A ‘culture’ change in catchment microbiology?

Abstract

The development of a robust evidence base to inform policy and practice related to catchment microbial dynamics, water quality and human health must be grounded on proven techniques used for microbial water quality analysis. Currently, water regulators are in an exciting transition period with new techniques borne out of the 'molecular revolution' beginning to offer a means of characterising microbial watercourse pollution that challenge 'tried and tested' culture-based reference methods. In this commentary we advocate caution regarding the reliability of quantitative molecular tools and stress the need to continue programmes of cross-validation between enumeration approaches. In turn, novel detection (molecular) methodologies can be validated over time at the larger landscape scale (i.e. the scale at which the policy is implemented) against well-established 'tried and tested' (culture-based) reference methods. This will ensure that hydrologically relevant research and policy questions under consideration still deliver a demonstrable impact for regulators. Indeed, the current European Union (EU) legislation for the microbial quality of bathing and shellfish harvesting waters demands that specific standards are derived from culture-based criteria, highlighting the need to sustain such approaches without their complete abandonment in the face of emerging molecular detection techniques (CEC, 2006a,b). Thus, paradoxically, new molecular technology may compromise the development of the existing, and rather immature, evidence base of catchment microbial dynamics if cross-validation is not properly undertaken. The danger then is that molecular approaches could move on to become the 'gold-standard' without a thorough understanding of the implications for regulation and aspects of modelling and applied research required to meet current water policy frameworks.Meeting these challenges has clear relevance to those working in the multi-disciplinary field of soil and water science. In this field, there is a drive to understand better the processes and impacts of land management on aquatic and terrestrial systems, and possible impacts on human health (McKergow and Davies

Selective Quantification of Viable Escherichia coli Bacteria in Biosolids by Quantitative PCR with Propidium Monoazide Modification

“…Oliver et al (26) emphasized the need for a program of cross-validation of techniques before a complete revamp. It is likely that molecular techniques such as qPCR will gain an industry standard and revolutionize sample analysis times.…”

“…However, cross-comparison of the results of traditional approaches (i.e., CFU) and units of DNA (equivalent to a total count) of appropriate indicators would offer more comprehensive, trusted, and validated data. The recent emergence of cross-validation literature has a strong potential to change future detection and quantification approaches (26). Thus, PMA-modified qPCR combined with culturing-based methods has a strong potential to enhance our understanding of pathogen behavior in biosolids, as well as a wide range of applications in other fields, including microbial source tracking, food safety, and medicine.…”

Impact of Freeze–Thaw Cycles on Die-Off of E. coli and Intestinal Enterococci in Deer and Dairy Faeces: Implications for Landscape Contamination of Watercourses

“…A proportion of both FIO cells may have entered into a VBNC state and it may be that some of the differences between the concentrations of E. coli and enterococci were attributable to VBNC cells [ 14 , 29 ]. While there is uncertainty over whether cells are therefore truly dead or just metabolically inactive, the ‘die-off’ parameters derived from studies such as ours remain crucially important given that models used to inform on landscape FIO fate and transfer, and guide environmental decision-making, are largely built on data derived from culturable counts in order to align with culture-based standards used by environmental regulators [ 30 ].…”

Developments in water quality monitoring and management in large river catchments using the Danube River as an example

“…Incorporating the emerging science of microbial source tracking into catchment studies to complement on-going monitoring and modelling activities can help in the identification of faecal pollution sources but it remains a largely qualitative approach. The availability of new molecular and enumeration techniques for FIOs is leading to increased interest in their potential for regulatory monitoring although there remains much debate in terms of practicality and cost associated with deployment (Oliver et al, 2010(Oliver et al, , 2014. With the increasing complexity of analytical methods that can, and may need to, be used in monitoring water quality in future in order to achieve effective management, alternative approaches to refining the scale (as described in Section 5.3) and complexity of monitoring programmes are becoming more important.…”