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UC Davis

Stefan’s group extends to UC Davis in California where he continues to collaborate with former colleagues in several projects that are centered around the topic of pathogen detection by molecular methods, in the context of risk assessment. The key researcher is Dr. Minji Kim who coordinates all activities.



With Dr. Karen Shapiro (PI) and others

Simultaneous Detection, Viability Discrimination, and Quantitative Risk Assessment of Shellfish-Borne Protozoan Pathogens.



Protozoan pathogens are microscopic parasites that can contaminate shellfish from overland runoff carrying fecal pollution from land to sea. Despite widespread contamination of shellfish with protozoan parasites, their importance as causes of illness in seafood consumers has been understudied. This project targets four protozoans identified as neglected pathogens in the context of seafood safety: Cryptosporidium, Giardia, Cyclospora, and Toxoplasma. The overall goal of this project is to validate novel molecular methods for i) efficient screening of shellfish using multiplex PCR to simultaneously identify these four parasites; and ii) discrimination of viable parasites that can cause illness from dead organisms that are detectable but no longer infectious using real-time PCR assays. We additionally aim to quantify the risk of contracting protozoan-borne disease from consumption of oysters using quantitative microbial risk assessment, and identify key steps within the shellfish production chain where intervention strategies can most effectively reduce this risk.




With Prof. Mike Kleeman (PI) and others

Evaluation and Identification of Constituents Found in Common Carrier Pipeline Natural Gas, Biogas and Upgraded Biomethane in California

California Air Resources Board Transportation and Toxics Division


Background:  Renewable energy sources are essential in California for reaching state goals for reducing greenhouse gas emissions.  Biogas is a source of renewable energy with great potential in California.  Biogas is produced by converting organic waste materials into a gaseous mixture of carbon dioxide and methane. Biogas can be used directly to produce electricity or it can be cleaned and upgraded to biomethane by removing carbon dioxide and other impurities so that it can potentially be used in all applications that currently use natural gas. Despite the great potential for biogas in California, the widespread adoption of any new fuel in the state must consider air quality implications and unintended outcomes for public health and infrastructure.  The first step in this process is the thorough characterization of biogas and upgraded biomethane produced by a variety of feedstocks and anaerobic digester approaches.


Methods: A comprehensive set of measurements was conducted for 10 different biogas / biomethane sample streams (each consisting of three different individual samples).  Sample streams were derived from 5 different production sources: two food waste digesters, two dairy farms, and one landfill.  The two food waste digesters had similar designs but used different feedstocks resulting in different biogas composition.  The two farms used different digester designs with one site using technology typical in California and the other site using technology typical in Europe.  The landfill had two different gas streams representing an older section and a newer section, effectively characterizing differences in landfills with different ages.


Results (biologicals):

Bacteria were less commonly detected in California biogas than in previous measurements made using biogas outside of California.  When cultivable bacteria were detected in Calfiornia biogas, the concentrations were generally comparable to previous measurements.  Acid forming bacteria and iron oxidizing bacteria were detected in raw biogas from agricultural digesters but not in most upgraded biomethane samples.


The concentrations of 16S rRNA gene copies of total bacteria in biogas and upgraded biomethane were below detection limits in about 90% of samples tested. The results from the genetic quantification of the filter and condensate samples indicate how many bacteria, either live or dead, have been aerosolized from anaerobic digestion and remained in the raw bioga stream. Few studies are currently available for quantifying the microbial composition of biogas using molecular methods. In the present study, the total bacteria concentration detected in biogas was approximately 104 gene copies per m3. Given that our detection limits were as low as 2 – 5 x103 gene copies per m3, it is not likely that the total bacteria gene copies were not detected due to the selected qPCR assay. Therefore, we demonstrated that total bacteria gene copy numbers found in the biogas and upgraded biomethane samples in the current study had 1-2 orders of magnitude lower concentrations than in the previously reported data.


Conclusions:  The composition of biogas and upgraded biomethane produced in California depends on the feedstock and the design of the anaerobic digester.  The upgrading process itself can also influence the trace composition of the gas by introducing alkanes.  The tests conducted to date suggest several mitigation strategies and/or best practices for management of feedstock, design of digesters, and strategies for upgrading biogas to biomethane in California.

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