Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey
Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project μAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives. Molecular tools are more rapid, accurate and reliable than traditional methods, which means faster mitigation strategies with less harm to humans and the community. We present microarray results for the presence of freshwater pathogens from a Turkish lake used drinking water and inferred cyanobacterial cell equivalents from samples concentrated from 40 into 1 L in 45 min using hollow fibre filters. In two companion studies from the same samples, cyanobacterial toxins were analysed using chemical methods and those dates with highest toxin values also had highest cell equivalents 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).
- Altüg, G., Yardimci, C. H., Okgerman, H., & Tarkan, S. A. (2006). Levels of bacterial metabolic activity, indicator (Coliform, Escherichia coli) and pathogen bacteria (Salmonella spp.) in the surface water of Sapanca Lake, Turkey. Journal of the Black Sea/Mediterranean Environment, 12, 67–77.Google Scholar
- Baudart, J., Guillebault, D., Meilke, E., Meyer, T., Tandon, N., Fischer, S., Weigel, W., & Medlin, L. K. (2016). Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters. Applied Microbiology and Biotechnology, 101, 871–886.CrossRefGoogle Scholar
- Certad, G., Dupouy-Camet, J., Gantois, N., Hammouma-Ghelboun, O., Pottier, M., Guyot, K., Benamrouz, S., Osman, M., Delaire, B., Creusy, C., Viscogliosi, E., Dei-Cas, E., Aliouat-Denis, C. M. & Follet, J. (2015). Identification of Cryptosporidium species in fish from Lake Geneva (Lac Léman) in France. PLoS One, 10. https://doi.org/10.1371/journal.pone.0133047.
- EPA. (2014). Cyanobacteria and cyanotoxins, information for drinking water systems. EPA 810F11001. Available online at https://www.epa.gov/sites/production/files/2014-08/documents/cyanobacteria_factsheet.pdf.
- Greer, B., McNamee, S. E., Boots, B., Cimarelli, L., Guillebault, D., Helmi, K., Marcheggiani, S., Panaiotov, S., Breitenbach, U., Akcaalan, R., Medlin, L. K., Kittler, K., Elliot, C. T., & Campbell, K. (2016). A validated UPLC–MS/MS method for the surveillance of ten aquatic biotoxins in European brackish and freshwater systems. Harmful Algae, 55, 31–40.CrossRefGoogle Scholar
- Griffitt, K. J., Noriea, N. F., Johnson, C. N., & Grimes, D. J. (2011). Enumeration of Vibrio parahaemolyticus in the viable but nonculturable state using direct plate counts and recognition of individual gene fluorescence in situ hybridization. Journal of Microbiological Methods, 85, 114–118.CrossRefGoogle Scholar
- Hill, V. R., Polaczyk, A. L., Hahn, D., Narayanan, J., Cromeans, T. L., Roberts, J. M., & Amburgey, J. E. (2005). Development of a rapid method for simultaneous recovery of diverse microbes in drinking water by ultrafiltration with sodium polyphosphate and surfactants. Applied and Environmental Microbiology, 71, 6878–6884.CrossRefGoogle Scholar
- Karlson, B., Cusack, C., & Bresnan, E. (Eds). (2010). Microscopic and molecular methods for quantitative phytoplankton analysis. IOC Manuals and Guides, no. 55 (110 pages). Paris: Intergovernmental Oceanographic Commission of ©UNESCO.Google Scholar
- Kegel, J. U., Del Amo, Y., Costes L. & Medlin L. K. (2016). Monitoring toxic microalgae in Arcachon Bay in France by microarrays. Microarrays, Featured Papers 2, 1–23.Google Scholar
- Lewis, J., Medlin, L. K., & Raine, R. (2012). MIDTAL (microarrays for the detection of toxic algae). A protocol for a successful microarray hybridisation and analysis. Germany: Koeltz., Koenigstein.Google Scholar
- Kurmayer, R., Blom, J. F., Deng, L., & Pernthaler, J. (2015). Integrating phylogeny., geographic niche partitioning and secondary metabolite synthesis in bloom-forming Planktothrix. The International Sosciety of Micorbial Ecology Journal, 9, 909–921.Google Scholar
- Lindahl, J. F. & Grace, D. (2015). The consequences of human actions on risks for infectious diseases, a review. Infection, Ecology, and Epidemiology, 5. https://doi.org/10.3402/iee.v5.30048.
