Richardson lab studies the activities of microbial communities through the study of genomics, transcriptomics and proteomics. While DNA-based techniques still serve as an anchoring point in bioenvironmental engineering, gene presence and characterization only provide insights into potential activity. Instantaneous activity levels are much more tightly tight to RNA and protein (particularly enzymatic proteins). With the wealth of information obtainable by querying RNA and protein pools, it is not only possible to determine whether a particular gene is being expressed under certain conditions, but it is also possible to use the data to develop molecular bioindicators of specific activities in environmental and reactor systems. The main techniques used by the lab are quantitative reverse transcription PCR (qRTPCR) to assay RNA pools and high throughput shotgun proteomics (via tandem mass spectrometry) of whole community peptides. Together these methods provide a wealth of information about the enzymes and other proteins being expressed by individual populations within a consortium of organisms. Additionally, the lab employs flourscence in situ hybridization with 16S rRNA-targeting probes in order to visualize and count specific populations in mixed communities. By applying multiple probes simultaneously, researchers are able to visualize biofloc and biofilm co-localization of different phylogenetic groups.
The main application of these "omics" is the study of consortia containing Dehalococcoides ethenognes - the first organism shown to bioremediate chlorinated ethenes (perchloroethene - PCE - and trichloroethene - TCE) to harmless ethene gas. This work builds on Cornell's expertise in this area which began two decades ago by Professor's James Gossett (CEE) and Stephen Zinder (Microbiology). The key challenges the lab is focused on are honing the list of key bioindicators of dehalorespiration and quantitatively relating net expression levels to bulk activity (in this case net dehalorespiration rates). This line of work is funded in part by the DOE/Westinghouse Savannah River Corporation's Monitored Natural Attenuation/Enhanced Passive Remediation program and in part in collaboration with Professor Stephen Zinder through the Cornell's Biogeochemistry and Biocomplexity Initiative.
A second project underway in the lab is the study of the effects of abiotic factors and biofilm coverage on the leaching of vinyl chloride (VC - which is a known human carcinogen) and organotin stabilizers (OTs - which are on the EPA's candidate contaminant list) from PVC pipe. PVC pipe, for many reasons, is attractive as a material for the replacement of water mains across the nation's aging water supply systems. However, the presence of VC and OTs make it important to determine what levels of these compounds could be expected in drinking water carried by PVC. This project, which is in collaboration with Professor Marc Edwards at Virginia Tech, is funded by the American Water Works Association's Research Foundation.
Richardson Lab group members:
Principal Investigator:
Prof. Ruth Richardson: I am an associate professor with a background in chemical engineering (BS) and environmental engineering. My general research interests are in understanding the behavior and activities of microorganisms in complex communities - and using molecular biological tools to explore these communities. The systems my lab group studies are dechlorinating communities, microbial fuel cells, microbial source tracking, and drinking water biofilms. In Ithaca, I also spend some time playing sports and I enjoy a wide range of music and dance.
Postdocs
Dr. Jeff Werner: I am a postdoctoral associate in the Richardson lab. I am an environmental chemist with a B.S. in chemistry and Ph.D. in water resources science. In general, I'm interested in the mechanisms and kinetics of chemical transformations in environmental systems, including the degradation of pollutants such as pharmaceuticals and chlorinated solvents, as well as reactions that link natural organic matter with local and global nutrient cycles. My current research is focused on using proteomics to monitor the bioremediation of groundwater contaminated with chlorinated ethenes. I also spend some of my time playing the guitar and the tenor banjo, going birding with my wife (who knows much more about birds than I), and breaking my computer and then fixing it again. For more information and CV, follow this link to my website: http://people.cornell.edu/pages/jjw58
Ph.D. students:
Annette Rowe (Microbiology): I received degrees from the University of California Berkeley in 2003, in Molecular and Cellular Biology and Microbial Biology. I am currently a graduate student in the feild of Microbiology, working on microbial interaction in dechlorinating microbial communities. I am working on how to measure and understand microbial competition for electron equivelents in both the dechlorinating community (and microbial fuel cells). In my free time I brew beer, play soccer and guitar.
Gretchen Heavner (Field of Civil & Environmental Engineering): I am a Ph.D. student with a background in chemsitry (BS) and environmental engineering (MS). I am interested in in-situ bioremediation, enhancing natural attenuation, and modeling the fate and transport of contaminants in the environment. More broadly, I want to investigate biological processes for the treatment of hazardous waste, fate and transport of organic contaminants in the environment, and microbiological processes in natural and engineered systems.
Po-Hsun Lin (Field of Civil & Environmental Engineering): I used to work with Prof. Richardson on a PVC project. In that project we tried to find vinyl chloride (VC) and organotin compounds from drinking water which contacts with PVC/CPVC pipes. These two chemicals have the potential to leach out from PVC/CPVC pipes. We also quantified the biofilm growing on the drinking water PVC pipes and explored the effect of different pipe types, pipe ages, and biofilms on VC and organotin leaching. Now I am working with Dr. Weber Shirk on a filtration project in which we used alum or other coagulants to improve the filtration efficiency.
Former Lab Members:
Brian Rahm (Field of Civil & Environmental Engineering): I am a PhD candidate with a background in biology and genetics. In the lab I tinker with the dechlorinating mixed culture, trying to correlate chloroethene respiration with expression of functional mRNA and protein molecules. My other duties include checking my email very, very frequently, often with little to no point, hoping simply to be surprised by something unexpected. I'm also in a band. That's pretty cool.
Rami Zahr (Chemical Engineering): I am a chemical engineer undergraduate pursuing a minor in environmental engineering. My research is determining the source of fecal coliform, indicator bacteria for more pathogenic strains of similar bacteria, in Cayuga Lake using microbial source tracking. I'm specifically using antibiotic resistance analysis and amplified fragment length polymorphism. I enjoy most sports and am very interested in political philosophy.
Michael Gifford (Civil & Environmental Engineering): I am an undergraduate student majoring in Civil Engineering with minors in Environmental Engineering and Engineering Management. My research is focusing on finding the sources of fecal contamination in Cayuga Lake. To decipher what organisms are contaminating the lake we use two techniques of microbial source tracking.
Robert Morris (Postdoc): Now at University of Washington, School of Oceanography, Box 357940, Seattle, WA 98195-7940; phone: (206) 221-7228; e-mail: morrisrm@u.washington.edu
Modeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solvents
Systems Biology of Dehalococcoides: Using Network Inference Modeling to Integrate Omics Datasets Under Varied Conditions
Detection of peptide bioindicators of bioremediation at contaminated field sites.
