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, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
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
Bradford SA, Schijven J (2002) Release of Cryptosporidium and Giardia from dairy calf manure: impact of solution salinity. Env Sci Tech 36:3916–3923
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
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
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
Caraux G, Pinloche S (2005) PermutMatrix:a graphical environment to arrange gene expression profiles in optimal linear order. Bioinforms 21:1280–1281
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
Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159
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
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
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
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
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
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
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
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
Lee DY, Seto P, Korczak R (2010) DNA microarray-based detection and identification of winterbourne protozoan pathogens. J Microbiol Meth 80:129–133
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
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
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
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
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
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
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
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
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
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
Utermöhl H (1958) Zur Vervolkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Ver Theor Angew Limnol 9:1–38
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
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
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
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
This work was supported by the EU μAQUA project (FP7-KBBE-2010-4, 265409).
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.
An erratum to this article is available at http://dx.doi.org/10.1007/s00253-016-8040-4.
About this article
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
- Freshwater pathogens
- Molecular barcodes