Microbial contamination of lakes, rivers, estuarine, and coastal waters poses a major risk to human health and it can lead to significant economic losses through closed beaches and shellfish harvesting areas.
When aquatic environments become contaminated with faeces, an important step in contamination management is identifying the source of the pollution. A research team at Cawthron is developing tools that will improve the microbial quality of water. Common bacterial indicators identify the presence of faecal contamination, but they fail to pinpoint the source of the problem. To address this issue Cawthron is providing novel microbial source tracking (MST) technologies to enable discrimination among different sources of faecal contamination, leading to effective management and remediation strategies.
We use molecular techniques to help identify the source of faecal contamination of water whether it is from farm, domestic or feral animals, humans or birds. DNA is extracted from a water sample and the sample is examined using the polymerase chain reaction (PCR) for DNA from source-specific organisms. The presence of certain micro-organisms indicates the source of the faecal contamination. Assays specific for humans, herbivores, dogs and wildfowl are in development.
This work is relevant to resource managers with water management responsibilities within local government authorities. Cawthron has helped councils and aquaculture companies identify sources of contamination within their waterways and growing waters. Some case studies are provided as examples.
Nelson City Council - Maitai River: High levels of faecal indicators in the Maitai River were identified as human faecal pollution and tracked to a stormwater drain. The Council is now working to resolve the situation: see Cawthron Report 1447 [PDF 5.9MB] produced with funding from Envirolink.
Motueka River Plume Study: Cawthron coastal scientists conducted a survey of the Motueka River plume during a flood event to assess the source and fate of faecal contaminants transported into Tasman Bay. The plume was delineated by towing a remotely operated CTD that continuously measured salinity, temperature, turbidity, and irradiance along transects extending into the Aquaculture Management Areas. The plume survey revealed a shallow low-salinity plume that extended at least 6 km into Tasman Bay. Water and mussels collected as far as the Aquaculture Management Areas had elevated counts of faecal bacteria. Using Microbial Source Tracking (MST) technology, Cawthron scientists were able to confirm the presence of faecal contaminants from ruminant animals such as cows and sheep within the mussels, revealing the close connection between land use and New Zealand’s highly valued coastal resources.
Recent funding through Seafood Innovation Ltd will assist in further developing MST technology for use in protecting shellfish resources.
Cawthron Institute has validated and deploys a wide array of MST tests targeting different gut bacteria and viruses. Tests currently available indicate presence or absence of a source within a given sample. Quantitative methods that provide a measure of abundance of a source within samples will be available in 2010.
The tests listed are currently available and additional tests targeting seabirds are under development and being validated.
Markers currently used at Cawthron
Human Methanobrevibacter smithii
Human Enterococcus faecium
Animal F-specific RNA coliphage
Human F-specific RNA coliphage
Human polyomavirus (JCV and PKV)
Cawthron provides two levels of service to clients. We are able to provide routine tests based on water samples sent to our laboratory for MST analysis. For a price list and order form please telephone 0-3-539 3265 or email: . Routine tests are best used for initial screening, or in situations where there is much known about the contamination problem and MST can be used to confirm the source of the problem (or rule out a given source such as humans).
High levels of temporal and spatial variability in the presence of markers can occur in natural systems, making contamination problems often difficult to solve. Replicate sampling, the use of multiple markers, and an understanding of the surrounding land uses and hydrology of the area are often required to more fully understand contamination problems.
Cawthron is able to design and implement investigative projects that use a range of tools, including MST, to answer questions about the source of faecel contamination in freshwater and marine environments. Depending on the question being addressed projects can vary between $5000 and $100,000. To discuss your project needs contact .
To ensure our research remains relevant and is connected to the best international science we collaborate with world leaders in Source Tracking Research.
Key collaborators include:
Dr. Warish Ahmed (CSIRO, Australia)
Dr. Brent Gilpin (ESR, NZ)
Dr. Valerie J. Harwood (University of South Florida, US)
Dr. Rachel T. Noble (University of North Carolina at Chapel Hill, US)
We are leading two research projects that aim to improve the application of MST tools to New Zealand-specific issues.
Microbial Source Tracking (MST) Tools for Water Quality Management
We are developing and validating MST tools for identifying the presence and relative contributions of human and ruminant sources of faecal contamination in coastal catchments and downstream nearshore waters. This project is being conducted in partnership with ESR and Regional Councils, via the Envirolink Tools Fund.
