology education for engineers at the University of Cincinnati may not be unique. Engineering students often do not have sufficient exposure to college-level biology, and engineering programs across the country need to reevaluate the emphasis placed upon chemistry and physics as part of ABET accreditation. Perhaps the time has come to encourage the study of biology to a degree equivalent to our current emphasis on chemistry and physics. The second course in our four-course series is offered to seniors in civil engineering who have elected to concentrate in environmental engineering. This course is entitled, Chemistry and Microbiology of Environmental Systems, and the primary objectives include introducing seniors to the biology of activated sludge sewage treatment including advanced topics related to biological nutrient removal. This course is intended to provide students interested in environmental engineering with sufficient background to excel in graduate work in environmental engineering. Accompanying the lectures for this course, students also participate in a term-long lab course. For two weeks during the lab course, pairs of students meet daily with a graduate student teaching assistant to perform maintenance, sampling, and analysis of pilotscale activated sludge systems. Also, the students tour a full-scale municipal activated sludge sewage treatment plant, and complete a two-week, extended homework assignment that requires the development of a preliminary design for an industrial activated sludge sewage treatment system. Thus, Chemistry and Microbiology of Environmental Systems provides our seniors opting for a concentration in environmental engineering with an opportunity to experience extensive hands-on activities in biology and engineering design related to biology. Two additional courses are offered each year as split-level and include both seniors as well as graduate students in environmental engineering. The first of these courses is Biological and Microbiological Principles of Environmental Systems. Following a lecture-discussion format, this course is intended to provide a broad-based overview of the biology and microbiology of environmental engineering including agents of infectious disease and specific microorganisms that are known to degrade pollutants. Significant emphasis is placed upon providing a basic understanding of the biochemistry and physiology of microorganisms. We have found that seniors from our program are well equipped to participate in this course because of the background they have received from our previous two courses covering biology. Typically, first year M.S. students represent the largest portion of students in this course. The M.S. students are taking this biology course concurrent with a graduate-level design course for biological treatment systems (e.g., the design of sewage treatment works). Most of our graduate students fit the model of typical civil engineering education as discussed briefly above. Therefore, this course often represents the first exposure of our graduate students to biology since high school. P ge 821.2 Proceedings of the 2003 American Society for Engineering Education Annual Conference & Exposition Copyright  2003, American Society for Engineering Education The final course in our four-course series is entitled, Molecular Biology in Environmental Engineering, and this course is the focus of this paper. Molecular Biology in Environmental Engineering is primarily a hands-on laboratory course that provides students with an opportunity to conduct a term-long experiment as part of a problem-based learning approach. Although the original intent of this split-level course was to provide a capstone experience in biology for seniors and graduate students in the department of civil and environmental engineering, we have found that many additional students opt to take advantage of this course. During the first three years of this course, participants have included students from civil and environmental engineering as well as the depart of chemical engineering and the department of electrical engineering from the College of Engineering, the department of environmental health and the department of molecular genetics from the College of Medicine, and the department of biological sciences from the College of Arts and Sciences. Enrollment in the first offering of our course was exclusively the intended target audience, namely civil and environmental engineering students, but enrollment in each subsequent offering has grown to include a cross-disciplinary pool of students. One reason for this increase in the breadth of enrollment is that students are drawn to the opportunity for a hands-on laboratory experience to learn about molecular biology as it can be applied to solve problems in a particular field, namely environmental engineering. Thus, we have found that providing an opportunity for hands-on laboratory work coupled with a problem-based learning approach is an effective strategy to attract crossdisciplinary participation in courses. An Introduction to Molecular Biology in Environmental Engineering and Science. Molecular biology refers to the science of studying molecules within and extracted from living systems. The primary classes of molecules that are of interest to environmental engineers include carbohydrates, lipids, proteins, and nucleic acid. Environmental engineers study carbohydrates and lipids because these molecules provide information about the physiology of microbial populations in bioreactors and bioremediation field sites. The study of proteins provides information about the biocatalytic properties of microbial populations, and nucleic acids provide a means of determining both the potential for biocatalytic capacity as well as the identity of specific microbial populations. Recently, studies of nucleic acids have been used extensively to document the identity of microbial populations in various environmental samples including soil, sewage sludge, and drinking water. This increased interest in molecular biology procedures targeting nucleic acid has been driven primarily by the interest of researchers to positively identify microbial populations. Before the development of nucleic acid-based microbial identification, the primary means of identifying microorganism

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Integrating Biological Principles in Environmental Engineering Education: Summary Results of a Three-Year Pilot Study

A population health perspective on America’s opioid addiction:

https://ascelibrary.org/doi/pdf/10.1061/%28ASCE%29EE.1943-7870.0001939

Daniel B. Oerther

Papers

Culture-Based MEMS Device to Track Gordonia in Activated Sludge

Respirometric evaluation of side-stream treatment of reject water as a source of nitrifying bacteria for main-stream activated sludge bioreactors

Integrating Biological Principles in Environmental Engineering Education: Summary Results of a Three-Year Pilot Study

A population health perspective on America’s opioid addiction:

Improved Health Diplomacy is Necessary for Resilience after COVID-19