Biodegradation of priority soil and water contaminants, including halogenated organics and benzene

Toxic compounds such as heavy metals, industrial solvents, dry cleaning liquids and pesticides are some of the most common and persistent soil and groundwater contaminants in the world, a dangerous legacy of negligent use and disposal in the past.  Removing these contaminants from the environment is a high priority to ensure access to clean drinking water.

One relatively new approach to this problem is to harness the natural ability of microorganisms to transform these chemicals, a technique known as bioremediation.  This method was successfully used by members of the BEEM research team who developed a microbial consortium called KB-1® that has been deployed at over 200 sites around the world to treat chlorinated solvents contamination.  The process of KB-1's development serves as a model for the BEEM project.

Some contaminated sites harbour microbes with the natural inherent ability to degrade the pollutant compounds.  BEEM researchers use soil and groundwater samples from these sites to create microcosms in the lab in which the microbial degradation of the compounds can be monitored using standard wet chemistry and chromatographic techniques.  When the desired activity is observed, more contaminant is added to the microcosms to encourage the growth of relevant microbial species.  Over time, the culture becomes enriched in the microbes responsible for this highly desirable activity.  Cultures can then be sequentially transferred to sterile synthetic media and fed regularly with the compound(s) of interest to further stimulate the growth of the desired microbes.

Many simultaneous microcosms will be created using samples from promising field sites to increase the chances of success.  The most promising enrichment cultures will have their metagenome and metatranscriptome sequenced to obtain a system level understanding of community function.  Computational analysis of the metagenome, transcriptome and enzyme activity data generated from the enriched cultures can then identify underlying biochemical pathways.

Once a useful and reliable culture has been developed, its biodegradation process will be optimized and scaled up for application in the field.

The BEEM project focuses particularly on anaerobic microbial processes, those that do not require the presence of oxygen.  Anaerobic (oxygen-free) conditions exist in many environments, including subsurface contaminated sites.  However, anaerobes are less frequently studied in the lab for practical rasons.  Working with them requires specialized equipment and patience, as their growth rates tend to be slower than those of aerobes.  The BEEM team has particular expertise and equipment for this purpose.  Because many anaerobes cannot be isolated due to syntrophic relationships with other microbes, members of the BEEM team have developed molecular techniques to unravel these complex, mixed communities.


Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Chan, W. Y., Wong, M., Guthrie, J., Savchenko, A. V., Yakunin, A. F., Pai, E. F., and E. A. Edwards
Chloroform respiration to dichloromethane by a Dehalobacter population. Grostern, A., Duhamel, M., Dworatzek, S., and E. A. Edwards
Effects of Elevated Temperature on Dehalococcoides Dechlorination Performance and DNA and RNA Biomarker Abundance Fletcher, K.E., Costanza, J., Cruz-Garcia, C., Ramaswamy, N.S., Pennell, P.D., and F.E. Loeffler
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. McMurdie, P. J., Behrens, S. F., Mueller, J. A., Goeke, J., Ritalahti, K. M., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S., Loeffler, F. E., and A. M. Spormann
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., and D. R. Lovley
Groundwater sampling for nucleic acid biomarkers Ritalahti, K.M, Hatt, J.K., Petrovskis, E., and F.E. Loeffler
RNA Extraction and cDNA Analysis for Quantitative Assessment of Biomarker Transcripts in Groundwater Ritalahti, K.M., Cruz-Garcia, C., Padilla-Crespo, E., Hatt, J.K., and F.E. Loeffler
Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae Wagner, D.D., Hug, L.A., Hatt, J.K., Spitsmiller, M.A., Padilla-Crespo, E., Ritalahti, K.M., Edwards, E.A., Konstantinidis, K.T., and F.E. Loeffler
Dehalococcoides and Reductive Dechlorination of Chlorinated Solvents Loeffler, F.E., Ritalahti, K.M., and S.H. Zinder