Network on Ecogenomics and Ecological Restoration (NEER)
Progress Report on Network-Building
Janet Atkinson-Grosjean,1 Justin Page,2 and Susan Baldwin3
February 28, 2011
A wide variety of people and organizations are working on aspects of ecological
remediation and restoration. As researchers involved in a mining-related project, 4 we
are pursuing the possibility of building a loose network of groups and individuals with
actual or potential interests in applying the new tools of ecogenomics5 in biological
approaches to ecological restoration (bioremediation). This document scopes out the
background, reports on network-building progress to date, and identifies future
directions.
Ecogenomics and bioremediation
The application of genomics to ecological problems (hence ecogenomics) is quite recent;
most of the literature dates from the late 1990s forward. Ecogenomics is proving
particularly fruitful in advancing biological remediation of soils and waters contaminated
with toxic metals and chemicals. The 2010 tailings dam breach in Hungary, and
consequent plume of toxic red sludge, reminds us of the necessity for complementary
mechanical, chemical, and biological responses to such disasters.
The first principle of bioremediation is that microbial communities, comprising bacteria
and other micro-organisms, can destroy or contain contaminants when appropriately
stimulated. Bioremediation occurs naturally if all essential materials are present on the
site. More often, the process is ‘engineered’ to accelerate biodegradation by optimizing
bacterial growth.6 Ecogenomics helps us understand the diversity and abundance of
microbial communities; the ecological relations that govern them, and the natural
abilities of some communities to thrive in contaminated environments.
There are important technical and epistemic differences between conventional
microbial genomics and ecogenomics. Genomics is a lab-based science while
ecogenomics is field-based, with laboratory support. In genomics, ‘purified’ microbial
species are cultured in the environs of the laboratory, then sequenced. Ecogenomics, in
contrast, is culture-independent; Random samples of wild-type microbial communities
are collected from a particular environment, such as a tailings pond or engineered
bioreactor. Then, using a powerful technique called phylotyping, researchers extract the
1 Senior Research Associate; Leader: Translational Genomics Research Group (TGRG); WM Young Centre for Applied
Ethics, University or British Columbia. janetat@interchange.ubc.ca
2 Postdoctoral Research Fellow, WM Young Centre for Applied Ethics and TGRG. jpage@interchange.ubc.ca
3 Associate Professor, Chemical and Biological Engineering, University or British Columbia.
sbaldwin@interchange.ubc.ca
4 The Development of Genomic Tools for Monitoring and Improving Passive Mitigation of Mine Drainage
5 Also known as metagenomics, community genomics, ecological genomics.
6 On the differences and principles of bioremediation see In situ bioremediation: when does it work? (US) National
Research Council. www.nap.edu
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ribosomal RNA (rRNA) of all of the microbes in the sample and use sequence-based
tools to determine what genes are present. An environmental sample that contains
many organisms will contain many rRNA sequences; their diversity is a measure of the
microbial community’s complexity. Tools such as microarrays assist gene expression
analysis. Researchers then screen the sample to identify a function of interest, such as
sulphate reduction.
In summary, the science of ecogenomics allows for the study of complex ecological
reactions and the composition, function, and dynamics of microbial communities. These
techniques contribute to the development of tools to monitor and mitigate industryrelated environmental damage.
A mining example
Mine drainage and other waste waters can contaminate many different aquatic
environments. Remediation usually requires large scale chemical treatment. Lime is
added to neutralize the acids and precipitate the metals into a high-density sludge
(HDS). But while solving one problem this method creates others—not least disposal of
the now toxic sludge. Additionally, such methods require capital investment in buildings,
plant and equipment, as well as ongoing operational costs for monitoring and
maintenance. The system demands tight controls and active interventions, hence
chemical treatment is called ‘active’ treatment.
In our current project, we are examining ‘passive’ biological alternatives to chemical
systems. Biological treatment systems project an environmentally-friendly image since
they blend into the natural setting and rely on natural processes. Many different forms
can be found, from existing wetlands and bogs to engineered bioreactors. In passive
systems only the flow of water into and sometimes through the system is controlled.
The part of the system where microbial treatment occurs is left to act on its own, i.e.
naturally or ‘passively.’ Passive systems are suitable for treating effluents that are less
heavily contaminated with metals or for remote areas where active treatment plants
cannot be built.
Bioremediation provides an alternative to active chemical treatment because microbial
consortia are effective in reducing metals to less toxic forms or to sequester metals as
part of their detoxification mechanism. In particular, sulphate-reducing bacteria (SRB)
are effective in bioremediation of mine drainage. However, SRB co-exist in microbial
communities that have complex biochemical interactions and rely on each other to
supply the necessary nutrients. In particular, SRB require other microorganisms to
degrade complex carbon compounds into simpler sources of electrons for their
metabolism.
Understanding the complex interactions, balance and composition of the microbial
community is essential if effective passive treatment strategies are to be implemented.