Microbial Source Tracking (MST) Technology for Shellfish
This project aims to expand the application of existing MST technology by developing and optimising methods for recovering a set of human specific bacterial and viral markers in shellfish flesh samples. This will provide the shellfish industry with improved tools to monitor the quality of their growing waters. This project is supported by industry through Seafood Innovations Ltd.
Recent Peer Reviewed Publications
Kirs M, Smith DC 2007. Multiplex Quantitative Real-Time RT-PCR for the F-specific RNA Coliphages: A Method for use in Microbial Source Tracking. Applied and Environmental Microbiology 73: 808-814.
Morris CA, Blackwood DA, Kirs M, Buttigieg ND, Morgan RR, Hogan J, Weeks I, Noble RT 2008. Comparison of Transcription-Mediated Amplification and growth-based methods for the quantification of Enterococcus in estuarine environments. Applied and Environmental Microbiology, 74(10): 3319-3320.
Converse RR, Blackwood AD, Kirs M, Griffith JF, Noble RT 2009. Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters. Water Research, 43(19): 4828-4837.
Kirs M, Smith DC (submitted). Differential replication of F+ specific RNA Coliphages.
Kirs M, Harwood JH, Fidler AE, Gillespie PA, Fyfe WA, Blackwood AD, Cornelisen CD (in prep). Evaluation of library independent microbial source tracking markers in New Zealand. In prep.
Kirs M, Cornelisen CD 2008. Shellfish Growing Area 1510: Review of microbiological data and technical advice on microbial source tracking. Cawthron Report 1435: 8pp.
Kirs M, Harwood JH, Fidler AE, Cornelisen CD, Gillespie PA, Fyfe WA (in review). Application of microbial source tracking (MST) technologies for identifying the source of microbial contamination in the lower Maitai River. Cawthron Report 1447: 42pp.
McCoubrey D-J, Kirs M, Cornelisen CD 2009. Advice on identifying sources of faecal contamination in Houhora Harbour. Cawthron Report 1646: 24pp.
Kirs M, Van Laanen A, Cotton D, Hadfield A, Van Loon N, DePaola Jr. A, Jones J, Krantz J, Fyfe WA (in review). Vibrio parahaemolyticus and Vibrio vulnificus in commercially harvested North Island oysters (Crassotera gigas). Cawthron Report.
Kirs M, Smith DC 2004. Microbial Source Tracking: Differential Coliphage Replication Leads To Biased Results in Enrichment Studies. In: Measure for Measure: How Do We Gauge Coastal Stewardship? Coastal Society Conference Proceedings, May 23-26, 2004. Newport, Rhode Island. pp. 300.
Kirs M, Smith DC 2005. Microbial Source Tracking: Multiplex Quantitative Real-Time RT-PCR Assay for F-Specific RNA Coliphages. 105th General Meeting of the American Society of Microbiology. June Atlanta, GA. Abstract and Poster.
Kirs M, Harwood JH, Fidler AE, Cornelisen CD, Gillespie PA, Fyfe WA 2008. Evaluation of library independent microbial source tracking markers in New Zealand. 108th General Meeting of the American Society of Microbiology. 1-5. June Boston, MA. Abstract and Poster.
Kirs M, Harwood VJ, Gillespie PA, Fidler AE, Cornelisen CD 2008. Application of microbial source tracking (MST) technologies for identifying the source of microbial contamination in the lower Maitai River and Little Sydney Stream. Conference Handbook, NZWWA’s 50th Annual Conference and Expo, 24-26. September, 2008, Christchurch. p80.
Habteselassie M, Kirs M, Blackwood AD, Kelly G, Noble RT 2009. Onsite Wastewater Treatment Systems and Their Impact On Surface Water Quality in Eastern North Carolina. Footprints in the Landscape: Sustainability through Plant and Soil Sciences. ASA-CSSA-SSSA International Annual Meetings, Pittsburgh, PA, 1-5 November 2009.
Cornelisen C, Gillespie P, Kirs M, Barter P, Goodwin E, Forrest R, Knight B, Young R, Quarterman A 2009. Cow poo swims the distance: Tracking faecal contaminants in the Motueka River plume. New Zealand Marine Sciences Society Annual Conference, Auckland, New Zealand, Sept 2009.
Microbial Source Tracking - Ensuring Water Quality for the Future Download [PDF 122 KB]