| Project objectives:
Biotool is an European Commission funded project (STREP) under the Sixth Framework Programme, Priority 6: Sustainable Development, Global Change and Ecosystems.
The objective of BIOTOOL is the assessment, evaluation and prediction of natural attenuation processes to implement natural attenuation as the accepted
key groundwater and soil remediation strategy in Europe.
This will require benchmarked monitoring tools for diagnosing biological status and predicting evolution of contaminated soil and groundwater, which
have to be rooted in biological processes. The generation and validation of such novel instruments will be materialized through the application of a suite
of state-of-the-art genomic, proteomic and analytical technologies to environmental samples and sites themselves. We will exploit the translocation of
indicator chemicals from below ground into above-ground vegetation as a cheap and rapid monitoring tool for subsurface contamination. Diagnosis of the biological
status and evolution models for polluted environments will be achieved through [i] the design and utilization of DNA and specifically DNA-array technology
for examining the catabolic potential of any given particulate sample and [ii] the identification of protein biomarkers as descriptors of soil and groundwater
conditions and biological attenuation. The progress in microbial community functional genomics and proteomics will be employed to gain a mechanistic understanding
of microbial responses to chemical insults, plant/microbe interactions and microbial community adaptations that determine microbial-driven soil and
groundwater attenuation processes. Such mechanistic understanding will add a considerable predictive power to the genomic and proteomic approaches. Determining
the links between environmental factors and expression of degradation abilities will be crucial for strategies aiming at an optimal expression of the catalytic
power of the indigenous microbial community. The robustness of diagnostic instruments for future normative applications will be validated in microcosms
and used for assessment of contaminated sites under study.
Chlorinated solvents and aromatic hydrocarbons represent the most prevalent organic groundwater contaminants in Europe. During the previous years, natural
attenuation, “naturally occurring processes in soil and groundwater that act without human intervention to reduce the mass, toxicity, mobility, volume
or concentration of contaminants in those media” has received increasing attention. It is generally accepted that microorganisms are the principal mediators
of the natural attenuation of many pollutants. They transform or mineralize pollutants thereby usually decreasing their masses and toxicities in contrast
to most other components of natural attenuation. The use of natural attenuation thus requires a detailed monitoring to determine how effective natural attenuation
is for attaining site remediation goals.
The key objective of BIOTOOL is to generate novel and reliable tools to diagnose soil status and predict evolution for contaminated soil and groundwater.
Emphasis is put on the assessment and evaluation of natural attenuation processes, which requires innovative monitoring tools and warning concepts to implement
monitored natural attenuation into soil and groundwater remediation strategies in Europe. The project focuses on halogenated solvents and aromatic pollutants,
since they are among the most abundant soil and groundwater contaminants in Europe. Particularly Eastern European countries contain huge aquifer contamination
with these compounds. Chlorinated solvents and aromatics are designated in the Water Framework directive and related documents (Directive 2000/60/EC)
and in the national legislation of the EU Member States as 'priority substances'.
The general objective is the development and validation of biological instruments and techniques for diagnosing the status of soil and groundwater polluted
with complex mixtures of aromatic and halogenated chemicals and predicting evolution of the afflicted sites. This will be materialized through the application
of a suite of genomic, proteomic and analytic technologies to environmental samples and sites themselves. A new technique is the exploitation of the translocation
of indicator chemicals from below ground into above-ground vegetation as cheap and rapid monitoring tool for subsurface contamination.
The specific objectives of the project are:
- Establishment of the correlation between soil/groundwater contamination and plant contamination. Such a correlation can directly be used for monitoring
purposes but is also very important for risk assessment.
- The design and utilization of DNA and specifically DNA-array technology for examining the catabolic potential of any given particulate sample. Such DNA-arrays
will provide information not only on microbial community profile, but, more important, on the overall biodegradative gene landscape present in a specific
location. The arrays will contain suitable functional probes to detect their target genes in soil/groundwater DNA extracts (biodegradation potential)
as well as cDNA from environmental mRNAs (activity profile).
- The access and analysis of the soil/groundwater meta-proteome as biomarker. Protein extracts of polluted soils and groundwaters with evolving degrees
of pollution will be employed to identify biomarkers as descriptors of soil and groundwater quality and biological 'clocks' for predicting the evolution
of the afflicted site.
- The use of lipid biomarkers as general prediction instruments of stress/toxicity on soil and groundwater microorganisms. Microbes in soil are often confronted
with multiple stresses, such as climate-induced shifts in osmotic pressure, oxygen tension and temperature, or pollutant-induced solvent and water stress,
some of which simultaneously combine a nutritional opportunity with a cellular stress. Microbes respond to such factors with a cascade of mechanisms, whereby
most of these adaptive responses are connected with changes in the composition of the cytoplasmic membrane. These shifts can be use to define soil and groundwater
- Elucidation of the roles of natural and chemical stresses and plant/microbe interactions on the metabolic activities of soil and groundwater microbial
catalysts. Recent progress in the area of microbial community functional genomics will be employed to gain a mechanistic understanding of prevailing stresses,
global regulatory responses, plant/microbe interactions and microbial community adaptations that determine microbial-driven soil and groundwater processes.
This will add a considerable predictive power to the genomic and proteomic approaches mentioned above. Determining the links between environmental factors
and expression of degradative abilities will be crucial for strategies aiming at an optimal performance of the indigenous community.
- The robustness of above diagnostic instruments will be validated in microcosms and used for assessment of contaminated sites under study.