Biological systems have many advantages but they have not been widely adopted in the
mining industry where they are viewed as an unstable emergent technology, too
technically challenging to implement at any but the smallest scales. However, we are
finding that ecogenomic methods offer important advantages over current monitoring
methods which tend to provide unreliable assessments. These methods also allow for
monitoring effects of changing environments on the composition of microbial
communities. Our research group is using microarray technology to develop ecogenomic
2
and phylogenetic profiles of the communities. We are assessing the diversity of the
different types of microbial species as well as the impact of changing environments on
community composition at two pilot passive systems in BC. Our goal is to show how the
tools of ecogenomics can overcome some of the technical challenges of passive
treatment, stabilize the technology, and contribute to overall improvements in function.
Conceptualizing the Ecogenomics Network
Our current research project is a modest example of what an ecogenomics network
might look like. We are driven by the twin concepts7 of utility and discovery that
characterize ‘translational praxis‘. In other words, we move knowledge between the
field and the lab, combining the work of natural and social scientists and the practical
needs of industry partners in an integrated research agenda. Our network extends
beyond ourselves and our industry partners to include community organizations,
regulators, environmental consultants, and First Nations governments. Although still a
work-in-progress, we nevertheless have a foundation on which to base future networkbuilding efforts.
We can look to the European Union (EU) for further examples. There, it is increasingly
common to convene a broadly constituted network of actors and interests—what
Michel Callon and colleagues (2010) call ‘hybrid forums’--early in the development of
emerging technologies. The purpose is to ensure that policy frameworks for new
technologies assess societal benefits and risks and not simply technical suitability. The
iterative and reflexive approach of such forums is often called constructive technology
assessment (CTA), to distinguish the process from conventional TA which is concerned
only with technical outcomes.
One model of what we have in mind is the Ecogenomics Consortium8 in Holland, a
research cluster established and funded by the Netherlands Genomics Initiative in 2003.
The Consortium brings together the needs and resources of public partners
(universities; national research institutes) and the private sector (industry; interest
groups) in an integrated, genomics-driven approach to sustainable use of soil
ecosystems. The Consortium’s founding rationale was to combine ‘hitherto fragmented
molecular research potential and capacities in these fields of science in the
Netherlands.’ We perceive similar fragmentation in approaches to ecological restoration
and see benefit in forming a network focused on genomics-driven solutions.
Network-building: progress to date9
(1) Working Group. In order to further our goal of building an ecogenomics network, we
convened a working group– comprising resource industry representatives,
environmental consultants, academics and government regulators – on October 18,
2010. The purpose of the meeting was to assess the needs that an ecogenomics
network could meet, the steps required to build such a network, the value that such a
network could provide, and the possibility of hosting a future Forum on Ecogenomics.
Discussion in the working group meeting helped to define many issues that would be
faced by an ecogenomics network, including its scope, purpose, how it may meet
7
More information on these mutually dependent concepts can be found at www.tgrg-ubc.org
See www.ecogenomics.nl
9 Initial work is being funded by our current project; under Theme 3 of the social sciences and humanities (SSH)
component: “novel technologies and translational praxis.”
8
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industry needs, and the role of the network in bridging divides. The scope of the
network was a consideration. Working group members put forward the view that while
many sectors face similar ecological issues, it may be desirable, in the first instance, to
focus on a single sector. They suggested we leverage the accumulated social capital
from our current project by focusing on the mining industry and issues of mine drainage
and metal leachate. Subsequently, the network could add nodes for other sectors, such
as forestry and agriculture, and the scope widened to encompass environmental
management more generally.
A number of divides were identified that could possibly be bridged by an ecogenomics
network, including those between academia and industry, regulators and industry, and
between industrial sectors. Members noted that the network could serve multiple
purposes, from addressing particular environmental problems, to supporting economic
growth, to fostering dialogue on developments in ecogenomics among industrial,
academic, and non-traditional stakeholders.
Working group members also recommended conducting a preliminary survey of BC’s
mining industry to identify pressing needs to which ecogenomics might apply, assess
levels of interest in an ecogenomics network, and opinions on whether such a network
might help solve actual problems faced by the industry. The group cautioned against
overselling what ecogenomics tools might offer and encouraged us to refine our
understanding in this regard. We were further encouraged to develop a preliminary web
presence ( or ‘storefront’) for the network.
(2) Survey construction and testing. We subsequently developed a web-based survey
instrument to address these questions. The survey collects background information on
respondents and their companies, environmental treatment technologies in use,
awareness of ecogenomics applications in the mining industry, barriers to development
of new discharge treatment technologies, factors that drive industry’s needs, interest in
the development of an ecogenomics network, and opinions on ideal network
membership. In late February 2011, we piloted the instrument10 with a small number
(N=10) of industry members, consultants and environmental professionals most of
whom are partners on our current project. The instrument piloted well. None of the
testers reported problems interpreting questions or responding to them. Some
recommendations for refinements were offered which will be incorporated into the
next revision.
