Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters
- 381 Downloads
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.
KeywordsPhylochips Microarray Freshwater pathogens Cyanobacteria Molecular barcodes
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.
- 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 71:27Google 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 4:390–408Google 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 77:6313–6322CrossRefPubMedPubMedCentralGoogle 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 63:2397–2402Google 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 71:6878–6884CrossRefPubMedPubMedCentralGoogle 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.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, KoenigsteinGoogle 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 12:5505–5527CrossRefPubMedPubMedCentralGoogle 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 107:563–593Google 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 12:7430–7443CrossRefPubMedPubMedCentralGoogle 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 pressGoogle Scholar
- Utermöhl H (1958) Zur Vervolkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Ver Theor Angew Limnol 9:1–38Google Scholar