Skip to main content
SpringerLink
Log in

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

  • Environmental biotechnology
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

An Erratum to this article was published on 14 December 2016

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Antunes JT, Leão PN, Vasconcelos VM (2015) Cylindrospermopsis raciborskii: review of the distribution, phylogeography, and ecophysiology of a global invasive species. Front Microbiol 6:473. doi:10.3389/fmicb.2015.00473

    Article  PubMed  PubMed Central  Google Scholar 

  • Bradford SA, Schijven J (2002) Release of Cryptosporidium and Giardia from dairy calf manure: impact of solution salinity. Env Sci Tech 36:3916–3923

    Article  CAS  Google Scholar 

  • Berndtsson, J.C, Paul, C.J. (2015) Microbiological pollution of the southern Baltic Sea from small urban catchments following rain events of different intensities. Vatten 71:27

  • Briand JF, Leboulanger C, Humbert JF, Bernard C, Dufour P (2004) Cylindrospermopsis raciborskii (Cyanobacteria) invasion at mid-latitudes: selection, wide physiological tolerance, or global warming? J Phycol 40:231–238. doi:10.1111/j.1529-8817.2004.03118.x

    Article  Google Scholar 

  • Brinkmann NE, Francisco R, Nichols TL, Robinson D, Scaheffere FW II, Schaudies RP, Villega EN (2013) Detection of multiple waterborne pathogens using microsequencing arrays. J App Microbiol 114:564–573

    Article  Google Scholar 

  • Campbell AM, Fleisher J, Sinigalliano C, White JR, Lopez JV (2015) Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida. Microbiol 4:390–408

    CAS  Google Scholar 

  • Caraux G, Pinloche S (2005) PermutMatrix:a graphical environment to arrange gene expression profiles in optimal linear order. Bioinforms 21:1280–1281

    Article  CAS  Google Scholar 

  • Chapman AD, Schelske CL (1997) Recent appearance of Cylindrospermopsis (Cyanobacteria) in five hypereutrophic Florida lakes. J Phycol 33:191–195. doi:10.1111/j.0022-3646.1997.00191.x

    Article  Google Scholar 

  • Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159

    Article  CAS  PubMed  Google Scholar 

  • DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Anderson GL (2011) PCR amplification-independent methods for detection of microbial communities by the high-density microarray phylochip. Appl Environ Microbiol 77:6313–6322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53:371–383

    Article  CAS  PubMed  Google Scholar 

  • Dittami SM, Edvardsen B (2013) GPR-analyzer:a simple tool for quantitative analysis of hierarchical multispecies microarrays. Environ Sci Pollut Res Int 20:6808–6815

    Article  PubMed  Google Scholar 

  • Gushin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mizrabekov AD (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63:2397–2402

    Google Scholar 

  • Hill VR, Polaczyk AL, Hahn D, Narayanan J, Cromeans TL, Roberts JM, Amburgey JE (2005) Development of a rapid method for simultaneous recovery of diverse microbes in drinking water by ultrafiltration with sodium polyphosphate and surfactants. Appl Environ Microbiol 71:6878–6884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kegel JU, Del Amo Y, Medlin LK (2013) Introduction to project MIDTAL: its methods and samples from Arcachon Bay, France. Env Sci Poll Res 20:6690. doi:10.1007/s11356-012-1299-9

    Article  Google Scholar 

  • Kegel JU, Guillebault D, Medlin LK (2016) Application of microarrays (phylochips) for analysis of community diversity by species identification. Persp Phycol 3:93–106.

  • Lee DY, Shannon K, Beaudette LA (2006) Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. J Microbiol Meth 65:453–467

    Article  Google Scholar 

  • Lee DY, Lauder H, Cruwys H, Falletta P, Beaudette LA (2008) Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens. Sci Total Environ 398:203–211

    Article  CAS  PubMed  Google Scholar 

  • Lee DY, Seto P, Korczak R (2010) DNA microarray-based detection and identification of winterbourne protozoan pathogens. J Microbiol Meth 80:129–133

    Article  CAS  Google Scholar 

  • Lewis J, Medlin LK, Raine R (2012) MIDTAL (microarrays for the detection of toxic algae): a protocol for a successful microarray hybridisation and analysis. Koeltz, Koenigstein

  • Lopes VR, Vasconcelos VM (2011) Planktonic and benthic cyanobacteria of European brackish waters: a perspective on estuaries and brackish seas. Eur J Phycol 46:292–304

    Article  CAS  Google Scholar 

  • Marcheggiani S, D’Ugo E, Puccinelli C, Giuseppetti R, D’Angelo AM, Gualerzi CO, Spurio R, Medlin LK, Guillebault D, Baudart-Lenfant J, Weigel W, Helmi K, Mancini L (2015) Detection of emerging and re-emerging pathogens in surface waters close to an urban area. Int J Environ Res Public Health 12:5505–5527

