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Applied Microbiology and Biotechnology

, Volume 101, Issue 2, pp 871–886 | Cite as

Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters

  • Julia Baudart
  • Delphine Guillebault
  • Erik Mielke
  • Thomas Meyer
  • Neeraj Tandon
  • Sabine Fischer
  • Wilfried Weigel
  • Linda K. Medlin
Environmental biotechnology

Abstract

Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project μAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health. Monitoring for organisms with molecular tools is rapid, more accurate and more reliable than traditional methods. Rapid detection means that mitigation strategies come into play faster with less harm to the community and to humans. Samples were collected from several waters in France, Germany, Ireland, Italy and Turkey over 2 years. We present microarray results for the presence of freshwater pathogens from brackish and freshwater sites in Northern Germany, and cyanobacterial cell numbers inferred from these sites. In a companion study from the same samples, cyanobacterial toxins were analyzed using two methods and those sites with highest toxin values also had highest cell numbers as inferred from this microarray study.

Keywords

Phylochips Microarray Freshwater pathogens Cyanobacteria Molecular barcodes 

Notes

Acknowledgments

This work was supported by the EU μAQUA project (FP7-KBBE-2010-4, 265409).

Compliance with ethical standards

LKM declares on behalf of all of the authors that there are no conflicts of interest, no research on humans of animals and no informed consents in this study.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Julia Baudart
    • 1
  • Delphine Guillebault
    • 2
  • Erik Mielke
    • 3
  • Thomas Meyer
    • 3
  • Neeraj Tandon
    • 4
  • Sabine Fischer
    • 4
  • Wilfried Weigel
    • 4
  • Linda K. Medlin
    • 5
  1. 1.Sorbonne Universités, UPMC University Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, (LBBM), Observatoire OcéanologiqueBanyuls/MerFrance
  2. 2.Microbia EnvironnementBanyuls sur MerFrance
  3. 3.MariLim Aquatic ResearchKielGermany
  4. 4.Scienion AGBerlinGermany
  5. 5.Marine Biological Association of the UKPlymouthUK

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