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Oscar Omondi DONDE, TIAN Cuicui, XIAO Bangding. Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems[J]. Journal of Oceanology and Limnology, 2018, 36(5): 1629-1642

Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

Oscar Omondi DONDE1,2,3, TIAN Cuicui1, XIAO Bangding1
1 Key Laboratory of Algal Biology of Chinese Academy of Sciences-Lake Restoration Research Group, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
2 International College, University of Chinese Academy of Sciences, Beijing 100049, China;
3 Egerton University, Department of Environmental Science, P. O. Box 536-20115, Egerton-Kenya
The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued efforts to improve the Faecal Contamination Source Tracking (FCST) techniques such as Microbial Source Tracking (MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DNA markers while accounting for seasonality and weather conditions' effects in tracking the major sources of faecal contamination in a freshwater system (Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DNA markers.
Key words:    assay|contamination|faecal bacteria indicator|source tracking|water quality   
Received: 2017-04-07   Revised:
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Articles by Oscar Omondi DONDE
Articles by TIAN Cuicui
Articles by XIAO Bangding
American Public Health Association (APHA). 2005.Compendium of Methods for the Microbiological Examination of Food and Water. 19th edn. Washington, DC. 350p.
Bej A K, McCarty S C, Atlas R M. 1991. Detection of coliform bacteria and Escherichia coli by multiplex polymerase chain reaction:comparison with defined substrate and plating methods for water quality monitoring. Applied and Environmental Microbiology, 57(8):2 429-2 432.
Boehm A B, Van De Werfhorst L C, Griffith J F, Holden P A, Jay J A, Shanks O C, Wang D, Weisberg S B. 2013. Performance of forty-one microbial source tracking methods:a twenty-seven lab evaluation study. Water Research, 47(18):6 812-6 828,
Campbell G R, Prosser J, Glover A, Killham K. 2001. Detection of Escherichia coli O157:H7 in soil and water using multiplex PCR. Journal of Applied Microbiology, 91(6):1 004-1 010,
Chase E, Hunting J, Staley C, Harwood V J. 2012. Microbial source tracking to identify human and ruminant sources of faecal pollution in an ephemeral Florida river. Journal of Applied Microbiology, 113(6) 1 396-1 406,
Dickerman B, Metzger J, Lee W T. 2006. Molecular identification of Aeromonas and coliform bacteria isolated on m Endo media from Lake Erie waters. World Journal of Microbiology and Biotechnology, 22(1):29-33,
Donde O O, Muia A W, Wanga L A, Shivoga A W, Trick G, Creed I F. 2015. Faecal pollution and solar purification of community water sources within Lake Naivasha Basin, Kenya. Journal of Water, Sanitation and hygiene for Development, 5(2):252-260,
Donde O O, Ojwang O W, Muia A W, Wanga L A. 2014.Bacterial abundance on the skin, gills and intestines of Cyprinus carpio in Lake Naivasha, Kenya:implications for public health and fish quality. Lakes & Reservoirs:Research and Management, 19(1):46-55,
Donde O O. 2017. Wastewater management techniques:a review of advancement on the appropriate wastewater treatment principles for sustainability. Environmental Management and Sustainable Development, 6(1):40-58,
Donde O O, Xiao B. 2017. Understanding wastewater treatment mechanisms:a review on detection, removal and purification efficiencies of faecal bacteria indicators across constructed wetlands. Environmental Reviews, (in Press)
Fatemeh D, Reza Z M, Mohammad A, Salomeh K, Reza A G, Hossein S, Maryam S, Azam A, Mana S, Negin N, Reza K A, Saeed F. 2014. Rapid detection of coliforms in drinking water of Arak city using multiplex PCR method in comparison with the standard method of culture (Most Probably Number). Asian Pacific Journal of Tropical Biomedicine, 4(5):404-409,
García-Aljaro C, Martín-Díaz J, Viñas-Balada E, CaleroCáceres W, Lucena F, Blanch A R. 2017. Mobilisation of microbial indicators, microbial source tracking markers and pathogens after rainfall events. Water Research, 112:248-253.
