• Research Cluster II: Ecological genomics

    The relatively new field of ecological genomics is a scientific discipline that studies the structure and functioning of a genome with the aim of understanding the relationship between the organism and its biotic and abiotic environments. Generally, it can be described as ‘the genomics revolution invading ecology’ (Van Straalen & Roelofs: An Introduction to Ecological Genomics).

    Featuring subjects, mechanisms and methods that are being developed and applied in this SENSE Research Cluster are, for example:

      • understanding ecological complexity, nutrient cycles, life-history patterns and responses of organisms to environmental stress at the genomic level
      • analysis of environmental genomes to improve our understanding of ecosystem functions and biodiversity and to contribute to define and measure environmental quality

    We welcome experts in ecological genomics to participate in this research cluster to exchange knowledge and stimulate new innovative developments (if you are not a member of the SENSE Research School but involved with this subject, then you are still welcome to enroll and participate in this research cluster).


    To read more about the SENSE research clusters in general, click HERE.

  • Instructions: Clicking on the section name will show / hide the section.

  • Coordinators:

    • Dr. D. (Dick) Roelofs (VU-IES-AE)
    • Prof. H. (Hauke) Smidt (WU-MIB)
    • Dr. J. (Juliette) Legler (VU-IVM-C&B)

    SENSE key experts:

    • Prof. Hauke Smidt (WU-MIB)
    • Prof. Jacintha Ellers (VU-IES)
    • Prof. N.M. (Nico) van Straalen (VU-IES-AE)
    • Dr. D. (Dick) Roelofs (VU-IES-AE)
    • Dr. Juliette Legler (VU-IVM-C&B)

    Contact information:

    For more information about this research cluster, please contact Dr. Monique Gulickx (

    • To illustrate the urgency and relevance of new developments in this field, below we present some of the emerging research questions that are currently challenging both science and society in the research domain of SENSE Research Cluster II:

      1. How can we incorporate Genomic tools into the common practice of environmental risk assessment and regulatory activities?
        Scientific and societal relevance: Genomics has enormous potential to improve ecological risk assessment. Risk assessment based on genomics tools will be very quick, automatable and high throughput. However, the current diversity of techniques and data analysis does not yet adequately support the use of genomics tools in regulatory testing (Ankley et al. 2006, ES &T p4055). This has lead the US Environmental Protection Agency to develop a new guidance that outlines best practice in the submission, quality assurance, analysis and management of genomics data for environmental applications (Dix et al. 2006. Nature Biotech 24. p1108). Such initiative is completely lacking in Dutch as well as EU environmental policy. It is extremely important and urgent to develop such initiative at the national and EU level.

      2. Can and should Genomics-based approaches (genetic engineering, synthetic biology) be used to generate improved and novel microbial traits for bioremediation?
        Scientific and societal relevance: A significant amount of chemicals resulting from former industrial activity is still in our environment. These heritages from the past can be degraded in a number of cases and/or converted to innocent products or otherwise neutralized, so that these compounds do not form a burden to present-day society anymore. It might even be possible to exploit microbially mediated transformation activities towards the valorization of industrial waste-streams. Genomics-based tools will play an essential role in the identification of organisms and consortia that exert such biodegradation and -transformation activity. Genomics analyses of their activity and their (trophic) relationships to each other can be applied to monitor and assess soil- and/or effluent remediation and valorization. Genes and gene products necessary for biodegradation and/or biotransformation will be identified and functionally characterized, so that the activity of the organisms and the degradation that is supported by them can be optimized.

      3. Can Genomics play an important role in the assessment of multi-generation effects of environmental pollutants?
        Scientific and societal relevance: Already 55 years ago two case-studies were published to become textbook examples of evolution in action: DDT resistance in houseflies and the rise of melanic forms of the peppered moth. Now, many years later, molecular studies have elucidated in detail the mechanisms conferring resistance. Some resistances are due to cis-regulatory change of stress combating genes. The discovery of these mechanisms has promoted the idea that resistance to environmental toxicants can be brought about by relatively simple genetic changes, involving up-regulation, duplication or structural alteration of a single gene. In our work on metal tolerance of Orchesella cincta, a soil-living hexapod, we have also followed this line and identified a cadmium-induced metallothionein (mt) in this species. However, a genome-wide gene expression profiling study reported earlier (Roelofs et al. 2009), shows that evolution of tolerance takes place in a complicated molecular network. In conclusion, current ecological risk assessment does not consider evolution of stress resistance. Genomics can unravel such multigenerational responses to prevailing environmental challenges and associated risks to affected natural populations.