    Article  PubMed  PubMed Central  Google Scholar 

  • Maynard C, Berthiaume F, Lemarchand K, Harel J, Payment P, Bayardelle P, Masson L (2005) Waterborne pathogen detection by use of oligonuceotide-based microarrays. Appl Environ Microbiol 71:8548–8557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Medlin LK (2013) Note: steps taken to optimise probe specificity and signal intensity prior to field validation of the MIDTAL microarray for the detection of toxic algae. Env Sci Poll Res 20:6683. doi:10.1007/s11356-012-1195-3

    Article  CAS  Google Scholar 

  • Padisák J (1997) Cylindrospermopsis raciborskii (Woloszynska) Seenayya et Subba Raju, an expanding, highly adaptative cyanobacterium: worldwide distribution and review of its ecology. Arch Hydrobiol Suppl Monogr Stud 107:563–593

    Google Scholar 

  • Panaiotov S, Simeonovski I, Levterova V, Karamfilov V, Brankova N, Tankova K, Campbell K, Jacob P, Helmi K, Boots B, D'Ugo E, Marcheggiani S, Mancini L, Breitenbach U, Mielke E, Kantardjiev T (2015) Two-year monitoring of water samples from Dam of Iskar and the Black Sea, Bulgaria, by molecular analysis: focus on Mycobacterium spp. Int J Environ Res Public Health 12:7430–7443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rajaniemi P, Hrouzek P, Kastovska K, Raphae KK, Willame RI, Rantala A, Hoffmann L, Komarek J, Sivonen K (2005) Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria). Int J Sys Evol Microbiol 55:1–26

    Article  Google Scholar 

  • Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL (2015) Waterborne pathogens: detection methods and challenges. Pathogens 4:307–334. doi:10.3390/4020307

    Article  PubMed  PubMed Central  Google Scholar 

  • Rodriguez I, Fraga M, Alfonso A, Guillebault D, Medlin LK, Baudart J, Jacob P, Helmi K, Meyer M, Breitenbach U, Holten NM, Boots B, Supiro R, Cimarelli L, Mancini L, Marcheggiani S, Albay M, Akcaalan R, Köker L, Botana, LM (2016) Monitoring of freshwater toxins in European environmental waters by using novel multi-detection methods. Water Res, in press

  • Schernewski G (2003) Nutrient budgets, dynamics and storm effects in a eutorophic, stratified Baltic Lake. Acta Hydrochim Hydrobiol 31:1–10

    Article  Google Scholar 

  • Shannon KE, Lee DY, Trevors JT, Beaudette LA (2007) Application of real-time quantitative PCR for the detection of selected bacterial pathogens during municipal wastewater treatment. Sci Total Environ 382:121–129

    Article  CAS  PubMed  Google Scholar 

  • Utermöhl H (1958) Zur Vervolkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Ver Theor Angew Limnol 9:1–38

    Google Scholar 

  • Wang Z, Vora GJ, Stenger DA (2004) Detection and genotyping of Entamoeba histolytica, Entamoeba dispar, Giardia lamblia, and Cryptosporidium parvum by oligonucleotide microarray. J Clin Microbiol 42:3262–3271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang ZH, Yang JQ, Zhang DJ, Zhou J, Zhang CD, Su XR, Li TW (2014) Composition and structure of microbial communities associated with different domestic sewage outfalls. Genet Mol Res 13:7542–7552

    Article  CAS  PubMed  Google Scholar 

  • Wilson WJ, Strout CL, DeSantis TZ, Stilwell JL, Carrano AV, Andersen GL (2002) Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes 16:119–127

    Article  CAS  PubMed  Google Scholar 

  • Zbikowska E, Walczak M, Krawiec A (2013) Distribution of Legionella pneumophila bacteria and Naegleria and Hartmannella amoebae in thermal saline baths used in balneotherapy. Paras Res 112:77–83

    Article  Google Scholar 

Download references

Acknowledgments

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

Author information

Authors and Affiliations

  1. Sorbonne Universités, UPMC University Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, (LBBM), Observatoire Océanologique, F-66650, Banyuls/Mer, France

    Julia Baudart

  2. Microbia Environnement, Avenue de Fontaule, 66550, Banyuls sur Mer, France

    Delphine Guillebault

  3. MariLim Aquatic Research, GmbH Heinrich-Wöhlk-Str.14, 24232, Kiel, Germany

    Erik Mielke & Thomas Meyer

  4. Scienion AG, Volmerstr. 7b, 12489, Berlin, Germany

    Neeraj Tandon, Sabine Fischer & Wilfried Weigel

  5. Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2PB, UK

    Linda K. Medlin

Authors
  1. Julia Baudart
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Delphine Guillebault
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Erik Mielke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thomas Meyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Neeraj Tandon
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sabine Fischer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wilfried Weigel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Linda K. Medlin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Linda K. Medlin.

Ethics declarations

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.

Additional information

An erratum to this article is available at http://dx.doi.org/10.1007/s00253-016-8040-4.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Baudart, J., Guillebault, D., Mielke, E. et al. Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters. Appl Microbiol Biotechnol 101, 871–886 (2017). https://doi.org/10.1007/s00253-016-7937-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-016-7937-2

Keywords

Search

Navigation