Ghimire N P, Jha P K, Caravello G. 2013. Physico-chemical parameters of high-altitude rivers in the Sagarmatha(Everest) National Park, Nepal. Journal of Water Resource and Protection, 5(8):35 827,
Horáková K, Mlejnková H, Mlejnek P. 2006. Direct detection of bacterial faecal indicators in water samples using PCR.Water Science & Technology, 54(3):135-140,
Horakova K, Mlejnkova H, Mlejnek P. 2008. Specific detection of Escherichia coli isolated from water samples using polymerase chain reaction targeting four genes:cytochrome bd complex, lactose permease, β-D-glucuronidase, and β-Dgalactosidase. Journal of Applied Microbiology, 105(4):970-976, https://org/10.1111/j.1365-2672.2008.03838.x.
Jahne M A, Schoen M E, Garland J L, Ashbolt N J. 2017.Simulation of enteric pathogen concentrations in locallycollected greywater and wastewater for microbial risk assessments. Microbial Risk Analysis, 5:44-52,
Jenkins C, Lawson A J, Cheasty T, Willshaw G A. 2012.Assessment of a real-time PCR for the detection and characterization of verocytotoxigenic Escherichia coli.Journal of Medical Microbiology, 61(8):1 082-1 085,
Kaoga J, Ouma G, Abuom P. 2013. Effects of farm pesticides on water quality in Lake Naivasha, Kenya. American Journal of Plant Physiology, 8(3):105-113,
Kirchman D L, Morán X A G, Ducklow H. 2009. Microbial growth in the polar oceans-role of temperature and potential impact of climate change. Nature Reviews Microbiology, 7(6):451-459,
Lee C, Kim J, Shin S G, Hwang S. 2006. Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. Journal of Biotechnology, 12(3):273-280,
Li J, Wang H, Liu Y, Lin M, Liu X, Hu X. 2014. Distribution and diversity of coliform bacteria in estuary of Jiahe River, China. International Journal of Environmental Research, 8(2):501-508.
Liu Y M, Yuan X P, Zhang Q Y. 2006. Spatial distribution and morphologic diversity of virioplankton in Lake Donghu, China. Acta Oecologica, 29(3):328-334,
Ma J C, Ibekwe A M, Yang C H, Crowley D E. 2013. Influence of bacterial communities based on 454-pyrosequencing on the survival of Escherichia coli O157:H7 in soils.FEMS Microbiology Ecology, 84(3):542-554,
Mieszkin S, Furet J P, Corthier G, Gourmelon M. 2009. Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. Applied and Environmental Microbiology, 75(10):3 045-3 054,
Nejman-Faleńczyk B, Bloch S, Januszkiewicz A, Węgrzyn A, Węgrzyn G. 2015. A simple and rapid procedure for the detection of genes encoding Shiga toxins and other specific DNA sequences. Toxins, 7(11):4 745-4 757,
Ohad S, Vaizel-Ohayon D, Rom M, Guttman J, Berger D, Kravitz V, Pilo S, Huberman Z, Kashi Y, Rorman E. 2015.Microbial source tracking in adjacent karst springs.Applied and Environmental Microbiology, 81(15):5 037-5 047,
Ojok W, Wasswa J, Ntambi E. 2017. Assessment of seasonal variation in water quality in River Rwizi using multivariate statistical techniques, Mbarara Municipality, Uganda.Journal of Water Resource and Protection, 9(1):83-97,
Paruch L, Paruch A M, Blankenberg A G B, Bechmann M, Mæhlum T. 2015. Application of host-specific genetic markers for microbial source tracking of faecal water contamination in an agricultural catchment. Acta Agriculturae Scandinavica, Section B-Soil & Plant Science, 65(S2):164-172,
Pimentel D, Berger B, Filiberto D, Newton M, Wolfe B, Karabinakis E, Clark S, Poon E, Abbett E, Nandagopal S. 2004. Water resources:agricultural and environmental issues. BioScience, 54(10):909-918,[0909:WRAAEI]2.0.CO;2.
Plante D, Bélanger G, Leblanc D, Ward P, Houde A, Trottier Y L. 2011. The use of bovine serum albumin to improve the RT-qPCR detection of foodborne viruses rinsed from vegetable surfaces. Letters in Applied Microbiology, 52(3):239-244, https://org/10.1111/j.1472-765X.2010.02989.x.
Public Health England (PHE). 2014. Enumeration of β-Glucuronidase Positive Escherichia coli:Pour Plate Method. Microbiology Services Food Water and Environmental Microbiology Standard Method. Public Health England, London.