      4. Can Genomics assess the ecological risks of complex toxicant mixtures?
        Scientific and societal relevance: Currently, effect assessment of chemical mixtures is through multiple dose–response analysis of single compounds and their combinations. Investigating whether such data deviate from the reference models of concentration addition and/or independent action to identify overall synergism or antagonism is becoming routine. However, recent data show that more complex deviation patterns, such as dose ratio–dependent deviation and dose level–dependent deviation, need to be addressed. Mechanistic information on toxicant activity in mixtures is scarce. A recent study on binary mixtures of a metal (cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene) showed an extremely complex pattern of gene regulation. Cadmium toxicity decreased in the presence of low concentrations of phenanthrene. Interestingly gene networks were identified that only responded to one of each toxicant. Such gene expression patterns exert high potential in identifying certain specific toxicant classes within an environmental sample that always consists of a mixture of potentially harmful compounds. In conclusion, genomics will become essential towards scientifically well established risk assessment of complex environmental samples (soil, effluents, water).

      5. Can Genomics aid in prevention of pollution by design/engineering of improved microbial consortia for treatment of industrial and domestic waste streams?
        Scientific and societal relevance: Recently, a consortium started research on bio-based, ecologically balanced sustainable industrial chemistry, within the Chemistry & Energy theme selected as one of the priority areas of the Dutch innovation programme. The scientific and technological focus of this program is on development of bio-based applications in environmental & industrial biotechnology for sustainable bio-based developments in industrial chemistry. An important theme within this Consortium is the bioremediation and/or valorization of industrial and domestic waste streams. Genomics research will identify the microbial consortia with high remediation activities. These organisms will be important tools in controlling waste streams and to minimize the ecological impact of industrial activity on ecosystem functioning in the future. Furthermore, microbial consortia can be tailored that can add value to waste streams by transformation of contaminants into useful products.
  • Here you will be able to find interesting articles, links to books that are worth reading, presentations that caught your attention, etc. To suggest items that should be placed here, please follow the instructions mentioned below or send an email to the (technical) coordinators.

  • Add a document to the Library

    Do you have any interesting articles, reports or other documents that you want to share within this research cluster? You can add the by clicking on Upload Documents below. Please note that your document will not be visible in the library immediately, because it first has to be approved by the coordinator. You can also contact him if you would like your suggested document to be brought under our attention in a different way or if you would like the document to appear differently in the library (there are some options available for that).

  • In this forum topics related to cluster I can be discussed, varying from scientific issues to organizational matters. The forum is very easy to use.

    To enter the forum, click on Forum RC II below. You will go to the overview page of the forum, where you can see all existing discussions. If you click on a discussion title, you will enter the discussion. You can read all posts and you can also respond to them, by clicking Reply.

    To add a new discussion topic, you can click on Add a new discussion topic on top of the overview page. Please make sure that your new discussion is really new and does not overlap with existing discussions, otherwise the forum will get messy.

    The forum is maintained by the technical coordinator of the research cluster, who will remove any inappropriate contributions to the discussions.

    Please note the following!

    Everyone who enrolls in this course, is automatically subscribed to this forum and will receive e-mail notifications of every post on the forum. If you do not wish to be subscribed to the forum, you can click Unsubscribe from this forum in the top right corner of the forum overview page.

    If you do not want to receive too many notifications, you can adapt the forum settings for your account. To do so, follow these steps:
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    b. Click Edit profile.
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    f. Scroll down and choose Update profile to activate your new settings.

    If you want to give feedback on the functioning of the forum or group page in general, then you are most welcome to leave a post in the discussion Technical feedback. The SENSE team will keep an eye on this discussion and will try to process your feedback as good as possible.