- Marcheggiani, S., D’Ugo, E., Puccinelli, C., Giuseppetti, R., D’Angelo, A. M., Gualerzi, C. O., Spurio, R., MedlIn, L. K., 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. International Journal of Environmental Research and Public Health, 12, 5505–5527.CrossRefGoogle Scholar
- Medlin, L. K. (2016). Mini review: molecular techniques for identification and characterization of marine biodiversity. Annals of Marine Biology and Research, 3(2), 1015.Google Scholar
- Medlin, L. K. (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. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-012-1195-3.
- Medlin L. K., Guillebault, D., Mengs, G., Garbi, C., Dejana, L., Fajardo, C. & Martin, M. (2017). New molecular tools, application of the mAQUA phylochip and concomitant FISH probes to study freshwater pathogens from samples taken along the Tiber River., Italy. Proceedings of 17 th Water Quality Conference, 221: in press.Google Scholar
- Paniel, N., Baudart, J., Hayat, A., & Barthelmebs, L. (2013). Aptasensor and genosensor methods for detection of microbes in real world samples. Methods, 64, 229–240.Google Scholar
- Rodriguez, I., Fraga, M., Alfonso, A., Guillebault, D., Medlin L., Baudart, J., Jacob, P., Helmi, K., Meyer, T., Breitenbach, U., Holden, N. M., Boots, B., Spurio, R., Cimarelli, L., Mancini, L., Marcheggiani, S., Albay, M., Akcaalan, R., Köker, L., & Botana, L. M. (2016). Monitoring of freshwater toxins in European environmental waters by using novel multi-detection methods. Environmental Toxicology and Chemistry, 36(3), 645–654. https://doi.org/10.1002/etc.3577.
- Sivonen, K., & Jones, G. (1999). Cyanobacterial toxins. In I. Chorus & J. Bartram (Eds.), Toxic Cyanobacteria in Water, A Guide to their Public Health Consequences., Monitoring and Management (pp. 41–91). London: E & F Spon.Google Scholar
- Suda, S., Watanabe, M. M., Otsuka, S., Chong, M. N., & Toze, S. (2002). Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria. Intternational Journal of Systematic Evolution and Microbiology, 52, 1577–1595.Google Scholar
- Tokat, B. (2010). Temporal and spatial distribution of picophytoplankton in Sapanca lake. MSc Thesis. Istanbul University, Institute of Graduate Studies in Science and Engineering.Google Scholar
- Utermöhl, H. (1958). Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mittleilungen Verhandlungen des Internationalen Verein Limnologie, 9, 1–38.Google Scholar
- Van der Gucht, K., Van de Kerckhove, T., Vloemans, N., CousIn, S., Muylaert, K., Sabbe, K., Gillis, M., Declerk, S., De Meester, L., & Vyverman, W. (2005). Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure. FEMS Microbiology Ecology, 53, 205–220.CrossRefGoogle Scholar
- Van Der Waal, D., Guillebault D., Alfonso D., Rodríguez, I., Botana, L. & Medlin L. K. (2017). μAqua microarrays for phylogenetic and toxin expression of cyanobacteria with validation by cell counts and UPLC/MS-MS. Harmful Algae, in press.Google Scholar
- WHO (2006). Guideline for drinking water quality, vol. 1, 3rd edn. Geneva: Recommendations Nonserial Publication, ISBN-13, 9789241546744.Google Scholar