Quirós P, Martínez-Castillo A, Muniesa M. 2015. Improving detection of Shiga toxin-producing Escherichia coli by molecular methods by reducing the interference of free Shiga toxin-encoding bacteriophages. Applied and Environmental Microbiology, 81(1):415-421,
Reischer G H, Ebdon J E, Bauer J M, Schuster N, Ahmed W, Åström J, Blanch A R, Blöschl G, Byamukama D, Coakley T, Ferguson C, Goshu G, Ko G, de Roda Husman A M, Mushi D, Poma R, Pradhan B, Rajal V, Schade M A, Sommer R, Taylor H, Toth E M, Vrajmasu V, Wuertz S, Mach R L, Farnleitner A H. 2013. Performance characteristics of qPCR assays targeting human-and ruminant-associated Bacteroidetes for microbial source tracking across sixteen countries on six continents.Environmental Science & Technology, 47(15):8 548-8 556,
Reischer G H, Kasper D C, Steinborn R, Farnleitner A H, Mach R L. 2007. A quantitative real-time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment area. Letters in Applied Microbiology, 44(4):351-356.
Reischer G H, Kasper D C, Steinborn R, Mach R L, Farnleitner A H. 2006. Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions.Applied and Environmental Microbiology, 72(8):5 610-5 614,
Rop K R, Donde O O, Muia A W, Makindi S M. 2016. Influence of rainfall intensity on faecal contamination in River Nyangores of Mara Basin, Kenya:an eco-health integrity perspective.AsianJournalofMicrobiology,Biotechnology and Environmental Science, 18(2):281-289.
Shanks O C, Atikovic E, Blackwood A D, Lu J R, Noble R T, Domingo J S, Seifring S, Sivaganesan M, Haugland R A. 2008. Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Applied Environmental Microbiology, 74(3):745-752,
Shanks O C, Kelty C A, Sivaganesan M, Varma M, Haugland R A. 2009. Quantitative PCR for genetic markers of human fecal pollution. Applied Environmental Microbiology, 75(17):5 507-5 513,
Sorensen J P R, Lapworth D J, Read D S, Nkhuwa D C W, Bell R A, Chibesa M, Kabika J, Liemisa M, Pedley S. 2015. Tracing enteric pathogen contamination in sub-Saharan African groundwater. Science of The Total Environment, 538:888-895,
Staley Z R, Edge T A. 2016. Comparative microbial source tracking methods for identification of fecal contamination sources at Sunnyside Beach in the Toronto region area of concern. Journal of Water and Health, 14(5):839-850,
Tian C, Wang C, Tian Y, Wu Q, Xiao B. 2015. Vertical distribution of Fe and Fe(Ⅲ)-reducing bacteria in the sediments of Lake Donghu, China. Canadian Journal of Microbiology, 61(8):575-583,
Tran N H, Gin K Y H, Ngo H H. 2015. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater. Science of the Total Environment, 538:38-57,
United Nation Environmental Management Program. 2001.Global drinking water quality index development and sensitivity analysis report. National Water Research Institute, Burlington, Ontario.
United State Environmental Protection Agency (USEPA). 2000. Risk characterization handbook, EPA 100-B-00-002. EPA, Washington DC.
USGCRP. 2016. The Impacts of Climate Change on Human Health in the United States:A Scientific Assessment. U.S. Global Change Research Program, Washington, DC. 312p.
Wang H, Zheng X W, Su J Q, Tian Y, Xiong X J, Zheng T L. 2009. Biological decolorization of the reactive dyes Reactive Black 5 by a novel isolated bacterial strain Enterobacter sp. EC3. Journal of Hazardous Materials, 171(1-3):654-659.
World Health Organization. 2003. Heterotrophic plate counts and drinking-water safety. IWA Publishing, London, UK.
World Health Organization. 2005. Water Recreation and Disease:Plausibility of Associated Infections:Acute Effects, Sequelae and Mortality. International Water Association Publishing, London.
World Health Organization. 2013. Water Quality and Health Strategy 2013-2020, Accessed on 2016-02-02.
Yamazaki Y, Fukasawa A. 2011. Multiplex polymerase chain reaction method discriminating Escherichia coli and Shigella sp. Archives of Microbiology, 193(2):83-87,
Zandagba J, Adandedji F M, Mama D, Chabi A, Afouda A. 2016. Assessment of the physico-chemical pollution of a water body in a perspective of integrated water resource management:case study of Nokoué Lake. Journal of Environmental Protection, 7(5):656-669,
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