Given the small pool of respondents and their familiarity with our research, pilot results
carry no significance. Nevertheless, responses are interesting. Compliance with
regulation was noted as the most important factor driving industry’s needs in relation to
discharge treatment. At the same time, regulators’ lack of familiarity with new
technologies was seen as a potential barrier to the adoption of new, ecogenomics-based
treatment methods. Respondents were either ‘enthusiastic’ (50%) or ‘cautious but
positive’ (50%) about participating in a network ‘to share information on scientific
advances and their translation into practical applications.’ No negative responses were
recorded. In terms of who should be involved in the network, respondents were definite
that mining companies, their consultants, and university researchers should be included
but more equivocal about other stakeholders.
10 The pilot survey may be viewed at https://www.surveymonkey.com/s/ecogenomics_and_mine_drainage_PILOT
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(3) Next steps. The Translational Genomics Research Group’s website (www.tgrgubc.org) is hosting a preliminary web presence for the network (http://www.tgrgubc.org/#/ecogenomics-network/4547345230) , where discussion documents and
working papers are posted for the time being. The plan is to establish an independent
address for the network as time, results, and funding permits.
We have begun to compile the sample frame for the next iteration of the survey, which
will be administered in the quarter ending June 30, 2011; analysis of results and
reporting will take place in the quarter ended September 30, 2011.
Concurrently, funding will be sought to support network-building efforts and to host a
first information-sharing forum in the final quarter of 2011 or spring 2012.
Summary
Translational praxis is the process that moves theory into practice, and vice versa.
Understanding and engaging translational praxis is essential if the natural and social
sciences are to be of practical use to industry. In the mining and minerals sector, for
example, the potential for lasting environmental damage from metal mine drainage
represents a major barrier to expansion. Sound or responsible practice demands swift
translation of research advances into measures that aid in remediation and restoration
of contaminated sites. The science and tools of ecogenomics may facilitate sound
practice by offering improved approaches to mitigation.
To advance these efforts, we have embarked on a process of mutual engagement
among academic researchers, industry representatives, research funders, and other
stakeholders. Initially focused on the mining industry, the aim is to build a network on
ecogenomics and ecological restoration (NEER) grounded in translational praxis, i.e.
through which practical needs can help shape the research agenda and research results
translate into real utility for industry and other users. This document represents the
initial report on our progress to date.
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Useful reading
The following materials provide background and introductions to the topics discussed in
this document
Atkinson-Grosjean, J., Justin Page and Sue Baldwin (2010) Toxic histories and
technologies of remediation. Conference paper (peer reviewed). Society for the
History of Technology. Tacoma, WA September 30 – October 3. See Powerpoint
presentation at http://www.tgrg-ubc.org/#/mining-andmetagenomics/4546551004
BC Wild and Environmental Mining Council of BC (2010) Acid mine drainage: mining and
water pollution issues in BC.
http://www.miningwatch.ca/sites/miningwatch.ca/files/amd.pdf
Callon, Michel , Pierre Lascoumes and Yannick Barthe (2009) Acting in an uncertain
world: an essay on technical democracy. The MIT Press
Larratt, Heather, Mark Freberg, Robert Hamaguchi (2007) Developing tailings ponds and
pit lakes as bioreactors and habitat: cost-effective successes at Highland Valley
Copper. British Columbia Mine Reclamation Symposium (31st), Sept 17-20,
Squamish, BC
National Research Council (1993) In situ bioremediation: when does it work?
Washington, DC: The National Academies Press. (Can be read online at
www.nap.edu
National Research Council (2007) The new science of metagenomics: revealing the
secrets of our microbial planet. Washington, DC: The National Academies Press.
(Can be read online at www.nap.edu
Ouborg, NJ and WH Vriezen (2007) An ecologist’s guide to ecogenomics. Journal of
Ecology. 95, 8-16
Province of British Columbia (ND) Ecological Restoration Guidelines Biodiversity Branch.
Available online at
http://www.env.gov.bc.ca/fia/documents/restorationguidelines.pdf
Rip, Arie, Tom Misa, Johan Schot (eds.) (1995) Managing Technology In Society. The
Approach of Constructive Technology Assessment London: Pinter Publishers
Roelofsen, A. JEW Broerse, T. de Cock Buning and JFG Bunders (2010) Engaging with
future technologies: how potential future users frame ecogenomics. Science and
Public Policy. 37 (3) April, 167 - 179
Roelofsen, A., RR Kloet, JEW Broerse, T. de Cock Buning and JFG Bunders (2010) Guiding
visions in ecological genomics: a first step to exploring the future. New Genetics and
Society Vol.29, No.1, March, 19-36
Sobolewski, André(1999) A review of processes responsible for metal removal in
wetlands treating contaminated mine drainage, International Journal of
Phytoremediation, 1: 1, 19 — 51. Available online at
http://dx.doi.org/10.1080/15226519908500003
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