BEEM -- Bioproducts + Enzymes from Environmental Metagenomes

Funding for the BEEM project ended in June 2015.

Project wrap-up summary

The goals of this project were to identify and harness the powers of naturally-occurring microbes and the enzyme catalysts within to develop processes that minimize energy and environmental impacts of industrial processes. For example, we looked for microbes and enzymes that transform low value waste materials into higher value products, or that can degrade and detoxify contaminants in our lands and waters.  


BEEM researchers, leveraging important collaborative efforts in the U.S. and in the E.U., have made high profile contributions that have clearly strengthened Canada’s global leadership position in environmental science and engineering and biotechnology.  BEEM researchers published over 90 peer-reviewed journal articles over the past 5 years, plus 6 book chapters or technical reports.  Ten master’s students and 6 PhD students graduated whose work was completely carried out under BEEM.  The four BEEM annual conferences stimulated active discussions while sharing and debating results and next steps, and the BEEM team was guided by a very engaged and forward-thinking Science Advisory Board.


Some of the most exciting results from BEEM include the discovery of novel microbes that can actually breathe toxic compounds like chloroform, or break down recalcitrant molecules found in wood and grasses. Many industrial sites are contaminated with solvents like chloroform, and the knowledge that certain bacteria can clean up this pollutant is already having an impact on remediation design and performance.   The organisms degrading lignocellulose wastes are contributing to new ways to recycle biomass into new products.


A large part of the project involved identifying novel ways to search for enzymes with useful catalytic properties. This research has already resulted in two new biotech start-ups driven by  our students and postdocs.  For example, we were able to identify enzymes that break bonds very effectively even at cold temperatures.  Interestingly, these enzymes often were found in the microbes that live in the deep cold ocean.  Two of these enzymes were found to be particularly good at degrading polylactic acid or PLA into its constituent parts. PLA is a plastic that can be made from renewable sources, and therefore is a great option to replace petrochemically-derived plastics, especially if it could be recycled easily as well.  The idea is so compelling that it is forming the basis of a commercial start-up called ZYMOMATICA to develop the technology.  Another start-up, ARDRA is just getting under way to use some of the many newly discovered enzymes to make chemical building blocks from renewable sources, again to displace fossil-fuel derived chemicals.


BEEM researchers have also founded Savant Technical Consultants Ltd. to provide Life Cycle Analysis of bioprocesses and expert advice to navigate biotechnological regulations in Canada.  This company is an outcome of GE3LSresearch into how policies and regulations, as well as technical constraints affect commercial outcomes and process viability. Savant has grown its business steadily since 2013.


Finally BEEM is not really over, as the most exciting projects will continue with new funding from an NSERC Strategic Network Grant on Industrial Biocatalysis (>$5M over 5 years), awarded in June 2014 and by researchers at BioZone.


Specific Project Outcomes:

  1. More than 90 publications, 6 book chapters, at least 10 Master’s theses and 6 PhD theses were produced during BEEM. 
  2. Novel microbial cultures that degrade chloroform (solvent), lindane & chlordecone (pesticides), lignocellulosic wastes & poplar hydrolysate (forest products), and their associated metagenomes;
  3. An array of enzyme and functional metagenome screens, several based on solid real substrates such as whole wood and ground plastic
  4. Hundreds of active enzymes (>788), many further characterized biochemically and structurally (see Table 1 for summary);
  5. Novel pathways to generate speciality and commodity chemicals, and enzymes screens to identify missing steps;
  6. Genome-scale metabolic models of individual anaerobes, as well as for defined microbial consortia
  7. Life Cycle Analysis (Cradle-to-Grave Economic, Environmental, and Technical Assessment) of processes such as Anaerobic Digestion and Bioethanol. 
Table 1:  Summary of types and numbers of enzymes identified and characterized from genomes and metagenomes (Total = 788 enzymes)

Enzyme Class Number to June_2015 Enzyme Class Number to June_2015
Aldo-keto reductases 32 Kinases 29
Beta-lactamases 4 Nucleases 76
Cellulases 71 Oxidases 20
Dehalogenases 20 Phosphatases 164
Dehydrogenases 36 Phosphodiesterases 40
Enoate reductases 26 Proteases 9
Esterases 182 Thioesterases 16
Glutaminases 4 Other enzymes 59