Hydrogenomics

Genomic techniques are developing at a very rapid pace in health, life, forensic and environmental science. These techniques provide very interesting new prospects for the water sector: fast detection of pathogens; determination of the relation between opportunistic pathogens in water and patients; and deeper insight into microbial communities and their function in water treatment processes, soils, biofilms. They can also be used to monitor sources and the fate of specific resistance genes, in new tools to monitor the efficacy of treatment processes, as well as for water quality and biodiversity monitoring. KWR develops DNA techniques for these purposes, supports the implementation, and evaluates the added value for effective and efficient water-quality management.

Applying genomic methods to look deep into the microbiome.

Fast-growing scientific field

KWR has been developing genomic tools for water (hydrogenomics) for two decades now. The speed, specificity and versatility of genomic methods, and the rapid developments, continue to increase and innovate the applications. Compared to traditional methods, DNA techniques are faster, more specific and more sensitive, and allow one to investigate the composition, function and activity of complex biological communities in water systems. Polymerase chain reaction (PCR) is a method now widely used in molecular biology.  We have developed quantitative PCR (qPCR) methods for rapid and specific detection of (opportunistic) bacterial pathogens (such as Legionella), viruses, fungi, cyanobacteria and protozoa, E. coli and enterococci, markers for specific contamination sources, antibiotic resistance genes, and for specific functional groups, such as iron oxidizing bacteria. Application of these techniques in the water sector has allowed for a more rapid assessment of drinking water quality (for example E. coli RT-PCR), water networks, cooling towers, wastewater systems (for example Legionella pneumophila qPCR), bathing water (enterococci qPCR, microbial source marker qPCRs). Our experience with hydrogenomics has expanded to eDNA of macrofauna and fish, to determine biodiversity to support NATURA2000.

Recent developments in

are now being translated to applications for water. These enable an improved understanding of the microbial community and processes in water treatment and biofilms in piped networks, of the integrity of groundwater abstraction systems and membrane filtration plants, of microbial degradation of contaminants, and of antibiotic resistance genes in water.

KWR has developed qPCR methods to identify and quantify toxic blue-green algae in bathing waters. We also provide the ecological knowledge needed to prevent blue-green algal nuisance.

Knowledge of the application of environmental DNA and metagenomics for water

KWR is fully abreast of DNA knowledge relevant to the water sector and agriculture. Development of genomic techniques and the interpretation of the results is embedded in our knowledge about microbial safety, biological activity and emerging contaminants.

• Fast and quantitative detection
  Application of Quantitative Polymerase Chain Reaction (qPCR) for the fast and selective conduct of detection of a large number of (opportunistic) pathogenic or bacteria, viruses, fungi and cyanobacteria.
• Understanding of bacterial and fungal population dynamics and function
  Application of Next Generation Sequencing (NGS) to gain insight into the composition and biochemical properties of bacterial and fungal populations; for example, to optimise water treatment processes or describe bacterial populations in greenhouse water.
• Tracing new microorganisms and their properties
  Detection of viruses, bacteria, fungi and protozoa for which ‘traditional’ (culture) methods do not suffice. Detection of antimicrobial resistance genes and genes associated with the degradation of contaminants.
• Risk assessment of bathing water
  Timely signalling of increased levels of blue-green algae and of bathing water parameters (E. coli, intestinal enterococci), including the tracing of contamination sources and risk analysis for humans and animals. Recognition and quantification of toxins produced by blue-green algae, and recommendations on preventing nuisance.
• Environmental DNA (eDNA)
  Analysis of DNA from traces of macro fauna and fish in water (skin cells, mucus, faeces) to determine biodiversity in support of NATURA2000.

Preparation of samples for RT-PCR analyses of E.coli in drinking water.

New opportunities to support efficient water management

Because of its versatility, hydrogenomics is widely applicable: the identification ranges from specific microbial pathogens to the macrofauna in the water ecosystem. The recent introduction of Next Generation Sequencing is opening many new avenues for research into better understanding of the microbial communities and their activities in water systems. This can be a basis for improved control of these communities, from suppressing growth of unwanted organisms or transfer of resistance genes, to supporting growth of microbial communities that are capable of degrading contaminants.