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Katharine Field
Associate Professor, Microbiology
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RESEARCH:
Research in my laboratory addresses fundamental questions in environmental microbiology and microbial evolution. Projects involve studying the effects of microbial contamination in water, developing markers to track the sources of fecal contamination, tracking the spread of antibiotic resistance genes from fecal bacteria in natural environments, and phylogenetic analysis of coevolution of fecal anaerobic bacteria with vertebrate hosts.
Pathogen contamination and fecal source discrimination. Pathogens and nutrients from fecal pollution impact the integrity of aquatic ecosystems, pose health risks and affect both recreational and fisheries use of the waters. Often the source of fecal contamination in water cannot be determined. My lab developed a PCR-based indicator system utilizing 16S rDNA markers from the Bacteroidales group of fecal anaerobic bacteria, to rapidly detect fecal contamination and identify its source(s). Real-time quantitative PCR allows us to quantify these markers. Our current research focus is on understanding the survival and spread of, and correlation among, fecal pathogens, anaerobes, and public health indicators in natural waters. By labeling fecal bacteria with BrdU, a thymidine analog, we can follow their persistence and survival in a culture-independent manner. We have also measured the co-occurrence of Bacteroidales source-specific fecal markers with particular pathogens such as E. coli O157:H7, Salmonella, and Campylobacter. We show that the addition of source-tracking data not only strengthens hypotheses about sources of pathogens in water (for example, E. coli O157:H7 comes from ruminant sources), but also provides a better estimate of human health risks from contaminated water.
Bacteroidales and the spread of antibiotic resistance in water. Bacteroidales bacteria bear conjugative transposons with genes for antibiotic resistance, such as tetQ for tetracycline resistance. These can be transferred via conjugation to even distantly-related groups of bacteria. We showed that these anaerobic gut bacteria conjugate and transfer antibiotic resistance under environmental conditions in cold aerobic seawater, when oysters are present to facilitate contact. In addition, we have also found that many different species of wild animals in Oregon (e.g. coyote, deer, fox) carry either a human or ruminant-type tetQ. A likely source is from fecally-contaminated water; an alternate hypothesis is that the gene occurs naturally in vertebrates. Current experiments in the lab aim to distinguish these hypotheses. We can identify tetQ from Oregon water samples. We are comparing occurrence of tetQ in coyote fecal samples from Oregon and Alaska; we are performing phylogenetic analyses of tetQ gene sequences from these sources
Coevolution of Bacteroidales with host species. The concept of “endemism” is usually applied to macroorganisms. Commensal bacteria may be the best models for endemic distribution among microorganisms. We have found strong evidence that Bacteroidales group has coevolved with host organisms; related host groups (animal species, for example) harbor related commensals. However, there is equally strong evidence pointing to horizontal transfer among hosts. We observed that humans from an isolated Alaskan village don't have some of the Bacteroidales groups that are widespread in the US and Europe. We are currently studying fecal Bacteroidales from the isolated population of humans. Future goals are to use comparative genomes approaches to characterize new groups of Bacteroidales bacteria from animals and humans, to cast light on their biochemical roles and evolution.
Importance of research. Our techniques have been successfully applied for rapid assessment of microbial water quality, and for microbial source tracking, in the United States and elsewhere. In addition, the Bacteroidales system is an excellent model for bacterial evolution by horizontal gene transfer versus adaptation, contributing to a fundamental understanding of the way bacteria evolve.